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Plant Transcriptomic Responses in a Diverse Organ and Stress Conditions

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Michal Rurek at Adam Mickiewicz University in Poznań
Michal Rurek
Mikołaj Smolibowski
Mikołaj Smolibowski
Mikołaj Smolibowski
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Abstract

Plant transcriptomes are an extremely dynamic entities shaped spatially and temporally by many intracellular and environmental cues. In this review, we first summarize the complexity and diversity of plant genomes and transcriptomes as a start point for the multitude of transcriptomic responses. Numerous alterations within various tissue and organ‐specific transcriptomes as well as the most relevant transcriptomic responses associated with plant acclimation to selected abiotic and biotic stress conditions, from the current studies employing highthroughput transcriptomic analysis are widely discussed. Understanding changes within plant transcriptomes, revealed by in silico functional analysis, allows for the characterization of stress affected genes and stress acclimatory mechanisms, as well as allows to perform plant metabolic engineering. The latter allow cultivars to produce more secondary metabolites in the future, which are often desirable substances in the biomedical industry. Accordingly, in this review special attention was also paid to characterize the potential of transcriptomic analyses of medicinal species, particularly to search for new cultivars. Extensive characterization of transcriptomic responses in stress would also result in the development of new cultivars that display physiological and molecular mechanisms that allow them to cope with adverse environmental conditions more adequately.
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Review Not peer-reviewed version
Plant Transcriptomic Responses in a
Diverse Organ and Stress Conditions
Micha
ł
Rurek * and Miko
ł
aj Smolibowski
Posted Date: 27 March 2024
doi: 10.20944/preprints202403.1654.v1
Keywords: differentially expressed genes; medicinal species; plant organs; secondary metabolites; plant
transcriptome; stress
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medium, provided the original work is properly cited.
Review
PlantTranscriptomicResponsesinaDiverseOrgan
andStressConditions
MichałRurek*andMikołajSmolibowski
DepartmentofMolecular&CellularBiology,InstituteofMolecularBiology&Biotechnology,Facultyof
Biology,AdamMickiewiczUniversity,Poznań,UniwersytetuPoznańskiego6,61‐614Poznań,Poland;
rurek@amu.edu.pl
*Correspondence:rurek@amu.edu.pl;Tel.:++48618295973
Abstract:Planttranscriptomesareanextremelydynamicentitiesshapedspatiallyandtemporally
bymanyintracellularandenvironmentalcues.Inthisreview,wefirstsummarizethecomplexity
anddiversityofplantgenomesandtranscriptomesasastartpointforthemultitudeof
transcriptomicresponses.Numerousalterationswithinvarioustissueandorgan‐specific
transcriptomesaswellasthemostrelevanttranscriptomicresponsesassociatedwithplant
acclimationtoselectedabioticandbioticstressconditions,fromthecurrentstudiesemployinghigh‐
throughputtranscriptomicanalysisarewidelydiscussed.Understandingchangeswithinplant
transcriptomes,revealedbyinsilicofunctionalanalysis,allowsforthecharacterizationofstress‐
affectedgenesandstressacclimatorymechanisms,aswellasallowstoperformplantmetabolic
engineering.Thelatterallowcultivarstoproducemoresecondarymetabolitesinthefuture,which
areoftendesirablesubstancesinthebiomedicalindustry.Accordingly,inthisreviewspecial
attentionwasalsopaidtocharacterizethepotentialoftranscriptomicanalysesofmedicinalspecies,
particularlytosearchfornewcultivars.Extensivecharacterizationoftranscriptomicresponsesin
stresswouldalsoresultinthedevelopmentofnewcultivarsthatdisplayphysiologicaland
molecularmechanismsthatallowthemtocopewithadverseenvironmentalconditionsmore
adequately.
Keywords:differentiallyexpressedgenes;medicinalspecies;plantorgans;secondarymetabolites;
planttranscriptome;stress
1.Introduction
Higherplants,knownasvascularortelomeplants(Thelomophyta),appearedduringplant
evolutionbackinthePalaeophyticera.Theyarecharacterizedbythepresenceoforgans,the
developmentoftissuesdistributingwater,mineralcompounds,andphotosynthesisproductsandthe
dominanceofthesporophyteoverthegametophyte[1,2].Duetothesessilelifecycle,higherplants
wereevolutionarilyforcedtodevelopmultipleadaptationsthatallowedthemtorespondtostress
[3],includingtranscriptomicalterations.Tobetterunderstandhowplantsrespondtoenvironment,
detailedtranscriptomicanalysesarestillnecessary.Thedevelopmentofhigh‐throughputRNA‐seq
platformswithasubsequentdecreaseinsequencingcosts,aswellasdatameta‐analyses,simplified
thetranscriptomicstudies.Theyallowfortheanalysisofthegeneexpressionprofilemanifestedbya
givenplantcell,tissue,ororgan.Seasonal,environmental,ordevelopmentaltranscriptomic
variationscanbealsoobserved[4].
Inrecentyears,planttranscriptomicreviewsfocusedmostlyonmethodologyissues[5–7].
Excellentstudieswithspecies‐specificomicsanalyses,includingthoseonstressresponseandfocused
ontherelevanceoftranscriptionfactors(TFs),hormones,translationalreprogramming,andthe
epigeneticlevel,aswellasphenotypicandphysiologicalanalyseswerealsopublished[8–13].
However,theydidnotalwaysreferexhaustivelytothetranscriptomicdata,andtheyweresometimes
limitedtothestudyofnoncodingRNAinacquiringstresstolerance[14].Owingtothosefactors,in
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© 2024 by the author(s). Distributed under a Creative Commons CC BY license.
2
thisreviewthediversityoftranscriptomicresponsesamongdiverseorgansinthedevelopmental
context,andresponsestovariousstressors,bothabiotic(includingUVradiation,chemical
treatments,drought,coldandheatstress)aswellasbiotic(fungalandbacterialinfections)stressors,
willbepresented.Thecitedstudiescomingfromrecenthigh‐throughputanalyses,willbediscussed
inthecontextofthecomplexityofplantgenomeandtranscriptomestructureasabasisforavariety
oftranscriptomicalterations.Wewillalsorevealtheapplicativeaspectsoftherecentsearchesfor
usefulnewmedicinalplantcultivarsresistanttostress.
2.TheDiversityofHigherPlantGenomesandTranscriptomesasaBasisfortheComplexityof
TranscriptomicResponsiveness
GenomeiscomposedofacompletesetofallDNAmoleculesinthecellcontainingthe
informationnecessaryforanindividualtofunctionanddevelop.Inplants,threegenomesare
recognized:nuclear,chloroplast(theplastome)aswellasmitochondrialgenome(themitogenome)
[15].
Plantnucleargenomesizeisnotcorrelatedwiththesizeoforganellargenomes.Ofallthemajor
taxonomicgroups,landplantscontainthemostconservedsizeofthenucleargenome.Forexample,
Genliseaaureaisacarnivorousplantspecieswithoneofthesmallestnucleargenomes,whichspans
43.3Mbps,whileoneofthelargestknownnucleargenomes(upto150Gbps)isknowninParis
japonica(TableS1).Currently,twomainfactorsarethoughttoberesponsibleforthelarge‐scale
variationofgenomesizeamonglandplants:therecurrentcasesofwholegenomeduplication(WGD),
i.e.,polyploidy,andthedynamicsofthelossandgainoftransposableelements.Eventhough
duplicationofchromosomenumberisanobviousreasonfortheincreasinggenomesize,transposon
gain‐and‐lossresultsinthegreatestvariationinthegenomesize.Insomenucleargenomes,
transposonscompriseabout3%oftheirsize;inotherones,theycanoccupyeven85%ofthegenome.
Interestingly,therelationshipbetweenplantnucleargenomesizeandtransposoncontentisgenerally
linear[16].Numerousevidencesuggeststhatplantspecieswithsmallnucleargenomesare
characterizedbybroaderphenotypicandecologicalfeatures,whilespecieswithlargergenomeslive
onlyunderconditionswithmorerelaxedpressureofnaturalselection.Interestingly,plantnuclear
genomecorrelateswiththenutrientavailability.Undernitrogenorphosphorusdeficiency,species
withlargergenomeswereunabletocompeteanddominateinecosystems[17].
AccordingtoMargulis[18]concept,plastidsandmitochondriaoriginatedfromtheengulfing
andmaintenanceofsingle‐celledorganismsintheearlyeukaryoticcellunderendosymbiosis.The
proofofsuchaneventwouldbethepresenceoftheirowngeneticmaterial,prokaryoticribosomes,
doublemembranedenvelopeaswellassize[19].Themitochondrialancestorswereprobably‐
proteobacteria,whiletheplastidancestorswereorganismssimilartocyanobacteria.Mostorganellar
genesunderwentanevolutionarytransfertothenucleus,andstillorganellarDNAinsertionscanbe
foundinnucleargenomes[20].Genome‐containingorganellesthusexhibitaparticularlycomplex
patternoftheirbiogenesis,dependingontheconcertedregulatedexpressionofnuclearand
organellargenesbyanterogradeandretrogradesignaling[21,22].
Althoughnucleargenomescanreach119.1MbpsinArabidopsisto150GbpsinsizeinParis
japonica,theplastomeisrelativelyconservedinlength,genecompositionandorganization,andin
angiospermstypicallyrangesinsizefrom120to180kbps[23,24].ThelengthoftheArabidopsis
plastome(withnucleargenomeof119.1Mbps)is154,478bps,whenP.japonica,theownerofthe
largestlandplantnucleargenome(150Gbps)hasaplastomeof155,957bp.Thedifferenceinsizes
betweenArabidopsisandP.japonicaplastomesisthereforeaboutonly~1,500bps(TableS1).Most
plastomesoflandplantencodealimitednumberofproteinsinvolvedprimarilyinphotosynthesis,
transcription,translation,andplastidsignaling.Similarlytomitogenomes,plastomesalsoencode
rRNAs,tRNAs,andvariousncRNAs[25,26].Multiplefactorsofnuclearoriginregulateandcontrol
theexpressionofplastidproteinsatdifferentstages,includingtranscription,RNAediting,post‐
transcriptionalmodification,splicing,andtranslation[27].Metabolitessynthesizedinplastidsare
oftensignalingmoleculesfordistantcommunicationpathwaysandplayanimportantroleinthe
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responseofplantstostress[25,28].Therefore,knowledgeoninteractionsbetweenthenucleusand
theplastidsmightcontributetounderstandingtheplantfunctioningunderstress.
Thesizeofcopiesofthegivenorganellargenomescanvaryinthesamespecies,e.g.,the
mitogenomeofpotato(Solanumtuberosum)iscomposedoffewmoleculesfrom49,171bps,49,230bps,
and112,800bpsto247,843bpsand297,014bps(TableS1)[29].Ingeneral,thesizeofplant
mitogenomesrangesfrom208kbpsforwhitemustard(Brassicahirta),366kbpsforArabidopsis,up
to2,500kbpsformuskmelon(Cucumismelo);evenlarger,fastevolvingmitogenomes(ca.11.3Mbps)
occursinsomeSilenespecies(TableS1),whilethegenenumber(ca.60genes)remainrelativelystable
[30–32].Mitogenomesofhigherplantsarethusparticularlylargeandpossessacomplexstructure,
whichcouldariseduringplantterrestrializationandoptimizeseedgerminationinnovelland
ecosystems.Boththestructureandtheexpressionpatternoftheplantmitogenomesimprovedthe
regulationoforganellarfunctionsandmitochondrialbiogenesisinseeddevelopment[21].
WhilethegenomeissetofallDNAmoleculesincells,thetranscriptomeissetofvariousRNA
molecules(mRNA,rRNA,tRNA,aswellasnumerusncRNAs,e.g.,miRNAs,siRNAs,etc.)atagiven
spatialandtemporalstep.AccordingtoImadietal.[33],thetranscriptomecanbeseenasatranslated
fractionofgenomeinformationrequiredbytheorganismtofunctionandrespondtoitssurrounding
environment.Forinstance,withthecomparisontomaize(Zeamays)nucleargenomesizingof
approximately2,2Gbps,theestimatedtranscriptomecapacityspansonly97Mbps,whichconsistsof
ca.4%ofthenucleargenomesize[34].
Todate,Bestetal.[35]havepublishedpreliminarymapsofArabidopsisandcauliflower
(Brassicaoleraceavar.botrytis)mitochondrialtranscriptomes.Arabidopsisandcauliflower
mitogenomesencode28and33protein‐codinggenes,3and3rRNAs,22and18tRNAs,andcover
approximately.85and35ORFsof>100aminoacidresidues,respectively.InadditiontorRNAs,
numeroustRNAs,andncRNAmolecules[26],plantmitogenomesencodeOXPHOSapparatus
(respiratorychaincomplexes),ATPsynthasesubunits,mitoribosomalproteins,fewproteins
indispensableforcyt.cbiogenesis,andthetranslocaseofthetwinarginineprotein.Uptoday,atleast
42and33transcriptionunitswerefoundbyRNA‐seqofArabidopsisandcauliflowermitogenomes,
respectively.TheexpressionofseveralArabidopsismitogenesleadstotheformationofmono‐or
bicistronictranscripts;forexample,OXPHOSandribosomalproteingenesareoftenexpressedat
variouslevels.Variousopenreadingframeswithinthesamepolycistronictranscriptcouldbe
diverselyexpressedwithinthepost‐transcriptionalRNAprocessing,whichinvolvesfewkeysteps,
includingcis‐andtrans‐splicingandRNAediting;thelatteronearosefromembryophytesseparated
fromancestralalgallineagesandisthereforebelievedtobeabsentingreenalgae[35,36].
Itisworthnotingthatthetranscriptomecompositionwithinthesameorganismdependsnot
onlyonthetissue,butalsoonthesamplingprocedure[6].Transcriptomicstudiesallowusnotonly
toknowwhatproteinsaresynthesizedinthecell;factorsthatregulatethetranscriptionalactivityof
agivenbiologicalsystemmaybealsocharacterized[37].Tissue‐specifictranscriptomesillustratethe
distinctnesswithingeneexpressionpatternsacrossvariousplanttissues.Thesetranscriptomesoffer
valuableinformationontheunderlyingmolecularprocessesthataffecttissue‐specificfunctions,such
asphotosynthesisinleaves,nutrientuptakeinroots,orreproductiveprocessesinflowers.
Furthermore,bydecipheringtissue‐specifictranscriptomes,specificgenesandregulatory
mechanismsthatdisplayuniqueattributesandrolesindiverseplanttissuescanbedescribed,thus
propellingadvancementsinplantbiologyandagriculture[38].Thetranscriptomecompositionalso
changesdynamicallyundervariousenvironmentalcues.Tissue‐specifictranscriptomesplayacrucial
roleinunderstandinghowplantsrespondtotheseconditions.Thisknowledgeisinstrumentalinthe
developmentofstrategiestoimproveplantacclimationunderchallengingenvironmentalconditions
[39].
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3.Tissue‐SpecificandOrgano‐SpecificAlterationsinPlantTranscriptomes
3.1.XylemandPhloemTranscriptomesasExamplesofTissue‐SpecificTranscriptomes
Well‐investigatedexamplesoftissue‐specifictranscriptomesaretranscriptomesofvascular
elements.Duringtheprimarygrowthofthestemsandroots,procambiumderivedfromtheapical
meristemsdividesanddifferentiatesintoxylemandphloem.Precursorxylemcellsformxylem
crumbcellsorfibers.Duringunaffectedangiospermdevelopment,inthevascularbundle,xylem,
procambiumandphloemcellsshowdorsoventralpolarization:xylemislocatedonthedorsal
(adaxial)side,phloemoccursontheventral(axial)side,whereasprocambiumislocatedbetweenthe
phloemandxylem(Figure1a)[40,41].Currenttranscriptomicstudiesindicateanantagonistic
influenceofTFsfromHD‐ZIPIII(e.g.,ATHB8,ATHB15/CNA,PHV,PHB,REV/IFL1TFs)andthe
KANADIfamilies(e.g.,KAN1,KAN2,andKAN3)inthedifferentiationofprocambiumcellstoxylem
andphloem,respectively.MutationsinREV,PHB,andPHVgenesforspecificTFshavebeenshown
toaffecttheorganizationofvasculartissuethatcontainsthephloem,whichsurroundsthexylem
(Figure1b)[42].However,inthecaseofmutationswithinKANADIgenes,xylemstartstosurround
phloemelements(Figure1c)[43,44].Roszaketal.[45]employedsingle‐cellRNA‐seqapproachto
studythedevelopmentofprotophloemfromtheprogenitorcell.Thisstudyunderlinedtherelevance
ofotherTFs,namelyPEARproteinsthatinitiatedifferentiation(lineagebifurcation)program,
controlledbyPLETHORATFs.PEARTFsmediateearlyasymmetricdivisionsduringphloemcell
biogenesisandinlaterallyadjacentcellsofprocambium.
Figure1.Modelsofthevascularelementdevelopmentinhigherplants.(a)Organizationofvascular
elementsinwild‐typeplants(withoutmutationsingenesfortranscriptionfactorsgoverningvascular
biogenesis);(b)Organizationofvascularelementsinplantspecieswithmutationsingenescodingfor
REV,PHB,andPHVtranscriptionfactors;(c)Organizationofvascularelementsinplantspecieswith
mutationingenescodingforproteinsoftheKANADIfamily.Moredetailsinthetext.
Transcriptomicanalysesofthebiogenesisofplantvascularelementsshowedthatmore
differentiallyexpressedgenes(DEGs)appearedtobeupregulatedinphloemthaninxylem([46];
TableS2).AmongDEGsupregulatedinphloem,genesforRNApolymeraseIIsubunitsB2,B7,B9,
ABC3andABC5,andRNApolymeraseIIIsubunitsC1andC2aswellasgenesinvolvedingalactose
metabolismandpolysaccharidesynthesiswereenriched.Onthecontrary,genesinvolvedinfatty
acidbiogenesis(ACOX1,ACOX3,ACADM,PAAF,andECHS1)wereupregulatedinxylem,
indicatingthedemandforhigh‐energycompounds.Furthermore,theelevatedexpressionofthe
mentionedabovegenesaccompaniedtheactivityofgenesforthesynthesisoffibrouselementsfrom
thephloem[46–48].
Nearly26,898DEGsinpotato(Solanumtuberosum)leafpetiolesofthe39,000genesidentifiedin
thepotatogenomewereidentified.However,onlyalimitednumberofgenes(mostly
downregulated)differentiatedallstudiedtissues(TableS2).Theexpressionpatternsbetweenthe
tissuesstudiedwereenrichedwithDEGsinvolvedinsignalingpathways,plantresponsetolight,
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hormonalresponse,flowering,orRNAbinding.Despitetissuesampling,geneexpressionvaried
dependingonwheretheplantmaterialwastaken[49].
Aninterestingstudyshowingtheseasonalvariationofchangesinthetranscriptomeduring
plantdevelopmentovermonthswascarriedoutbyMishimaetal.[50],whosequenced
transcriptomesoftissuesofthemeristemcambiumandderivativecellsofJapanesecedar
(Cryptomeriajaponica)fromafewdevelopmentalstages.Almost55,051DEGswerefound,with10,380
DEGsinvolvedinxylemformation.Moregeneswereexpressedduringinhibitionofcelldivisions
thanduringpeakxylembiogenesis(xylogenesis)atspringreactivation(TableS2).During
xylogenesis,genesassociatedwithprimarycellwallbiosynthesis,secondarycellwalldeposition,and
lignificationweremarkedlyupregulated.Theexpressionofgenes,codingforenzymesinvolvedin
thelignificationprocess,e.g.,PAL,4CL,C4H,HCT,CCOAOMT,andCCRintheperiodfromMarch
toAugustalsoincreasedbutdecreasedsinceSeptember.Therefore,thisstudyconfirms
environmentalanalyses,indicatingthatseveralcambiumcellsincreaserapidlybetweenMarchand
June.Suchresultssuggestthatthegenesinvolvedinlignificationbelongtothemaingenesinvolved
inthebiogenesisofJapanesecedarxylem[50].
3.2.SelectedOrgano‐SpecificTranscriptomes
Thespecializationofindividualplantorganstoperformspecificfunctionsisaconsequenceof
differencesintheexpressionlevelsofnumerousgenefamilies.Forexample,distinctgeneexpression
patternsarepresentedinroottissuesandleavesoringenerativeorgans[51].Detailsonaffectedgenes
fromdevelopmentalandorgano‐specificstudiesweresummarizedinTableS2.
3.2.1.RootandLeafTranscriptomes
Themainfunctionofrootsistostoreenergyintheformofhigh‐energycompounds,i.e.,complex
carbohydrates,whileleavesconvertsolarenergyintochemicalenergyduringphotosynthesis[52,53].
Ahigh‐resolutionsingle‐cellRNA‐seqexpressionatlasofArabidopsisrootwasconstructedby
Denyeretal.[54].Itallowsinunprecedentedmannertoretrieveexpressionfeaturesofallmajorcell
typeswithinroots(withfinelyresolvedmarkergenesdefininguniqueclusteridentitiesandgene
expressionwaves)andtocharacterizekeydevelopmentalregulatorsandgenesgoverningroot
morphogenesis.Amongthem,expressionprofilesofatleast239TFsweredistinctive,includingthe
onesforroothairbiogenesis.Inaddition,Shulseetal.[55]profiledArabidopsisroottranscriptome
bysingle‐cellRNA‐seqacrossmajortissuesanddevelopmentalstages(inparticular,during
endodermishistogenesis,whichresultedintheidentificationofatleast800dynamicallyresponding
genes).Thoseauthorsalsoinvestigatedtheimpactofsucrosesupplementationontheroot
transcriptomeunderitsdevelopment.Intheearlierstudy,Efronietal.[56]employedsingle‐cell
RNA‐seqtostudyrootcellsregenerationafterexcisionofroottip.Authorsconcludedthatthe
transcriptomeofregeneratingcellspriortostemcellactivationresemblesthatofanembryonicroot
progenitorcell.Plantrootregenerationfollowsthedevelopmentalstagesofembryonicpatterning
andisgovernedbyspatialinformationprovidedbycomplementaryhormonedomains.
Thepatternofthelateralrootsandcell‐specifictranscriptomicalterationsweresummarizedin
Kortzetal.[57]review.Intissue‐specifictranscriptomesinArabidopsisleaves,thenumberofDEGs
decreasedfromtheleafvasculature(thehighestone)totheepidermisandmesophyll,indicatingthe
variablecomplexityofthesetissuesandtheirdecreasedsensitivitytotranscriptionalresponsiveness.
Interestingly,boththeepidermisandmesophyllexpressionprofilesweremainlyenrichedwith
downregulatedDEGs.Genesspecificforepidermalbiogenesiscodedproteinsforlipidmetabolism,
stomataldevelopment,auxinsignaling,andcuticlewaxsynthesis.Genesactivespecificallyin
mesophyllcodedproteinsthatparticipateinhormonesignaling,oxidativestressresponse,defense,
andphotosynthesis(afewgenesonlyforthelatterGO:term)aswellasvariousDNAbinding
proteins(notably,ERFandWRKYTFs).Incontrast,vasculature‐specificgeneswereindispensable
forthebiogenesisofvascularelements,thecellwall,genesresponsiblefortheproteinfate,plant
development,andmorphogenesisaswellasfortheaccumulationofTFscontainingMYBandNAC
domains[39].
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Recently,TenorioBerríoetal.[58]investigatedtranscriptomesofover1,800Arabidopsisleaf
cellsbysingle‐cellRNA‐seq.Thisstudycharacterizedatleast14diversecellpopulations(notonly
fromthecoretissues)inyoungleavesanddetectedatleast19,000variousmessengersfocusingon
thecellulardiversityofdevelopingleavesintertwinedbydevelopmental,metabolic,orstress‐
responseroutes.Mainleaftissueswerewell‐identifiedbytranscriptomicanalysis(whichindicated
forthewhighsensitivityofmesophylltranscriptometolowwaterpotential)anddevelopmental
gradientsinleafepidermiswereanalyzed.Resultsindicatedalsoforthediversityofcellsbuilding
thevasculararchitecture.Thisstudyprovidedalsovaluablesetofgeneticmarkersfordistinctcell
populations.Incontrast,during3‐week‐longsenescence,thetranscriptomeofArabidopsisleaves
becamenotablydifferentfromtheoneofmatureleaves[59].SeveraldifferentTFsactiveindifferent
stagesofdevelopmentwereidentified.DEGsactivebetween29and33daysaftersowingwere
groupedintotwoclusters.Ingeneral,duringArabidopsisleafsenescenceDEGsrelatedwith
photosynthesis,chlorophyllbiogenesis,cytokininsignaling,ribosomebiogenesis,aminoacid
metabolism,theutilizationofcarbonskeletonsandcellcycleappeareddeclinedinexpressionlevel,
whilegenesforjasmonicacid(JA)andethylenesignaling,responsetostimulus,caspaseand
pectinoesteraseactivity,lipiddegradation,catalyticactivity,cytoskeleton,metalbindingand
transportwereupregulated.Thoseregulatedgenesperformprotectivefunctionsthattheplanttakes
instressacclimation.Novelgroupsofco‐regulatedgeneswerealsodiscoveredamongupregulated
DEGs.Moreover,Chroboketal.[60]performedthemeta‐analysisofBreezeetal.[59]data,that
allowedfortheidentificationofmorethan1,000genesformitochondrialproteinsactiveatleastata
singletimepoint;thosealterationswereespeciallyvisibleattheinitialstagesofsenescence.Few
clusterswereproposedbasedonexpressionvaluesofthemitochondrialcluster,particularlyenriched
ingenesforOXPHOSfunctions,auxinsignaling,reactiontonutrientandlightdepletion,plastid
functions,stressresponse,proteinfate,transport,andassembly.Thoseresultsindicateforthe
relevanceofmitochondrialbiogenesisduringplantsenescence.
Inthesugarcane(Saccharumspp.hybrids)transcriptome,moreorganspecificDEGswere
expressedinleaves,contrarytoroots;duringanalyses77,359geneswereidentified[61].Intheleaf
transcriptome,messengersforphotosyntheticproteinswereupregulated.Onthecontrary,theroot
transcriptomewasenrichedwithtranscriptsencodingproteinsforpolysaccharidebiogenesis,
aminoacidmetabolism,orinvolvedinhigh‐energycompoundcatabolism.Althoughorganospecific
differencesresultedfromvariousfunctionsofbothorgans,somegeneralcharacteristicsofexpression
profilesremainedunchanged[51,61].
Themaize(Zeamays)leaftranscriptomeshowedwell‐noteddifferencesingeneexpression
consistentwithleafaxialsymmetry[62].Inbasaltissues,genesforcellwallbiosynthesis,DNA
synthesis,cellcycleregulation,auxinbiosynthesis,andcellulartransportwereupregulated.In
contrast,intheapicalpartoftheleaves,photosyntheticgenesappearedvisiblyupregulated,
especiallygenesencodingenzymesforthebiosynthesisofisoprenoids(e.g.,carotenoids),Calvin
cycle,redoxhomeostasis,starch,andsucrosemetabolism.Thesedatashowthatglobalchangesinthe
levelofgeneexpressionalsooccurinsuchaseemingly‘uniform’organastheplantleaf.During
analysis,Lietal.[62]identifiedalmost25,800maizeunigenes.
3.2.2.TranscriptomesofGenerativeOrgans
Sexualreproductionofhigherplantsisperformedbygenerativeorgans‐ flowers.Their
morphologyisspecies‐specificanddependsmostlyonthepollinationstrategy.Despitethe
differencesbetweentheformationofgenerativeorgans,thetransitionfromthevegetativetothe
generativephaseisundoubtedlythemostimportantstepinplantdevelopmentandthusgenetically
controlled[63].Multiplestudieshaveshownthatfloweringdependsonthephotoperiod,
vernalization,activityofplanthormones(includingGA),thermosensing,andavarietyofageing‐
associatedprocesses[64–66].Boththephotoperiodandthevernalizationcontroltheinitiationof
flowering,whichprotecttheplantfromtheenergy‐consumingflowerdevelopmentinunfavorable
conditions[67,68].
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AnanalysisoftheAnnonasquamosatranscriptomeshowedelevatedexpressionlevelsofgenes
involvedinvernalizationandphotoperiodinduction[68].Morethan71,948A.squamosageneswere
identified,ofwhichaboutathirdweredifferentiallyexpressed.Genesinvolvedinthephotoperiod
pathwayembracedsomephytochrome(PHY)andcryptochrome(CRY)genesaswellasearly
floweringgenes(EF1,EF3).DistinctDEGsappearedtobehomologoustogenesinvolvedin
vernalization,includingFIEandVIN3genes.AnotherstudyshowedthatMADSproteingeneshave
alargemorphogeneticeffectonflowerformation.MADSbelongtotranscriptionallyimportant
regulators[69],forexample,SOC1andFULfactors.Disturbancesintheexpressionpatternofthese
genescontributedtodelayedflowerformation,despitetheunaffectedphotoperiod[64].
Atthestageofcolorfulpetalformation,genesresponsibleforencodingenzymesforpigment
synthesis,genesinvolvedinthesynthesisofsecondarymetabolitesintissue,suchascarotenoidsor
anthocyanins,weresignificantlyupregulatedinAchimenes[70].Othergenefamilieswereinvolved
duringthedevelopmentofbroccoli(Brassicaoleraceavar.italica)floralbuds[71].DEGsinvolvedin
broccolicurdheterosisactiveinlightandH2O2‐mediatedsignalingappearedamongnewly
discoveredfunctionalclassesthatcontrolcropyield,hormonesignalingstressresponse,and
flowering.Overall,expressedgenes(especiallytheupregulatedones)seemedtoprevailinhybrid
linesratherthaninparentallines.NumerousDEGsfromthisgroupencodedproteinsimportantfor
growthanddevelopment,fattyacidandcarbohydratemetabolism,proteinsynthesisand
modifications.
3.2.3.SeedTranscriptomes
Seedsperformareproductivefunctionamongangiospermsandallowthedevelopmentofanew
plantgeneration,resultingfromsexualreproduction,aswellasprotecttheembryofromadverse
conditions.Theseedendospermandembryoaredevelopingafteradoublefertilization.Incontrast,
theseedcoverisformedfromembryostemcells.Seedsoftencontainhigh‐energycompounds,
allowingforthegermination.Analysisoftheseedtranscriptomeappearsthusextremelyimportant
forthecharacterizationofgenesactiveinseedbiogenesisandgermination[72,73].
Recently,aspatialtranscriptomicprofilingofgerminatingbarley(Hordeumvulgare)seedswas
exhaustivelystudiedbyPeirats‐Llobetetal.[74].Suchmethodology(VisiumGeneExpressionslides,
10xGenomics)allowedforacompletestudyofgeneexpressionprofilesacrossindividualcelltypes
withintheplantseeds.Forsequencing,8m‐thicklongitudinalsectionsofthebarleygrainswere
prepared.Thestudyallowedtoobtainspatiallyresolvedcellularmapforbarleygerminationand
identifiesspecificfunctionalgenomicstargetstocharacterizebettercellularprocessesduring
germination.ResultsofPeirats‐Llobetetal.[74]studyextendspreviousattemptsofusingsingle‐cell
RNA‐seqfordecipheringofrootandotherorgantranscriptomes[55,75],astime‐seriesspatial
transcriptomicanalysisoftranscriptomeallowsfarmorecomplexoutputfromallcelltypesinthe
investigatedtissue/organwithpreservedinformationontheirspatiallocation.Visiummethodology
allowedalsofordetectionof83‐90%transcriptsreportedfromtheprevious,tissue‐specificstudies
[76],howeveronlyaportionofseedtissuewassubjectedtoRNA‐seq.Thisapproachallowedclear
distinguishingoftissuesandtissueregionsbothbytheirphysicallocationandgeneco‐expression
patterns.Variousfunctionalgenecategorieswererevealedamongover14,000DEGsattheinitial24
hafterseedimbibition(at0[dry],1,3,6and24hour‐timepoints).Selectedgenefamilies,including
aquaporins(highlyexpressedinmesocotyl,scutellumandcoleorhiza),thionins(inendospermand
aleurone),starchcatabolismenzymes(invariousseedtissues,includingaleuroneandendosperm),
cellwallmodificationproteins(inradicleandscutellum),transporters(includingmitochondrialones
incoleorhiza,embryo,andscutellumduringearlyimbibition),ribosomalproteins,RNA‐binding
proteinsandelongationfactors(thelastthreecategoriesinembryotissues)andTFs(includingbZIP,
bHLH,andDREBproteins)displayedaspatiallytemporalexpressionpattern.Distinctgeneclusters
wereobservedincoleorhiza,radicleandscutellum,andembryowasdividedinto3expression
clusters.Mostgenesencodingtranscriptionandtranslationfunctionswereexpressedintheembryo.
Thespatialgeneexpressionpatternssuggestedthattheabilityofgerminationtoproceedwithout
transcriptionisaspecificembryofunction.Genesformitochondrialbiogenesiswerenotexpressed
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ataveryhighlevelsuntil24hafterimbibition,however,genesformitochondrialexpression
machinerywereinitiallyexpressedandgenesforglycolyticenzymesappearedevenmoreactive.
LEAgenesweremostlyexpressedatearlyimbibitionstages.Endospermandaleuronetranscriptomes
weredistinct.
AvaluableanalysisoftheArabidopsisseedtranscriptomeatmultipledevelopmentalstages
allowedtheidentificationofactivegenesbefore,duringandafterseedripening.Thehighly
expressedgenesforseeddevelopmentweredetectedintheglobularembryoandthedeveloped
cotyledon.Alower,butnoticeable,expressionlevelofgenesspecificforseeddevelopmentwas
observedinthematureandpost‐maturestagesofthegreenembryo,associatedwiththetransitionof
theseedintodormancy.Ofthegenesfor48diverseTFs,LEC1,LEC1‐LIKE,LEC2,FUS3,MEDEAand
PEI1wereactive.Mutationsthatoccurredinthesegenesresultedinembryodefects,whichconfirmed
theirkeyroleinseeddevelopment[77].Furtherstudiesofthettranscriptionalreprogrammingin
ArabidopsisgerminatingseedsresultedinthefirstdynamicTFnetworkmodelofseedgermination.
NumerousalreadyknownaswellasnovelTFswerefound.AfterseedstratificationgenesforbZIP
andAP2/EREBPTFsappeareddownregulated.TheDEGsaffectedbyseedgerminationcountfor
significantlynoveldatainthefield.AmongthefunctionaltermsrelatedwithDEGsinseeds,the
functionsofRNAsplicing,andhistoneprevailed,unlikethefunctionsrelatedtolightandroots.
Genesencodingproteinsthatinteractwithnucleicacidsandmetabolicenzymeswerealsoenriched.
Moreover,geneticisoformsvariedbetweendryandpost‐imbibedseeds[78].
AnanalysisofthePolygonatumcyrtonemaseedtranscriptomerevealedupregulatedgenesforthe
synthesisofsecondarymetabolites;theothergenesforproteinsactiveinthesynthesisoflignininthe
germinatedseedstageweredownregulated.Inaccordancewithpreviousanalyses,upregulationof
genesinvolvedinstarchcatabolism,whichcanprovidetheenergyforPolygonatumseedlings,were
evident[79].
3.3.TranscriptomicAnalysesofPlantSpecieswithMedicinalApplications
Transcriptomicstudieshavefoundapplicationsinmedicinalplantresearch,e.g.,forthe
functionalgenecharacterizationandtheidentificationofkeymetabolicpathwaysofpharmaceutical
importance.Althoughmostmedicinalspeciesdonotbelongtothemodelones,transcriptomicdata
fromvariousplantstudiesallowacomparisonofnewlydiscoveredgeneswithexistingdata,helping
todeterminethepotentialfunctionofgeneexpressionproductandtofindgenesresponsibleforthe
synthesisofbioactivecomponents[80,81].Forinstance,understandingtissuesresponsibleforthe
increasedsynthesisofgivencompoundsmayallowoptimizationoftheproductionofmedicinal
substancesproducedbyaloe(Aloevera),whichcanbeused,forexample,inthepharmaceuticalor
cosmeticindustries.Analysisofaloerootandleaftranscriptomesidentifiedintotal113,063and
141,310unigenes,respectively.DEGsinleaves(butnotinroots)weremainlydownregulated.Some
DEGswereinvolvedinlignin,saponin,andalloinbiosynthesis[82].Incontrast,analysisofTrillium
govanianumroot,leaf,fruit,andstemtranscriptomesrevealedthehighestnumberofDEGsbetween
leavesandroots[83].Amongthem,severalgenesinvolvedinthebiosynthesisofsteroidsaponins
andothersecondarymetabolites,includingbrassinosteroids,carotenoids,terpenoids,flavonoids,
phenylpropanoids,andsteroids,wereenriched.Almost141DEGswereinvolvedinthemetabolic
pathwaysofthesemetabolitesand78genesappearedtissuespecific.Genesfortheflavonoid
synthesiswereupregulatedprimarilyinfruitsandstems.Contrarytothat,genesinvolvedinthe
synthesisofterpenoidhadincreasedexpressioninleaves,whilegenesresponsibleforthesynthesis
ofsteroidsappearedtobeupregulatedinroots.Thoseresultsillustratethefact,howdiverse
compoundswiththepharmaceuticalpotentialmaybesynthesizedintissue‐ ororgan‐specific
manner.Ingeneral,thestudybySinghetal.[83]mayallowtheproductionandextractionof
medicinalsubstancesfromT.govanianum.
Transcriptomicanalysesoftheroots,stems,andleavesofEntadaphaseolidesallowedthe
identificationof61,046DEGsintotalinthesethreeorgans.Atleast26genesforcytochromeP450
biogenesisand17genesforuridinediphosphateglycosyltransferaseisoformsinvolvedinthe
biosynthesisoftriterpenoidsaponinswereupregulatedinstemscomparedtorootsandleaves.The
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elevatedexpressionlevelofthesegenesinstemscorrespondstothefactthatthecontentof
triterpenoidsaponinsinthisplantorganishigherthaninrootsandleaves[84].
TranscriptomicstudiesofmedicinalspeciesalsocoverDEGsforanthocyaninbiogenesis.
AnalysisoftheleaftranscriptomeofTetrastigmahemsleyanum,aspeciesfromwhichanimportant
extractwithantibioticpropertiesisobtained,allowedforidentificationofalmost100,540unigenes
andDEGsinvolvedmainlyinanthocyaninbiogenesis(e.g.,CHS,CHI,F3H,DFR,AS,UF3GT).The
resultsofthisstudyalsosuggestedthedifferentialparticipationofsecondarymetabolitebiogenesis
pathwaysinleafmetabolismdependedonthedevelopmentalstage[85].
Duetoitsbroadpharmacologicalactivities,Dendrobiumhuoshanensestemsbelongtothewidely
usedmedicalherbamonghealthcareproducts.However,thebiosyntheticpathwaysofbioactive
substancesandthemolecularregulationofstemdevelopmentareoftenunclearinfewpoints.The
studyontranscriptomesofleaves,stems,androotsofD.huoshanenserevealedcandidategenes
involvedinstemdevelopmentandpolysaccharidebiosynthesis(atleast103genes).Thecollected
datawasenrichedin27genesrelatedtofructoseandmannosemetabolismaswellas74genesfor
glycosyltransferasesand15genesinvolvedinthebiosynthesisofflavonoids.Forphotoperiodcontrol
andmaintenance,genescodingforspecificTFs,includingCO,MADS‐box,andAP2‐likeones,were
notable.Othergenescodedproductsrelatedtohormonebiogenesis[86].Ingeneral,thosedatamay
provideanimportantresourceforfuturestudies,inparticularfortheinvestigationofmolecular
processesengagedintheactivecompoundbiogenesisandtheorganogenesis.Foradditionalanalysis
ofgenesnecessaryforpolysaccharidebiosynthesisamongmedicinalplants,transcriptomesofleaf,
root,andrhizomeofPolygonatumcyrtonema,anedibleplantusedintraditionalChinesemedicine,
wereinvestigated.Inthisstudy,164,573genesintotalwereidentified,while59,271,52,184and45,893
geneswereexpressedinleaves,roots,andrhizomes,respectively.Upregulatedgenesinvolvedin
polysaccharidemetabolismwerenotablyenrichedinrhizomes.Furthermore,1,131genesfor
candidateTFsgoverningexpressionofgenesforpolysaccharidebiosynthesiswerefound,e.g.,for
MYB,AP2‐EREBP,WRKY,bHLH,zincfingerC3HandC2H2,andNACTFs[87].
AnotherspeciescontainingsecondarymetabolitesusedinmedicineisPolygonumcuspidatum.It
containsresveratrolandbioactiveanthraquinones,emodinandphysicon,displayingantimicrobe
andanticanceractivities[88].DuetothelackofavailabilityofP.cuspidatumwholegenomicdata,
functionalstudiesarehampered.Toaddressgeneticinsightsintothemetabolicpathwaysofnatural
products,acomprehensiveanalysisofP.cuspidatumroot,stem,leaf,flower,andfruittranscriptomes
revealed27,18and20genesthatencodeenzymesforthemevalonate,methylerythritolphosphate,
andshikimatebiosynthesispathways,respectively.Fewgenescodingimportantenzymesinvolved
inresveratrolsynthesis(PAL,C4H,4CL,aswellasSTS/CHSsynthasesforthelaststepofresveratrol
condensation)wereidentified.SomeSTS/CHSgeneswereupregulatedinroottissuesofP.
cuspidatum,suggestingthattheycouldbespecificallyinvolvedintheresveratrolandflavonoid
metabolism[89].
Basedonthegeneinventoryinvolvedintheprocessesoccurringinvariousplantorgans,itwas
possibletoselectgenescodingproteinsparticipatingingivenmetabolicpathways,andthusit
becamepossibletooptimizetheoccurrenceofachosenprocess,ortomanipulateagivenmechanism
ofspecificmetabolitebiogenesisbygeneticengineering.Furthermore,analysisofthetranscriptome
ofmedicinalspeciesallowedustounderstandthemetabolicpathwaysofsecondarymetabolites,
whichplayanimportantroleintheadaptationofplantstoenvironmentalconditionsandhave
therapeuticeffectsonvariousplantorgansatdifferentdevelopmentalstages.Dataobtainedfrom
thesestudiescanprovideinformationontheaccumulationofsecondarymetabolitesandtheefficient
productionofactiveingredientsindifferentpartsofmedicinalplants,aswellascanbeusedto
developnovelgenotypeswithenhancedstressresistance[81].Furtheranalysisofmetabolic
pathwayswillhelptounderstandhownaturalproductsaresynthesizedandprovideresourcesfor
engineeringlarge‐scaleproductionofnaturalproductsandgeneratingnovelchemicalsinfuture
syntheticbiologyapplications.
ResultsoftranscriptomicanalysesofmedicinalspeciesweresummarizedinTableS2.
4.PlantTranscriptomicResponseunderStressAcclimation
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Stresscanbedefinedasinternalandexternalfactorsthataffecttheefficiencyofphysiological,
metabolic,andmolecularplantprocessesthatleadtoareductionintheefficiencyofenergy‐to‐
biomassconversion.Thesestressorscanbedividedintoabiotic(Section4.1)andbiotic(Section4.2)
ones[90].Duetothesedentarylifestyle,plantshavedevelopedadaptiveabilitiesatmultiplelevels
tocopewithadverseconditions.Plants‘sense’externalcues,whichinturngenerateacellular
responsetransmittingstimulifromthecellsurfaceorcytoplasmicreceptorstothetranscription
machinery.Thislinksspecific‘cellularsensitivity’toenvironmentalfactors.Studiesonplant
transcriptomes,whichparticipateinsuchresponsemaythusallowforbetterunderstandinghow
plantsadapttochangingenvironmentalconditions[91].Figure2showsthewidelyused
methodologicalpipelineforstudyingthetranscriptomicresponseunderstressinplantspecies.It
combinesbothexperimentalandinsilicoanalysestoidentifysystematicallystress‐responsivegenes
incultivarsvaryingwiththestressresistance.Belowdiscussedarethemostinterestingalterations
thatoccuringeneexpressionprofilesunderdiversestressconditionsfromselectedbasicandapplied
studies.
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Figure2.Thegeneralpipelineforthehigh‐throughputanalysisoftheplanttranscriptomeunder
stressacclimationbetweengenotypesvaryingwithstressresistance(stresssusceptibleandresistant
lines).Keysteps,fromstressdosage(top)totheidentificationofdifferentiallyexpressedgenesets
(bottom)wereshown.Inthistypeofanalysis,expressionpatternsareoftencomparedpairwise
betweenthestresstreatedandcontrolgrownplantsforeachgenotypetestedandthelistofaffected
geneswithfoldchange(FC)valuesisgenerated.Moredetailsinthetext.
4.1.AlterationsinPlantTranscriptomesduringAbioticStress–theSelectedExamples
Abioticstress(e.g.,drought,suboptimaltemperatureincludingcoldandheat,salinity,heavy
metals,radiation,nutrientdeficiency,andmechanicaldamage)resultsfromtheactionofmultiple
physicalorchemicalstimuli[80,92].Duringacclimationtoabioticstress,planttranscriptomes
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respondparticularlydynamically.Detailsongenesaffectedunderabioticstressfromhigh‐
throughputtranscriptomicstudiesaregiveninTablesS2andS3andthesummaryofthecellular
functionsgovernedbydiversestressorsaffectinggeneexpressionprofilesinvariousplantspecies
wasdepictedinFigure3.Inpublictranscriptomicrepositories,e.g.,ExpressionAtlas[93],relatively
completeArabidopsistranscriptomicdataisavailable.Theg:Profileranalysis[94]offunctionalGO:
termsrelatedtoArabidopsisstress‐responsivegenescollectedfromExpressionAtlasshowedthehuge
variabilityofgeneresponseunderthoseconditions,evenbetweensimilartreatments.However,
stressresponseinvolvesnotonlydistinct,butalsosimilargenefamilies,especiallyacrossdiverse
durationofthegiventreatment,althoughdependingonstressorqualityanddosage(Figure4,Table
S3).Regardingorgan‐specificresponse,leavesareparticularlyaffectedbyvariousstressconditions.
Theybelongtoplantorgansinvolvedincarbonskeletonmetabolismandphotosyntheticenergy
capture;however,studiesregardingtheimpactofstressonleaftissues,contrarytoroots,maybestill
underrepresentedincertainaspects[39].
4.1.1.ChemicalTreatmentandUVRadiation
Dataontheinfluenceofchemicalstimulionplanttranscriptomescomefrequentlyfromleaf
studies.AvariabilityofArabidopsisleaftissuetranscriptomicresponsesunderUVradiation,aswell
asunderchemicaltreatments(antimycinA,3‐amino‐1,2,4‐triazole,methylviologenandsalicylicacid
[SA])wascharacterizedbyBerkowitzetal.[39].Theepidermisandmesophyllcellshadahigher
numberofpoorlyexpressedgenesthanthevasculatureafteralltreatments(comparewithSection
3.2.1data).Inthoseconditions,thetissue‐specificgenesrangedbetween20and80%innumber.The
responsepatternsofthosetissuestostresswerecomplexandhighlyspecificforeachtreatment.For
example,antimycinAresultedinsimilarresponsesinalltissuesstudied;however,UV‐affectedgenes
wereexpressedmainlyinthevasculatureandepidermis.Genesforphotosyntheticproteinswere
downregulatedinallArabidopsistissuesafter3‐amino‐1,2,4‐triazoleandSAtreatments,whileonly
thegenesthatencodethecomponentsofPSIandPSIIwereupregulatedbymethylviologen,andUV
radiationdownregulatedphotosyntheticgenesintheepidermisandupregulatedtheminthe
mesophyll.InArabidopsis,UVcanalsoaffecttheexpressionlevelofgenesforproteinsnecessaryfor
chlorophyllbiogenesis,proteinfolding,oxidoreductaseandligasegenes,andgenesfor
glyceraldehyde‐3‐phosphatedehydrogenaseindiverseextentbetweenUV‐AandUV‐Btreatments;
however,participationofTFsinbothradiationresponsesisnotable.Tissuesstudiedalsohave
distinctmitochondrialresponsestoantimycinA[39],whichaffecttheexpressionpatternof
respiratorygenes(includingalternativeoxidase),generaloxidoreductaseactivitygenes,glutathione
transferase,aswellasgenesrelatedtoSer/Thrkinaseactivityandexportacrosstheplasma
membrane.Onthecontrary,SAtreatmentresultedingenesaffectedforpolysaccharideandheme
binding,lactoperoxidaseactivity,H2O2scattering,Ca2+bindingandgenesforERresponseproteins
(Figure4,TableS3).
ToprotectthemselvesagainsttheharmfulactionofUV‐BonDNA,plantsaccumulatevarious
compounds,includingflavonol,anthocyanin,andproanthocyanidin.Flavonoidsareeconomically
importantsubstancesinfruitsthatarealsobeneficialforhumanhealth.Accordingly,Songetal.[95]
observedthatamongtheupregulatedDEGsinV.corymbosum,genesforthephenylpropanoidand
flavonoidbiosyntheticpathwaysprevailed.Genesinvolvedinplanthormonesignaltransduction
weresignificantlyenrichedafter1h,followedbygenesinvolvedinphenylpropanoidbiosynthesis
after3h,andbygenesinvolvedintheflavonoidanthocyaninpathwayafter6hofUV‐Bexposure.
Theseresultssuggestthatphytohormone‐relatedgenesmayconstitutetheprimaryresponsetoUV‐
Bradiation.Thealteredexpressionofseveralgenesinvolvedinflavonoidbiosynthesiswas
characterized.Genesinvolvedinproanthocyanidinandflavanolbiosynthesis,includingthePal1,
4CL2,CHS,CHI3,VcFSLandVcUFGTgenes(forphenylalanineammonialyase,4‐coumarateCoA
ligase,chalconesynthase,chalconeisomerase,flavanolsynthase,andanthocyanidin3‐O‐
glucosyltransferase,respectively)wereallupregulatedunderradiation,andtheirexpressionlevel
lastedhighafterthe24htreatment.Arabidopsisgenesessentialforoxidoreductaseactivity,
porphyrinmetabolism,plastidorganization,andcarbohydratemetabolismregulationalso
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respondedtoUV‐B(Figure4,TableS3),however,accordingtoDongetal.[96]transcriptional
analysis,inUV‐BresponseofPachycladoncheesemanii,anativeNewZealandspeciescloseto
Arabidopsis,multiplegenesactiveinthewoundhealing,regeneration,flavonoidbiosynthesisare
specificallyenrichedandtheproductionofanthocyaninsbelongtothemostimportantstrategyof
acquiringoftolerancetoradiation.Nevertheless,commongenesforUV‐BresponseinArabidopsis
andP.cheesemaniiincludedtheonesfortheaminoacid,vitamin,pigment,andsecondarycompound
metabolism[96].Toexplorethemolecularmechanismunderlyingtheincreaseinflavonoid
biosynthesisunderUV‐Bradiation,Songetal.[95]investigatedthetranscriptomesofVaccinium
corymbosumexposedtovariousdosages(1‐24h)ofUV‐Bradiation.Comparativeanalysisofthedata
obtaineddetected16,899DEGsbetweendifferenttreatments,while806commongeneswere
differentiallyexpressedinallsamplestested.ThehighestnumberofDEGsappearedamongplants
exposedtoUV‐Btreatmentfor24h.
Lettuce(Lactucasativa)growningreenhouseconditionsusuallycontainsaloverlevelofascorbic
acid(ASC)comparedtoplantsgrowninfieldconditions.ASCisanantioxidativenutrientfor
humangrowth,reproduction,andhealth.AstheaccumulationlevelofASCiscorrelatedwithlight
intensity,lettuceplantsweretreatedwithlow,intermediate,andhighdoseofUV‐Btoinvestigate
itseffectontheASClevelinplants.Thesubsequenttranscriptomicanalysisresultedinthe
identificationofnumerousDEGswithinthelow‐doseandthehigh‐doseradiationtreatedgroups.
Furthermore,thecomparisonofthesetwogroupsrevealed809DEGsthatoverlappedbetween
them,ofwhich351geneswereupregulatedand458genesappeareddownregulated;twoMIOX
genes(formyo‐inositoloxygenase,importantenzymeinmyo‐inositolpathway)geneswere
significantlyupregulatedwithinthehigh‐doseUV‐Btreatedvariant.TheexpressionoftheMIOX
genewaselevated2‐3timesbyASCinArabidopsis.GenessuchasAPXandMDHARthatare
relatedtotherecyclingofASC,werealsosignificantlyupregulatedinthisvariant[97,98].In
general,resultsofthosestudiessuggestthatexpressionoftheMIOX,APXandMDHARgenesmay
contributetotheregulationoftheASClevelinducedbyUV‐Bradiation.Inthismodel,UV‐Bmight
notdirectlyincreaseASCsynthesis,butratherindirectly‐byaffectingotherbiologicalpathways
thatleadtoanincreaseintheASClevelinplanttissues.
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Figure3.Summaryofthecellularfunctionsgovernedbystressaffectedgenesinvariousplantspecies.
Inaddition,abbreviationsforthekeygeneaswellasgenefamilies(particularlyformostrelevant
transcriptionfactors)wereindicatednexttoeachstressoridentifier.Onlymostrelevant,joindatafor
bothupregulatedanddownregulatedgeneswereindicated(peripherally).Literaturereferences,cited
inthetext,wereshown(nexttoeachstressoricons).Signalingroutesbetweenactivelytranscribed
nuclear,plastidandmitochondrialgenomes(smallarrowswithinmarkedorganelles)thatare
indispensable,forinstance,fortheproperorganellarbiogenesisunderstressacclimationwerealso
depicted(center).Moredetailsinthetext.
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Figure4.InsilicofunctionalprofilingofdifferentiallyexpressedArabidopsisgenesundervarious
stresstreatments.Countsofaffectedgenes,experimentaccessionnumbers,linkstotheExpression
Atlasdataandexperimentdescriptors(italicized,inquotes)wereallshown(aboveeachtable).The
experimentdescriptorscarrytheinformationonthecomparedvariants(treatmentvscontrol
conditions).Forinsilicoanalysis,treatmentidentifiers(‘UV‐Aradiation’,‘UV‐Bradiation’,
‘antimycineAʹ,‘salicylicacid’,‘drought’,‘cold’,‘heat’)wereusedforbrowsingoftheExpressionAtlas
dataunderʹBiologicalconditionsʹ option.ThecompleteArabidopsisdataweretakenfromthe
ExpressionAtlas(https://www.ebi.ac.uk/gxa/home;[93])andplacedinTableS1.Next,theretrieved
ArabidopsisGenomeInitiative(AGI)locuscodes,representingaffectedgenesetsfromthegiven
experimentwithwild‐typeArabidopsis,wereusedasqueries(organism:Arabidopsisthaliana)for
thesearchofthemostrelevantdriverfunctionalterms(thefunctionalprofiling)ing:Profiler
(https://biit.cs.ut.ee/gprofiler/gost;[94]).DuringGO:termenrichmentanalysis,termswereextracted
anddepictedintables,togetherwiththeirIDsandthesource(BP‐biologicalprocess;MF‐molecular
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function;CC‐ cellularcomponent).Thecountsfortheuniqueandthecommondifferentially
expressedgenesfromvariousexperiments(indicatedbydiversecolors)withplantstreatedwithdiverse
UV‐A,UV‐B,antimycinA,salicylicacidandcolddosageswerecomparedonDeepVenndiagrams(at
thebottomornexttotheg:Profilertables).DeepVenndiagrams(circleareaproportionaltogenequantity)
weregeneratedusinganonlinetoolfromthehttp://www.deepvenn.com/Webpage[99].Colorson
diagramsarethesameaswithincompareddatasets.AlllinkswereaccessedJanuary9,2024.(a)The
dataforUVandchemical/hormoneresponse;(b)Thedatafordrought,heat,andcoldstressresponse.
4.1.2.WaterDeficiency(drought)
Toacclimatetowaterdeficiencies,plantsundergoseveralbiochemical,physiological,and
molecular(ABA‐dependentorindependent)responses,including,forexample,stomatallimitation
ofgasexchangeduetostomatalclosure,whichisaconsequenceofreducedosmoticpressureand
decreasedcellturgor[100]aswellasmultiplealterationsingeneexpressionprofiles.Asdrought
belongstoenvironmentalfactorsthataffectmostcropproductivity,thecharacterizationofthose
adjustmentsbyomicsstudieswouldrevealdroughtmechanismsincropsthatresultinrational
developmentofstressresistantcultivars[101].Characterizationofsweetpotato(Ipomoeabatatas)
transcriptomeindroughtallowedforthedetectionofalmost73,636unigenesandvariousgenesfor
ABA(IbZEP,IbNCED,IbABA2andIbAAO2),ethylene(IbACS,IbACO)andJA(IbLOX,IbAOS,IbOPR,
IbACOX1I,IbACOX3,IbMFP2)biosynthesis,whichappearedallupregulated.Thoseresultsindicate
fortheinvolvementofhormonalsignalingunderwaterdeficit.Interestingly,thoseanalysesalso
showedthatgenesassociatedwithSAsynthesiswerenotaffectedwhileamongthemaingenes
affectedindrought,genesforsomeenzymessuchasABIphosphataseorCa2+‐ATPasewereidentified
[102].
Analysisofthetranscriptomeoftwodrought‐resistantchickpea(Cicerarietinum)cultivarsunder
droughtrevealedaveryfewDEGswhichwerecommonforthoselines.Interestingly,
downregulationsinthetranscriptomesofbothgenotypesprevailed,showingdetrimentaldrought
impactonthetranscriptomiclevel.MultiplegenesforAP2‐EREBP,bHLH,bZIP,C3H,MYB,WRKY
orMADSTFswereinvolvedindroughtacclimation.ThoseTFsgovernedsignalingregulation,
secondarymetabolism,ortransitiontothegenerativephase[103].Thetranscriptomicresponseof
Phoebebournei,aChinesewoodspecies,todroughtemployedalsonumerousgenesforTFsfrom25
families,includingWRKY,AP2,HLH,bZIP,CCAAT‐binding,GATAzincfinger,SBPdomain,TCP,
Dof,GRFzincfinger,HD,andNAMTFs.Interestingly,AP2domaincontainingTFsaswellassome
NAMTFswerepreferentiallyexpressedat30hand45h‐longstress.Moreover,POD,SOD,andCAT
geneswereupregulatedandgenesnecessaryforplant‐hormonesignaltransduction,MAPK
signaling,phenylpropanoidbiosynthesis,flavonoidbiosynthesis,andstarchandsucrosemetabolism
weresignificantlyaffected,especiallyafter15d‐longdrought.Inaddition,genesfortwolight‐
harvestingcomplexIchlorophylla/bbindingproteins(LHCA1andLHCA2),light‐harvesting
complexIIchlorophylla/bbindingproteins(LHCB1,LHCB2,LHCB4)andporphyrinbiosynthesis
proteinsweredifferentiallyexpressedacrosstreatments[104].
Anotherstudy[105]includedadifferentialanalysisoftranscriptomesfromtwowheat(Triticum
aestivum)varietieswithcontrastingdroughtsensitivities.Duringthecomparativeanalysisofboth
transcriptomes,asignificantdifferencewasshowningeneexpressioninthedroughtresistant
cultivar,whichinvolvedgenesforthesynthesisofsecondarymetabolites.Genesnecessaryforthe
droughtacclimationincluded,amongothers,thosecodingimportantTFs(e.g.,asMT,FT,AP2,ABA2,
ARF6,WRKY6,AOS,LOX2).Furthermore,therecentinvestigationofgenesandpathwaysinvolved
intranscriptomicresponseoftworice(Oryzasativa)cultivars(stress‐susceptibleandresistant)in
terminaldroughtrevealedthegeneralprevalenceofdownregulatedgenesacrosstestedlinesand
organs[106].Notably,thenumberofaffectedDEGsdecreasedinstress‐resistantline.Thedifferential
expressionofgenesforNACandZIPTFs,ABAsignaling,LEAproteinsandproteinsrelatedwith
redoxhomeostasisplayedcrucialrolesinachievingofstresstolerance.Tyagietal.[106]concluded
thatthosegenesaregoodcandidatesforthegeneticimprovementofdroughttoleranceinrice.
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DenovosequencingofthetranscriptomeofMedicagofalcataseedlingssubjectedtodrought
revealedalmost4,460DEGsinresponseto2h‐longwaterdeficiency;theupregulatedDEGs
prevailed.M.falcatahousekeepinggeneswereexpressedatarelativelyhighlevel,althoughwithlittle
variation.ThesignalingpathwaysofthehormoneandNodfactors(interplaywithlegumesymbiosis)
wereprimarilyenrichedamongDEGs.GenesfornumerousTFs(e.g.,NACfamily)werealso
enrichedandgenesforABAbiosynthesiswereupregulated,incontrasttogenesforABAcatabolism.
Also,genesforABFTFs(e.g.,ABF1),JAbiosynthesis,ERFs,nucleicacidhelicasesanddiversegenes
forRNApolymerasesandDNArepairproteinsappearedupregulated.Incontrast,gibberellin
biogenesisgeneswereantagonisticallyexpressedcomparingtoABA‐relatedgenes,exceptforGID1
gene[107].FortheglobalanalysisoftranscriptomeofanotherFabaceaemember,Glycinemax,inthe
progressingdrought,Transcriptogramertoolwasemployed[108].Sixtosixteendiversefunctional
categorieswereenrichedamongDEGsat1‐,6‐and12h‐longdrought,includingcelldivision,cell
cycle,cellwallorganization,stressresponses,hormonesignaling,signaltransduction,andregulation
ofgeneexpression.TheparticipationofgenesforCa‐bindingproteinsinthestressresponsewas
notable.AnalysesofDeOliveira‐Busattoetal.[108]indicatedalsoforthepresenceofmostobservable
responsesinthefirsthourofdroughtaction,includingdownregulationsinDEGsforFemetabolism
andoxidativestressresponseandupregulatedgenesforchaperonebinding/proteinfolding,helicase
activity,nucleotide‐bindingsite,leucine‐richrepeatproteins,programmedcelldeath(PCD),
proteasome,cellcycle,DNAmetabolism,proteinbiosynthesisandRNAregulatorymechanisms.
However,mostfunctionalcategorieswererepressedafter6h‐longdrought.
Atranscriptomicreprogrammingunderrecurrentdehydrationandrehydrationcyclesin
Ceratostigmaplantagineum,aresurrectionspecies,wasstudied[109].DEGsweregroupedintoseven
functionalgroups.Themostabundantinfunctionaltermswasclusterwithgenesactiveduringstress
response,hormonesignaling,aminoacidcatabolism,sucroseandfattyacidbiogenesis,energyand
respiratorymetabolism,proteinmodificationandtransport,andmembraneorganization.Insilico
analysesindicateddownregulationofphotosyntheticgenesforlightreactionsandCalvincycle
proteinstodecreasephotooxidativedamageduringdehydration.Notably,amongthemultitudeof
genesinducedintheinitialstagesofdehydration,theOXPHOSgenesweredistinctive,allowingthe
recoveryofrespiratorymetabolismrecovery.Understress,numerousgenesforRNAprocessingand
regulationwereenrichedandgenesfortheubiquitinproteasomesystemweresignificantly
upregulated.Overall,datafromXuetal.[109]indicatetheflexibilityofprimaryandsecondary
metabolisminwatershortageandrewatering,using,amongothers,analternativerespiratory
pathway,theC3‐CAMswitch,andtheGABAshunt.
Drought‐affectedArabidopsisgenescodevariousproteinsforcellwallbiogenesis,carbohydrate
andhemebinding,transmembraneproteins,waterchannels,detoxificationprocesses,secondary
metabolism,extracellularregion,cell‐celljunctions,andsecretoryactivities(Figure4,TableS3).
TranscriptomicanalysisofanotherrepresentativeofBrassicaceae‐rapeseed(Brassicanapus)revealed
thatmostsignificantlyenrichedGOtermsoftheupregulatedDEGswererelatedwiththeresponse
towaterdeprivation,ABAsignaling,osmoticstress,andotherabioticstimuliandlipidmetabolism
aswellascutin,suberin,andwaxbiogenesis,fattyaciddegradationandsecondarycompound
metabolism.Onthecontrary,downregulatedDEGswereconnectedmainlywithphotosynthetic
activities,porphyrinmetabolism,carbon,andnitrogenmetabolism[110].
Duetothegrowingtrendofglobalwarmingandthesimultaneousseverescarcityofwater
resources,discussedanalysescanhelpdevelopnewvarietiesofcropsthatareresistanttodrought
andwillbeabletogrowinareaswithlimitedwaterresourcesinthefuture[80].Inaddition,theusage
ofstress‐alleviatingcompoundsmaybealsobeneficial.Forinstance,thegrowthregulator5‐
aminolevulinicacid(ALA)hasbeenusedtoalleviateabioticstressconsequences,includingattempts
tomitigatedroughtingrapevine(Vitisvinifera),bytheincreaseofanti‐oxidativeresponses[111].
Transcriptomicandphysiologicalanalysesallowedtoestablishthatchlorophyllmetabolismand
photosyntheticapparatusareprimarilyaffectedbyALA,whichusessynergisticmechanismsto
alleviatedrought.Underdrought,intheALApresence,alterationsintheexpressionpattenofDEGs
forchlorophyllsynthesis(upregulatedgenes)anddegradation(downregulatedgenes),Rubisco‐
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relatedgenes(upregulated)andphotorespiratoryDEGs(attenuated)playedimportantrolesthat
enableALAtomaintaincellhomeostasisinthewaterscarcity.
4.1.3.ElevatedTemperature(HeatStress)
Elevatedtemperatureaffectscerealdevelopmentandproductivity,especiallythedevelopment
ofmalereproductiveorgansandtheviabilityandmaturationofpollengrains[112,113].Heatstress
leadstotheincreasedlipidperoxidationanddegradation,membranedamage,elevatedamountof
reactiveoxygenspecies(ROS),andsimultaneousdecreaseinROSscavengeractivity,leadingto
nucleicaciddamageandconsequentlytoapoptosis[114,115].Assengetal.[116]intheirmodeltested
theimpactofgrowingtemperatureonwheatyield;whentheaveragetemperatureincreasedby2°C
duringthegrowingseason,thepossibilityofadecreaseinyieldincreasedbyupto50%.Itispossible
toalleviatetheconsequencesofheattreatmentbychemicaltreatmentofplants,forexample,by
endogenousmelatonin.Chrysanthemumleaftranscriptomesinheatwithorwithoutadditional
supplementationwithmelatoninwerecomparedbyXingetal.[117].Ingeneral,heattreatmentalone
downregulatedmoregenesthanupregulatedothers.Doubletreatments(melatonin+heat)
significantlyincreasedtheexpressionlevelofseveralDEGs.Interestingly,melatonintreatment
regulatedtheexpressionpatternoftheHSFandHSPgenes,genesforstarchandsucrosemetabolism,
signaling,andchlorophyll,flavonoid,carotenoidbiosynthesis.,andthelevelofvariousTFs,
includingMADS,MYB,NAC,TCP,WRKY,andbHLH(Figure3).
Thecomparisonofmicrosporetranscriptomesinheatstressintwotomato(Solanum
lycopersicum)genotypeswithcontrastingheattolerancerevealedamongtheupregulatedDEGsat
least11HSPgenes,whichencodecytosolic,mitochondrial,plastid,andERHSPs.Theincreased
expressionofHSPgenessuggestsitskeyroleinresponsetoplantheat.FiveAPXgenes(which
expressionproductsallowustocombattheincreasedROSlevelmoreeffective)werenotably
upregulatedinmaturingmicrospores[118].
Sometranscriptomicreportsfocusedontheroottranscriptomeinheat.Thedynamicsofthe
transcriptomeinroothairswasstudiedbyValdés‐Lópezetal.[119]insoybean(Glycinemax)plants
subjectedtoelevatedtemperatureatdiversetimepoints.Theauthorsidentified46,366soybeangenes
expressedinallvariants,aswellasonaverage1,849and3,091DEGsinheatedroothairsandstripped
rootspergiventimepoint.Interestingly,alimitednumberofDEGswascommonforalltimepoints
(465genesonly)within10functionalmodulesregulatedbyafewTFs(HSF,AP2/EREBP,MADS‐box
andWIRKY).Ingeneral,heataffectedtheexpressionpatternofgenesforsoybeanrootmetabolism,
proteinfoldinggenes,chromatinremodeling,andlipidandATPsynthesisveryefficiently.
Arabidopsisleaftranscriptomeundervariousstressconditions(salinity,osmoticstress,andheat
stress)wasrecentlyinvestigatedbySewelametal.[120].Ofallthesetreatments,theelevated
temperatureappearedtohavethemostnotableeffectontranscriptomicprofiles(withthedominant
upregulatedDEGs).Interestingly,onlytripletreatmentreachedthemaximumDEGnumber.
However,eightclusterscontainedresponsivegenesandselectedconditions(osmoticandheatstress)
actedantagonistically,whiletogethertheylargelyreprogrammedthegeneexpressionpattern.The
DEGsaffectedbyheatcoveredmultiplegenesthatencodedHSPs(11genesinduced,exceptHSFA1E,
HSF3andHSFA5),lateembryogenesisabundant(LEA)proteins,receptor‐likekinases(RLKs),
glutathioneS‐transferasesandWRKYTFs.Furthermore,heatstressaffectedArabidopsisgenesfor
carbohydratebinding,UDP‐galactosyltransferases,membranetransporters,andPCD(Figure4,
TableS3).Heatanditscombinationswithotherstressorsinducedvariousmitochondrialgenes,
presumablyasacompensativeresponsetoexcessiveproteindegradation,whichwaspreviously
suggested[121].However,heatalsorepressedseveralcellcyclegenes,ribosomalproteingenes(234
genesinthetripletreatment)aswellasgenesinvolvedinDNAsynthesisandrepair[120].
Thetranscriptomesinthepreexistedleavesofriceunderheatacclimation(afterashiftfrom
30/25oCto40/35oC[day/night])werealsostudied[122].Notably,afterthethermalshift,atransient
adjustmentinmetabolicgenetranscriptlevelinpreexistedleavesbeforehomoeostasiswasreached
within1day,whichaccompanieddeclineintheabundanceofsomeproteins.Atleast19,308rice
geneswereretainedforexpressionanalysisbyRNA‐seqinthreetimepointsaftertransferringof
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plantstotheheattreatment.1,818and1,465genesinpreexistedleavesappeareddifferentially
expressedafter2and6hafterthethermaltransfer,respectively,andmultipleDEGsoverlapped
betweenthosetimepoints.Numerousgenesforprimarymetabolismandrespondingtoabiotic
stimuli,andformetabolitebiosynthesiswereaffected,includingonlyfewphotosynthetic/respiratory
geneswereaffected(genesforcomplexIIsubunits,externalNAD(P)Hdehydrogenase,uncoupling
proteins,alternativeoxidase,andsomeglycolyticenzymes).
Theelevatedtemperatureoftenactssimultaneouslywiththewaterdeficit.Afewrecentstudies
focusedoninvestigationoftheimpactofheatstress,drought,andthedoubletreatment(heatplus
drought)ontotalplanttranscriptomes.Thediscussedresponsesinbarley(Hordeumvulgare)flag
leaveswererecentlystudiedbyMikołajczaketal.[123].Heataloneresultedinanotablylower
numberofDEGsinthreetimepointsandacrossthreesizegroupsofflagleaves,thanthedrought;
however,thedoubletreatmentengagedalmostasmuchDEGsasdroughtstress.Inmedium‐sized
leaves,heatstress(similarlytodrought)affectedthehighergenenumber,irrespectivelyofstress
duration.However,duringlongerheatanddroughttreatments,moreDEGswerealsonotablefor
large‐sizedleaves.Genesetsassignedtovariousprocessesunderlyingthedroughtandheat
response,includingphotosynthesis,theabscisicacidpathway,andlipidtransportwereidentified.
InvestigatedstressorsaffectedespeciallyexpressionlevelofLEAandHSPgenes.Overall,
Mikołajczaketal.[123]studyprovidednovelinsightintothemolecularmechanismsofbarleyflag
leafthatdeterminedroughtandheatresponse,aswellastheirco‐occurrence.Furthermore,according
totheMahalingametal.[124]study,thenumberofDEGsincreasedinbarleyheads(butnotinflag
leaves)instress‐tolerantgenotypeasheatprogressed.Onthecontrary,instress‐sensitivegenotype,
DEGsdeclinedinnumberinthoseconditions.Heatresponseengagedtransporterproteingenes,
genesforABAresponseaswellasresultedindifferentialexpressionofLEAgenesinstress‐sensitive
genotype;incontrast,genesfornon‐specificlipidtransferproteinsandcarbonatedehydratase
activitywereenrichedinstress‐tolerantgenotype.Onlyprolongeddroughtresultedintheincreased
numberof(mostlydownregulated)affectedgenesirrespectivelyfromthetissueorgenotype.The
combinedtreatment(heatwithdrought)resultedinthenotableincreaseofDEGnumberonlyin
stress‐sensitivebarleyline,howeveralterationsinDEGpatternwereverydistinctfromthesingle
treatments.Ingeneral,multiplegenesforRNAmetabolismandHsp70chaperonecomponents
(HsP70,ClpBandHsp70‐dependentnucleotideexchangefactor)appearedhubgenesforheat,
droughtandthedoubletreatmentinco‐expressionnetworkanalysisthatcanbeusefulforfuture
attemptsinengineeringstresstolerance.Atleast900TFsaidedtranscriptionalreprogrammingintwo
linesofbarleyacrossalltreatments.Anotherstudy[125]pointedouttohighernumberofDEGs
affectedindouble(heatanddrought)treatmentofLoliumtemulentum,whichcodedforproteins
necessaryforthetranscriptionalregulation,proteinfolding,cellcycle,organellarbiogenesis,binding,
transport,oxidoreductase,andantioxidantactivity,andcellularsignaling.Affectedgenescodedalso
forTFsfromAPETALA2/EthyleneResponsiveFactor,NAC,WRKY,bHLH,MYB,andGATA
familiesaswellasmultiplezincfinger‐typeproteins.
WhenheatstresswascombinedwiththeelevatedCO2level,thedetrimentaleffectofheatwas
alleviatedonlybypartialderegulationofprimaryandsecondarymetabolismgenes.The
transcriptomeofflagleavesofdurumwheat(Triticumdurum)inheat,elevatedCO2,andthe
combinationofthosestimuliwasinvestigated.Theirdatacoveredalmost60,209transcripts,ofwhich
29%ofmessengersspecificallyrespondedinabundancetoheat.MostDEGscodedproteinsinvolved
instressresponse,nucleicacidmetabolism,miscellaneousenzymes,andcellularsignaling.Genes
upregulatedbyCO2wereoftendownregulatedbyheat(theycoded,interalia,photosynthetic,and
OXPHOSproteins,enzymesoflipidandaminoacidmetabolismandglutathione‐ascorbatecycle,
hormonesignaling,nucleicacidmetabolism,andtransportproteins).However,heatupregulated
surprisinglyRubiscosubunits[126].
ChenandLi[127]studyincludedBrachypodiumdistachyonleaftranscriptomeanalysis,showing
DEGsparticipatinginprocessessuchasthespliceosomeandPSI,andPSIIbiogenesis,orinprotein
folding.Notably,morethan43upregulatedgenescodedmachineryforalternativeRNAsplicing.
Accordingtothoseanalyses,theupregulationofgenesinvolvedinalternativesplicingindicatesan
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increasedabilityofplantcellstoperformalternativesplicinginresponsetohightemperaturesto
createalternativeformsofproteinsthatcanalleviatephysiologicalconsequencesofheatexposure.
Todescribethermotoleranceandprotectivemechanismsagainstthermalstressindesertspecies,
Obaidetal.[128]studiedthetranscriptomeofRhizyastricta,theevergreenshrub,atelevated
temperature.DEGsweregroupedinto32and38groupsformatureandapicalleaves,respectively.
Massivedownregulationsincluded,amongothers,genesforcyclin,cytochromep450/secologanin
synthaseandU‐box‐containingproteins.Onthecontrary,theupregulatedgenescoveredthosefor
HSPs,chaperones,UDP‐glycosyltransferase,aquaporinsandtransparentproteintesta12,indicating
thatthermotoleranceinR.strictaleavesiscontrolledmainlybyimprovingproteinfoldingand
preventingproteindegradation.TFsputativelyregulatingexpressionofHSPgenesunderheat
includedHSFA,AP2‐EREBP,andWRKYTFs(Figure3).Ingeneral,numerousmetabolites,including
polyols,sugars,methionine,andphenolicswereinvolvedinthedevelopmentofR.stricta
thermotolerance.
4.1.4.LowTemperature
Similarly,toelevatedtemperature,alsoreducedtemperature(e.g.,coldtreatmentandfreeze)
cancontributetoplantgrowthanddevelopmentaberrations.Thecoldresponsecovers,interalia,the
directinhibitionofmetabolicreactions,andbecauseofthelimitedosmosis,celldehydrationandthe
oxidativestressoccursimultaneouslywithotherloweredtemperatureeffects.Theformationofice
crystalsunderconditionsofreachingthefreezingpointisthegreatestthread,whichresultsinprotein
degradationandmechanicaldamage.Mostplants,however,canadapttothecoldandgaintolerance
toiceformationintheircellsbygraduallybeingexposedtoreduced(non‐freezing)temperatures
undercoldacclimationprocess[129].
AnalysisofAmurvine(Vitisamurensis)transcriptomeundercoldtreatmentallowedforthe
categorizationofDEGproductsindiversefamilies,includingsignaltransduction,transcription
regulation,andalternativesplicing.Atleast38majorfamiliesofTFsinvolvedintheregulationof
coldresponseinV.amurensisweredetected,includingnovelTFs(e.g.,PLATZ,LIM,EIL,NIN‐like,
TUB,WHIRLY,andPcG).Regardinggenesforthesignaltransduction,CIPK8,CXIP4,CDP,and
CRK2genes,whoseexpressionproductsareresponsibleforCa2+binding,appearedupregulated.
Notably,resultsofthoseanalysesmayfurtherallowustoelucidatethemechanismsofcoldtolerance
[130].
ManyearlycoldresponsegenesencodeTFsthatinducetheexpressionofgenesforthe
subsequentstressresponse[92].Chengetal.[131]studiedeffectsoftheoverexpressionofMeTCP4
(aspecificTFfromcassava[Manihotesculenta])inArabidopsisplantsduringcoldstress.Theaffected
geneswereclassifiedasstress‐responsiveinallconditionstested,toTFactivityandDNAbindingin
control,andtooxidoreductase,peroxidase,andantioxidativeactivityundercoldstress.Duetal.[132]
analyzedthetranscriptomeofAgropyronmongolicumseedsatdifferentdevelopmentalstages.191,204
unigenesweredetected,whichwereclassifiedinto25functionalgroups.TheresponsetocoldofA.
mongolicumengagedABAreceptorsandincreasedthelevelofexpressionofgenesforbZIPandNAC
TFs.Thisresultsinthedownregulationoftargetgenesascoldtoleranceincreases.DEGswere
assignedto136metabolicpathways,ofwhichthemajoritywereenrichedincarbohydrate
metabolism,hormonalandphosphatidylinositolsignalingaswellastobiogenesisof
phenylpropanoids,flavonoids,stilbenoids,diaryloheptanoids,gingerolsandisoflavonoids.
ThecoldtreatmentappeareddetrimentalalsotoMedicago.falcataseedlingtranscriptome
(downregulatedtranscriptsprevailed).ThestudyofM.falcatastressresponsesfocusedon
phytohormoneandnodulationsignaling,revealingsomesimilaritieswithdroughtresponses
(Section4.1.2),however,ABF1andGID1transcriptsdecreasedinabundance.Interestingly,theGH3
auxin‐responsivegenewasintenselyupregulatedincold(similarlytoDIMI1,butcontrarytoDIMI2
andDIMI3,allofwhichencodeimportantnodulationfactors).Onthecontrary,theAUXtranscripts
encodingtheauxinreceptordecreasedinabundance.Furthermore,atleast16genesforMYBand12
genesforNACTFswereinducedbycold,indicatingtheirparticipationintheacquisitionofcold
tolerance[107].
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Arabidopsisdataforchillingresponse(contrarytosub‐zerocoldresponse)coveredparticularly
ahighnumberofaffectedgenes;interestinglythosetworesponsesoverlappedsurprisinglylittle
(Figure4).Chillingengaged,interalia,secondarymetabolism(e.g.,flavonoidbiogenesis)genesand
genesfortransporterproteins.Instead,duringsub‐zeroArabidopsisacclimation,genesforproteins
participatinginhormonesignaling,especiallyJAsignalingandABAreceptors,wereaffected.In
general,Arabidopsisresponsetocoldstressinvolved,interalia,genesforPSIbiogenesis,
carbohydrate,andsecondarycompoundmetabolism,O‐glycosylcompoundhydrolases,flavonoid
biosynthesis,nitratetransporteractivity,andpigmentmetabolism(Figure4,TableS3).Interestingly,
inP.cheesemanii,Arabidopsiscloserelative,thecoldresponseemploysmorefunctionalgenefamilies
thaninArabidopsisleaves,includingthespecificallyaffectedgenesfortheglycosinolatemetabolism
[96].However,inbothArabidopsisandP.cheesemanii,genesforwound‐like,circadianclockaswell
asforflavonoid,trehalose,phenylpropanoidandoxylipinmetabolismbecomeimportantunderthe
earlycoldresponse.
Animportantstageduringcoldacclimationisalsotheregulationofmetabolicprocesses
occurringinplantcellorganelles.Naydenovetal.[133]investigatedmitochondrialandnuclear
transcriptomesofgerminatedwheat(Triticumaestivum)germ.Somegenesencodingmitochondrial
proteins,includingMnsuperoxidedismutase(SOD)andalternativeoxidase(AOX),appeared
upregulated;however,thelevelofexpressionofnucleargenesessentialformitochondrialbiogenesis
visiblydecreased.Thisindicatesmutualcontrolofgeneexpressionbetweenmitochondrialand
nucleartranscriptomes,executedbyanterogradeandretrogradesignaling.
4.2.PlantTranscriptomicResponseunderBioticStress
Tocopewithbioticstress,plantshavedevelopedseveraldefensiveresponses,manyofwhich
arepreciselyinducedbythepathogenattack[100].Plantcellscontainplasmamembranereceptors,
thepurposeofwhichistorecognizethepathogenassociatedmolecularpatterns(PAMPs).Whena
pathogenisrecognizedbyareceptor,PAMP‐triggeredimmunity(PTI)isinitiated,whichusually
stopstheinfectionbeforeitspreadsthroughouttheplant.However,duetotheconstantcombat
betweenpathogensandtheirvictims,pathogenscanneutralizePTIbysecretingspecialproteins
calledeffectorsintothecytosoloftheplantcell.Plants,inresponsetotheeffectorssecretedby
pathogens,developedtheabilitytodetectmicroorganismsbyrecognizingaspecificeffector,which
iseffector‐triggeredimmunity(ETI).Thisresponseconsistsoftheproductionbytheplantof
intracellularreceptorsdesignedtorecognizeeffectormoleculesproducedbypathogens.The
interactionbetweenthereceptorandtheeffectortriggersacomplexnetworkofcellresponsesaimed
atdetermininginfectionresistance[134].
Higherplantsdonotpossessspecializeddefensecells,andtoprotectagainstpathogens,they
useʹoxidativeoutbreakʹ.Furthermore,ahighlevelofROSisrequiredtoinitiatethehypersensitive
response(HR).ThisreactionbelongstoPCDmanifestations,whichissupposedtolimittheaccessof
thepathogentowaterandnutrientsandisaimedatlimitingthespreadofthepathogen[135].Details
ongenesaffectedunderbioticstress(fundalandbacterialinfections)describedacrosshigh‐
throughputtranscriptomicstudiesweregiveninTableS2andthesummaryofthecellularfunctions
governedbybioticstressaffectedgenesinvariousplantspecieswaspresentedonFigure3.
4.2.1.FungalInfections
Pathogenicfungicanbedividedintobiotrophicandnecrotrophicfungi.Biotrophicfungifeed
onlivinghosttissue.Necrotrophicfungikillthehostandthen,secretingspecialenzymes,‘digest’
hosttissuesandfeedonthem.Numerousspeciesofpathogenicfungi,dependingonthe
developmentalstage,behaveasbiotrophicornecrotrophicones.Dependingonthestageoffungal
infection,differentresistancesignalingpathwayscanbeactivated.SAsignalingisbelievedtobe
involvedinresistancetobiotrophicandhemibiotrophicpathogens(pathogensthatareearly
biotrophsandnecrotrophslater).JAandethylenesignalingappearedtobeindispensablefor
necrotrophicresistance[136].
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Recently,transcriptomicanalysesbroadenedourknowledgeonplantaffectedgenesunder
attackoffungalpathogens.Analysisofthetranscriptomeofpumpkinleaves(Cucurbitamoschata)
infectedwithpowderymildew(Blumeriagraminis)24and48haftertheonsetofinfectionshoweda
downregulationofmultipleDEGsincludingbHLH87,WRKY21,ERF014(codingTFsforethylene
signaling)aswellastheHSFandMLO3genes(codingpowderymildewresistance).GenesforPSI
andPSIIsubunits,oxygen‐enhancingproteins,chlorophyll‐bindingproteins,andmagnesium
chelatasewereadditionallyregulated.Upregulationofgenesassociatedwithfoliarphotosynthesis
after48hofinfectionindicatesforuntouchedphotosyntheticactivityduringinfectionandassociates
withtheappearanceofinitialfungalhyphae.Theupregulationofgenesassociatedwiththe
photosynthesiswasalsoshowninthecaseoffungal‐infectedwheat(Triticumaestivum)[137].
Thetranscriptomeofwheatleavesinfectedwithpowderymildew(Erysiphalesspecies)aswell
aswithstripedrust(Pucciniastriiformis)werecomparedwiththeonefromsamplenotinfectedwith
anypathogenandamongthemselves[138].Intotal,186,632unigenesweredetected.Comparative
analysisofpowderymildew‐ andwithstripedrust‐infectedsamplesshowedaderegulationof
numerousgenesamongthreevariants.Theresponsetopowderymildewinfectioninducedstronger
changesinthegeneexpressionpattern.Genesforphenylalaninemetabolism,phenylpropanoid
biosynthesis,alpha‐linolenicacidmetabolism,flavonoidbiosynthesis,andphenylalanine,tyrosine
andtryptophanbiosynthesisweredifferentiallyregulatedunderpowderymildewinfection.
However,inthecaseoftheattackbystripedrust,genesinvolvedinmetabolicprocessessuchas
carbonbindinginthephotosynthesis,carotenoidsynthesis,PSantennaproteinsynthesis,and
ubiquinonebiosynthesiswereallupregulated.Thisindicatestheuseofdifferentialgeneexpression
patternsassociatedwithdefensemechanismsinresponsetovariousfungalinfections[138].
Twotranscriptomedatasetsoffungus‐infectedsilkofmaize(Zeamays)obtainedfromNational
CentreforBiotechnologyInformation‐SequenceReadArchive(NCBISRA)databasewerecompared
byKumaretal.[139].EachdatasetconsistedofresultsofRNA‐seqanalysisforleavesofmaize
infectedbydifferentfungalspeciesbelongingtoHypocreaceae(e.g.,Trichodermaatroviride),Nectriaceae
(e.g.,Fusariumverticillioides,F.graminearum),andUstilaginaceae(e.g.,Ustilagomaydis).SetAcontained
dataforsilksamplesaffectedbyF.graminearumandU.maydis,whilesetBcontaineddatafrom
samplesinfectedbyF.verticillioidesandT.atroviride(everydatasetalsocontainedthecontrolresults).
Analysisofsuchdataresultedintherevealof14,694and14,808DEGsbetweencontroldatasetsofA
andB,respectively.Almost4,519upregulatedand5,125downregulatedgeneswereidentified,
however,only21genesweredifferentiallyexpressedinthefourdifferentvariantsoffungalinfection.
Amongthesegenes,thegenesencodingtheperoxidase(POD)enzymethatcontrolsthelengthening
ofgermtubetoprotectmaizekernelsfromfungaldiseasewereupregulated.Strongexpressionof
SKIP19genesthatinfluenceandrespondtobioticandabioticstressconditions.Differential
expressionpatternwasfoundfortheOSM34(osmotin‐likeprotein)gene,whichimproveshost
defenseandimmunedefenseagainststress,andtheDUF26geneforthereceptor‐likeproteinkinase
subfamily(itsdomainplayscrucialroleinstressresistanceandantifungaldefense);thosetwogenes
wereupregulatedinF.verticillioides,F.graminearum,andU.maydisinfectedsamples,however,they
appeareddownregulatedinsamplesaffectedbyT.atroviride.Genesaffectedbetweenthree,two,and
afterinfectionbyasinglefungalspecieswerealsorevealed.
Identifyinggenesexpressedduringinfectionbyvariousfungalspeciescanhelptofindgenes
essentialfordefenseagainstthosemicrobes.Astheglobalclimateisaltered,importantagriculturally,
plantspeciesbecomegraduallyexposedalsotoincreasingbioticstress.Thefindingsdiscussedabove
wouldhelpdevelopplantcultivarsthatarehighlyresistanttofungalinfections.
4.2.2.BacterialInfections
Analysisofthetranscriptomeofriceplants(Oryzaindica)infectedwithXanthomonasoryzae
revealedmultipleDEGs;theupregulatedoneswereclassifiedinto10functionalgroups,among
whichgenescodingproteinsinvolvedinprocessessuchassignaltransduction,carbohydrate
metabolism,andtranscriptionregulationwereenriched.Onthecontrary,downregulatedgeneswere
assignedto12functionalgroups,amongwhichthegroupsofgenescodingforTFsandproteins
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involvedinlipidcatabolism,oxidativeburst,andassociatedwiththecellcycleormetabolicpathways
werethemostdistinctive[140].
Analysisofthetranscriptomeoftomatoplants(Solanumlycopersicon)infectedwithClavibacter
michiganensisallowedabetterunderstandingoftheresponseoftheplanthosttoinfection.
Upregulatedgenescodedproteinsthatparticipateinprocessessuchasproteinphosphorylation,
plantdefenseresponse,andhormonalsignaling.Theresistancegeneanalogues(RGAs)inresponse
toC.michiganensiswereupregulated,alsoincludinggenesRLKgenes.Theexpressionofgenes
encodingTFs,suchasWRKY,NAC,HSF,andCBP60,whichbelongtofactorsinvolvedinthe
antibacterialplantresponse,wasalsoelevated(Figure3).Inaddition,anincreaseintheSA
accumulationintomatotissuesduetobacterialinfectionwasshowed.Moreover,theuseof
exogenousSAresultedintheinductionofgenesforWRKYTFs.Thissuggeststheappearanceofgene
regulationbySAinresponsetoinfectionwithC.michiganensis,resultinginimprovedqualityofthe
plantimmuneresponse[141].
Inturn,Luetal.[142]investigatedtranscriptomesofrice(Oryzasativa)cultivarsresistantand
susceptibletoinfectionwithXanthomonasoryzaena.Thispathogencausesacerealdiseasecalled
bacterialleafstreak(BLS).Dataanalysisshowedthat,generally,moretranscriptsrespondedin
abundanceamongtheinfection‐susceptiblecultivar.Theseanalysesrevealedelevatedlevelsof
expressionofgenesencodingproteinsinvolvedinphenylpropanemetabolicpathways,
phenylalaninemetabolism,andflavonoidbiosynthesis,whichwerecloselyrelatedtoresistanceto
plantdiseases.Furthermore,theresultsofthestudybyLuetal.[142]alsosuggestedtheparticipation
ofselectedWRKY,NAC,MYB,andbHLHTFsinplantresponsetobacterialinfection(Figure3).
Recentresearchonresistant(IBL2353)andsusceptible(Ohio88119)tomato(S.lycopersicum)
cultivarsinfectedbyC.michiganensispresentednewgenefamiliesindefensemechanismsand
confirmedtheimportantroleoftheWRKYfamilyofTFsintheresponsetobioticstress.Comparison
oftranscriptomicdataderivedfromresistantandnon‐resistanttomatocultivarsaffectedbyC.
michiganensisrevealedthat215geneswereupregulatedandfurther362genesappeared
downregulatedamongallstressvariants(12h‐ and24h‐post‐infection)inbothgenotypes,
respectively.FromtheanalysesoftheGOandKEGGpathwayofgenesassociatedwithresistance,
almost25tomatogeneswereselectedforfurtheranalysis.Tocomparethedifferencesinthosegenes
betweensusceptibleandresistantgenotypes,aheatmapwascreated.Thankstothis,outof25genes
codingproteinsassociatedwiththeplantdefenseresponse,aWAKL20gene(forthewall‐associated
receptorkinasesimilartowall20)wasparticularlycharacterized,duetoitsincreasedexpressionlevel
intheIBL2353cultivar.TheWAKL20proteinistheonlymemberoftheWAKSsubfamilythatplays
animportantroleininnateresistancetomultiplepathogens.Thevirus‐inducedsilencingofthe
WAKS20geneintheIBL2353tomatocultivarresultedintheappearanceofsusceptibilitytoC.
michiganensisinfection.TheseresultsseemtoconfirmanimportantrolefortheWAKS20geneinthe
defensemechanismofplantsandestablishthefoundationforfurtherresearchintothesearchfornew
moreresistantplantvarieties[143].
5.ConclusionsandFuturePerspectives
Planttranscriptomecanbedynamicallyshapedbymanyfactors,functioningondiverselevels
ofbiologicaldiversity[81,91,93].Understandingthecompositionofthetranscriptomeallowsto
recognizemechanismsandgenesinvolvedinacclimationtoadverseenvironmentalconditionsto
whichplantshavebeensubjected.Inplantcells,inadditiontothetranscriptomebeingaproductof
nucleargenomeexpression,plastidandmitochondrialtranscriptomesarealsopresent,contributing
totheoveralldynamicityandcomplexityofplanttranscriptomes[25–27,35,121].Diversenuclearand
organellargenesareinducedinvariousorgansandunderacclimationtonumerousabioticandbiotic
stressors[121,133].Inthecurrentreview,wefocusedmainlyonsuchdiversityofglobalplant
transcriptomicresponsestovariousabiotic(UV,chemicaltreatments,drought,heat,low
temperature)andbiotic(bacterialandfungalinfections)stressconditionsassayedbyhigh
throughputtranscriptomesequencingstudies.Inaddition,wecharacterizeddistincttissue/organ‐
specifictranscriptionpatternsalsoanalyzedbyRNA‐seq,includingsinglecellRNA‐seqapproach
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andothercurrentmethodologies.Forthat,wefocusedmostlyonthetranscriptionalbiogenesisof
vascularelementsaswellasonseed,leaf,andgenerativeorgantranscriptomes.Wecommentedalso
onperspectivesofapplicationofbiomedicinallyimportantspeciesintranscriptomicanalyses.
Extensiveresearchontheplanttranscriptomeisbeingdevelopedatvariouslevels.
Transcriptomicdatacanbeacquiredbothfromdifferentialexpressionstudiesontissue/organsor
evenfromsinglecells,andmodernRNA‐seqapproachesconsiderablyextendedourknowledgeon
transcriptomecontentandsize.OwingBestetal.[35]study,moreorganellartranscriptomesfor
importantcropspeciesshouldbeanalyzedinthefuturethatwouldallowforthebetter
understandingofplastomeandmitogenomeresponsesinstressandtheirrelevanceinparticular
developmentalsteps.Also,moretranscriptomicstudiesemployingsinglecellRNA‐seqcoupledwith
microscopicanalyzesareexpected,inorder(1)tobroadenthespatio‐temporaldataoftissue/organ
transcriptomes,(2)toexplorediversityoftranscriptomesindistinctcellscontributingtotheorgan
architecturalintegrity,and(3)tobuildcompleteexpressiondatasets/atlasesforagriculturally
importantspeciesinthefuture.Duetotheunderrepresentationofthetranscriptomicdatainstress
forsomeplantorgans,furtherstudiesarestillexpected[39].Inafuture,cleardistinguishingoftissues
andtissueregionsbothbytheirphysicallocationandinvestigatingofgeneco‐expressionpatternsin
transcriptomicanalyseswouldbealsonecessary[76].
Higherplants,ascomplexorganismswithspecializedstructures,showdiverseandvery
dynamicallychanginggeneexpressionpatternsdependingontheorganorconditionstowhichthey
aresubjected,whichleadstothemetabolicflexibility[80,109].Inaddition,stressresponseatthe
transcriptomiclevelisactivelymodulateddependingonthestressorqualityanditsduration(for
somestressors,likedrought,affectingtranscriptomicpatternmostlyafteraprolongedexposure
[108]).Inthisreview,transcriptomicdatacomingnotonlyfromArabidopsis(TableS3),butalsofrom
diverseplantspecieswithvariouspotentialsofagriculturalapplicationswerediscussed.Notably,
DEGsconnectedwiththegivenstressresponsesincropspeciesvariedfromtheArabidopsisones,
employingdiversegenefamiliesorgenesfordiverseregulatoryproteins;nevertheless,commonly
regulatedgenesoftencoveredtheonesforthelow‐molecularcompoundbiogenesisandfor
secondarymetabolismenzymes[96].
Evensimilarenvironmentalcuesresultedinthediversityofgeneresponses,leadingtothe
inductionorupregulationofdistinctgenes.Transcriptomicstressresponsesengagedinductionof
bothcommongenesfordiversestressorsaswellasspecificgenemodules,codingcertainprotein
familiesactiveinselectedtreatmentsonly.Thiswasalsoevidentinthediscussedmeta‐analysisof
Arabidopsistranscriptomicdata(Figure4),whereonlylimitednumberofDEGsappearedcommon
fordiverseabioticstresstreatments;evenmultipledosageofthegivenstressorresultedinahigh
variabilityoftranscriptomicresponse.Somegenesforthegivenhormone(e.g.,SA)signalingwere
unaffectedbycertaintreatments,forinstance,bywaterdeficitwhichappearedparticularly
detrimentalalsoatthetranscriptomiclevel[102,103,106].Amongaffectedtranscripts,numerous
mRNAsencodedforaplethoraoftranscriptionfactorsfromdiversefamilies(Figure3).Itseemsthat
somemostdetrimentalstressors(forinstancehightemperaturetreatments)employedparticularly
highnumberoftranscriptionfactorsregulatinggeneexpression[124].
Doublestresstreatmentsresultedinhighlyspecificresponses,insomecasesincreasingthe
numberofaffectedDEGs[120,125]asmuchasthemostdetrimentalstressor[123],indicatingthatstill
thereisaneedformultiplestressoranalyses.Generally,stress‐sensitivecultivarsengagemoreDEGs
intheirstressresponses,however,thosepatternshighlydependonactualtissue/organstressed
(TableS3)[124].However,mostofthetranscriptomicdatadiscussedherecamefromplantmaterial
cultivatedunderhighlycontrolledlaboratoryconditions.Therefore,inouropinion,fieldexperiments
testingthevariationsofmultiplestressresponses(whichactsimultaneouslyonfieldcultivated
plants)inplantnuclearandorganellartranscriptomeswillbecontinuouslyawaited.Additionally,
plantresponsesonbioticstressindicatedfortheimportanceofplant‐microorganisminteractions
whichcanoverallinfluencestresstolerance[144],andthiswouldbechallengingpointalsoforfuture
transcriptionalstudies.Thus,impactoftheplantmicrobiomeonstressresponseonthe
transcriptionallevelshouldbeinvestigatedinmorebroadenedcontext.
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Withtheknowledgeofindividualgeneprofilesandmechanismsresponsible,forexample,for
thesynthesisofsecondarymetabolites,itwouldbepossibletousethempractically(1)duringgenetic
engineeringofmedicinalplantspecies,(2)toinvestigateofprocessesengagedintheactive
compoundbiogenesisandtheorganogenesis,and(3)tounderstandbetterhowmetabolicpathways
contributetovariousstressacclimationstrategies.Thiswouldalsoallowanexemplarymanipulation
ofplantmetabolicpathwaysinthefuturetoobtainmoresecondarymetabolites,whichoftendepends
onthedevelopmentalstage[83,85].Last,butnotleast,understandingmetabolicpathwaysandplant
responsestounfavorableconditions,suchasdrought,reducedorelevatedtemperature,orpathogen
infection,cancontributetothedevelopmentofnewmorestress‐resistantplantcultivars.Those
pendingactionswillincludemodernmethodologicaltools,includingadvancedgeneticengineering
andgeneeditingstrategiestoalleviatefuturecroplossesduetosuboptimalweatherandthe
increasedfooddemandsinthefuture[81,145].
SupplementaryMaterials:Thefollowingsupportinginformationcanbedownloadedatthewebsiteofthis
paperpostedonPreprints.org.thissubmissioncontainsthreeSupplementaryTables:TableS1:Comparisonof
theselected,differentlysizedplantnuclearandorganellar(plastid,mitochondrial)genomes,TableS2:
Differentiallyexpressedgenes(DEGs)instudiesonorgan‐/tissue‐specifictranscriptomes(lines3‐26)aswellas
planttranscriptomesunderstressacclimation(lines27‐64),TableS3:Arabidopsisdifferentiallyexpressedgenes
(DEGs)forvarioustreatmentsandstressconditions.
AuthorContributions:M.R.andM.S.:carriedouttheliteraturereview;M.R.:conceptualization;M.R.andM.S.:
writing—originaldraftpreparation;M.S.:preparationofFigures1‐2andTableS1;M.R.:preparationofFigures
3‐4,andTablesS2‐S3;M.R.:writing—reviewandediting;M.R.:supervision;M.R.:fundingacquisition.All
authorshavereadandagreedthesubmittedversionofthemanuscript.Authorsagreetobepersonally
accountablefortheirowncontributionsandforensuringthatquestionsrelatedtotheaccuracyorintegrityof
anypartofthework.Allauthorscontributedtothearticleandapprovedthesubmittedversion.
Funding:ThisresearchwasfundedbytheExcellentInitiative–ResearchUniversity(ID‐UB)programatthe
AdamMickiewiczUniversity,Poznań andKNOWRNAResearchCenteratAdamMickiewiczUniversity,
Poznań,grantno.01/KNOW2/2014.
InstitutionalReviewBoardStatement:Notapplicable.
InformedConsentStatement:Notapplicable.
DataAvailabilityStatement:Publiclyavailabledatasets(TablesS1andS3)wereanalyzedinthisstudy;those
datacanbefoundhere:https://www.ncbi.nlm.nih.gov/datasets/genome/,https://www.ebi.ac.uk/gxa/home,
https://biit.cs.ut.ee/gprofiler/gost,
Acknowledgments:WewouldliketothankcolleaguesfromourInstituteforthevaluableremarksduringthe
preparationofthemanuscript.
ConflictsofInterest:Theauthorsdeclarenoconflictsofinterest.
Abbreviations
AAO aldehydeoxidase
ABAabscisicacid
ABFABSCISICACIDRESPONSIVEELEMENT‐BINDINGFACTOR
ACADMmedium‐chainacyl‐CoAdehydrogenase
ACO 1‐aminocyclopropane‐1‐carboxylicoxidase
ACOXacyl‐CoAoxidase
ACS1‐aminocyclopropane‐1‐carboxylicsynthase
ALA5‐aminolevulinicacid
AOSalleneoxidesynthase
AOX alternativeoxidase
APAPETALA
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APXascorbateperoxidase
ARFauxinresponsefactor
ASanthocyanidinsynthase
asMTacetylserotoninO‐methyltransferase
ASCL‐ascorbicacid
ATHBsmallhomeodomain‐leucinezipperfamily
AUXauxinreceptor
bHLHbasichelix–loop–helix
BLS bacterialleafstreak
bZIP basic(region)leucinezipper
CAM crassulaceanacidmetabolism
CATcatalase
CBP CALMODULIN‐BINDINGPROTEIN
CCOAOMTcaffeoyl‐CoAO‐methyltransferase
CDP CAATdisplacementprotein(transcriptionalrepressor)
CCR cinnamoyl‐CoA:NADPreductase
C3H zincfingertranscriptionfactor
CHI chalconeisomerase
CHS chalconesynthase
C4H 4‐cinnamatehydroxylase
CIPK CBL‐interactingproteinkinase
4CL 4‐coumarate:CoAligase
Clpcaseinolyticprotease
CO CONSTANS
CRK cysteine‐richreceptor‐likekinase
CRY cryptochrome
CXIP CAX‐interactingprotein
DEGs differentially‐expressedgenes
DFR dihydroflavonol4‐reductase
DIMI DIMINUTO
DofDNA‐bindingwithonefinger
DREBdehydration‐responsiveelement‐binding
ECHS shortchainenoyl‐CoAhydratase
EF earlyflowering
EIL ethyleneinsensitive‐like
ER endoplasmicreticulum
EREBP ethylene‐responsiveelementbindingprotein
ERF ethyleneresponsefactor
ESTs expressedsequencetags
ETI effector‐triggeredimmunity
F3H flavanone‐3‐hydroxylase
FIE fertilization‐independentendospermia
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FSL flavonolsynthase
FT FLOWERINGLOCUST
FUL FRUITFUL
FUS fusedinsarcoma
GABA g‐aminobutyricacid
GID GA‐INSENSITIVEDWARF
GRF GrowthRegulatingFactor
HCT hydroxycinnamoyltransferase
HDhomeodomain
HLHhelix‐loop‐helix
HR hypersensitiveresponse
HSF heatshockfactor
HSP heatshockprotein
IFL INTERFASCICULARFIBERLESS
JA jasmonicacid
KAN KANADI
LEA late‐embryogenesisabundant
LHClight‐harvestingcomplex
LEC littleelongationcomplex
LIM homeoboxtranscriptionfactor
LOX lipoxygenase
MADS MINICHROMOSOMEMAINTENANCE1/AGAMOUS/DEFICIENS/SERUMRESPONSE
FACTOR
MAPKmitogen‐assiociatedproteinkinase
MDHAR monodehydroascorbatereductase
MEDEA motifenrichmentindifferentialelementsofaccessibility
MFP multifunctionalprotein
MIOX myo‐inositoloxygenase
MLO mildewlocuso
MYB myeloblastosis
NAC noapicalmeristem/ATAF1/cup‐shapedcotyledon
NAMnoapicalmeristem
NCED 9‐cis‐epoxycarotenoiddioxygenase
NIN noduleinception
OPR 12‐oxophytodienoicacidreductase
OSM osmotin‐likeprotein
OXPHOS oxidativephosphorylation
PAAF 23‐dehydroadipyl‐CoAhydratase
PAL phenylalanineammonialyase
PAMP pathogen‐associatedmolecularpattern
PCD programmedcelldeath
PcG Polycombgroup
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PEAR PHLOEMEARLYDNA‐BINDING‐WITH‐ONE‐FINGER
PEI Cys3Hiszincfingerdomain‐containingprotein
PHB PHABULOSA
PHV PHAVOLUTA
PHY phytochrome
POD peroxidase
PS photosystem
PTI PAMP‐triggeredimmunity
PLATZ plantAT‐richsequenceandzinc‐bindingprotein
REV REVOLUTA
RGA resistancegeneanalogue
RLK receptor‐likekinase
ROS reactiveoxidativespecies
SA salicylicacid
SBPSQUAMOSA‐pROMOTERBINDINGPROTEIN
SOC suppressorofoverexpressionofconstans
SOD superoxidedismutase
STS stachyosesynthase
TCP bHLHDNA‐bindingdomain
TF transcriptionfactor
TUB transcriptionfactorfamily
UF3GT UDP‐glucose:flavonoid3‐O‐glycosyltransferase
WAKL20 wall‐associatedreceptorkinase‐like2
WGD whole‐genomeduplication
WRKYtranscriptionfactorfamily
VIN VERNALIZATIONINSENSITIVE
ZEP zeaxanthinepoxidase
ZIPleucinezipper
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Drought stress has been known to adversely affect growth, development, and productivity of plants to varying extent. Being a multifaceted trait, drought tolerance involves interaction of an array of genes, pathways, and mechanisms. A unique regulatory scheme is adopted by different plants, which provides tolerance to drought stress in association with biochemical and physiological mechanisms. Transcriptome analysis of a drought tolerant [Nagina 22 (N-22)] and drought sensitive (IR-64) cultivars provides insights into the genes/pathways/mechanisms involved in terminal drought stress tolerance. In the present study, comparative physio-biochemical analyses of the rice cultivars under terminal drought stress substantiated their performance. Whole transcriptome analysis of leaf and root from the rice cultivars exposed to terminal drought stress revealed 6077 and 10050 differentially expressed genes (DEGs) in leaf of N-22 and IR-64, respectively, under drought stress. A maximum of 2682 genes were up-regulated exclusively in N-22 while 7198 genes were down-regulated exclusively in leaf of IR-64. Interestingly, the highest number (2594) of genes was down-regulated exclusively in roots of IR-64, while only 1497 gene were up-regulated exclusively in root of N-22. Differential expression of OsNAC10, OsbZIP23, OsABA8ox1, OsCPK4, OsLEA3, and OsNCED4 along with the GO terms enriched with up-regulated genes for transcription factors (TFs), redox homeostasis, and ABA signaling in N-22 under terminal drought stress play crucial roles in stress tolerance. The stress-responsive genes for transcription factors, redox homeostasis, and ABA signaling up-regulated in N-22 were mainly responsible for terminal drought tolerance. These stress-associated genes can be utilized for genetic improvement of rice for drought tolerance.
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