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8 FiguresCharacterization of mango (Mangifera indica L.) transcriptome and chloroplast genome
Abstract
We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80 % of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37 %) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.
Figures
1 3
Plant Mol Biol
DOI 10.1007/s11103-014-0179-8
Characterization of mango (Mangifera indica L.) transcriptome
and chloroplast genome
M. Kamran Azim · Ishtaiq A. Khan · Yong Zhang
Received: 26 October 2013 / Accepted: 4 February 2014
© Springer Science+Business Media Dordrecht 2014
by a combination of Sanger and next generation sequenc-
ing. The draft mango cp genome size is 151,173 bp with
a pair of inverted repeats of 27,093 bp separated by small
and large single copy regions, respectively. Out of 139
genes in mango cp genome, 91 found to be protein cod-
ing. Sequence analysis revealed cp genome of C. sinensis
as closest neighbor of mango. We found 51 short repeats in
mango cp genome supposed to be associated with extensive
rearrangements. This is the first report of transcriptome and
chloroplast genome analysis of any Anacardiaceae family
member.
Keywords Transcriptome analysis · RNA-seq ·
Anacardiaceae · Plant genome
Introduction
Mango (Mangifera indica L.), a member of family Anac-
ardiaceae is an important fruit crop which is commer-
cially grown in over hundred tropical and subtropical
countries (Mukherjee and Litz 2009). According to Food
and Agriculture Organization (FAO) of United Nations,
after banana, mango is the dominant tropical fruit vari-
ety produced worldwide, followed by pineapples, papaya
and avocado (http://www.fao.org/docrep/006/y5143e/
y5143e1a.htm). Major mango growing countries are India,
China, Thailand, Pakistan, Australia, Indonesia, Bangla-
desh, Philippines, Nigeria, Myanmar and Egypt.
The mango tree is considered to have evolved in the
rainforests of South and South-east Asia (Krishna and
Singh 2007). Full-grown mango trees reach a height of
40 m and can stay alive for several 100 years. Mango leaves
are exstipulate, simple and usually alternate; depending on
the cultivar, leaf morphology is highly variable (Mukherjee
Abstract We characterized mango leaf transcriptome and
chloroplast genome using next generation DNA sequenc-
ing. The RNA-seq output of mango transcriptome gen-
erated >12 million reads (total nucleotides sequenced
>1 Gb). De novo transcriptome assembly generated 30,509
unigenes with lengths in the range of 300 to ≥3,000 nt
and 67× depth of coverage. Blast searching against non-
redundant nucleotide databases and several Viridiplantae
genomic datasets annotated 24,593 mango unigenes (80 %
of total) and identified Citrus sinensis as closest neigh-
bor of mango with 9,141 (37 %) matched sequences. The
annotation with gene ontology and Clusters of Ortholo-
gous Group terms categorized unigene sequences into 57
and 25 classes, respectively. More than 13,500 unigenes
were assigned to 293 KEGG pathways. Besides major
plant biology related pathways, KEGG based gene annota-
tion pointed out active presence of an array of biochemical
pathways involved in (a) biosynthesis of bioactive flavo-
noids, flavones and flavonols, (b) biosynthesis of terpenoids
and lignins and (c) plant hormone signal transduction. The
mango transcriptome sequences revealed 235 proteases
belonging to five catalytic classes of proteolytic enzymes.
The draft genome of mango chloroplast (cp) was obtained
Electronic supplementary material The online version of this
article (doi:10.1007/s11103-014-0179-8) contains supplementary
material, which is available to authorized users.
M. K. Azim (*) · I. A. Khan
Jamil-ur-Rehman Center for Genome Research, International
Center for Chemical and Biological Sciences, University
of Karachi, Karachi 75270, Pakistan
e-mail: kamran.azim@iccs.edu; mkamranazim@yahoo.co.uk
Y. Zhang
BGI-Shenzhen, Beishan Road, Yantian District,
Shenzhen 518083, China
Plant Mol Biol
1 3
and Litz 2009). The inflorescence of mango flowers is
rigid and erect, usually 30 cm long, widely branched and
is always cymose. Mango fruit varieties have been known
for attractive colours, savouring smell, delightful taste and
high nutritional value (Mukherjee and Litz 2009). Mango
is an ever green dicot angiosperm. Although several tetra-
ploid individuals were reported, mango is usually a diploid
tree (Mukherjee 1950; Duval et al. 2005; Viruel et al. 2005;
Schnell et al. 2005, 2006). It has 2n = 40 chromosomes
with estimated genome size of 441 mega basepairs (http://
data.kew.org/cvalues/).
During last few years, a number of reports addressed
the genetic diversity of mango for application in culti-
var identification using PCR and sequencing based tech-
niques viz. RAPD, ISSR, DAMD etc. (Srivastava et al.
2012; Chinag et al. 2012; Souza et al. 2011; Rocha et al.
2012; Ravishankar et al. 2011; Hirano et al. 2010; Khan
and Azim 2011). Despite its global importance, genomic
sequence resources available for the mango tree are scarce.
As of October 2013, there are only 684 highly redundant
sequence entries in the GenBank for mango. Large scale
discovery and characterization of functional genes via
genome sequencing or global exploration of the transcrip-
tome are required for better understanding of fundamental
molecular biology of mango.
Recently development of RNA sequencing (RNA-seq)
methodology has facilitated the analysis of transcriptomes
of a number of crop and medicinal plants (Xu et al. 2013;
Duangjit et al. 2013; Sara et al. 2010). RNA-seq is char-
acterized by sequencing of the transcriptome using mas-
sively paralleled next generation DNA sequencing tech-
nology. It is among the most popular techniques of NGS
(Strickler et al. 2012). RNA-seq generate millions of short
cDNA reads which either aligned to a reference genome
or reference transcripts, or assembled de novo to produce
a genome-scale transcription map that consists of both the
transcriptional structure and/or level of expression for each
gene (Mortazavi et al. 2008). Sequencing of RNA has long
been recognized as an efficient method for gene discovery
and remains the gold standard for annotation of both cod-
ing and non-coding genes (Adams et al. 1991; Haas and
Zody 2010). Furthermore, the RNA-seq method offers a
holistic view of the transcriptome, revealing many novel
transcribed regions, splice isoforms, single nucleotide poly-
morphisms (SNPs) and the precise location of transcription
boundaries (Li et al. 2010; Wilhelm et al. 2010). RNA-seq
is expected to revolutionize the manner in which eukaryotic
transcriptomes are analyzed (Wang et al. 2009).
Here we report the characterization of mango leaf tran-
scriptome and chloroplast genome using next generation
sequencing. We generated over 1.0 billion bases of high
quality DNA sequence of mango using RNA-seq tech-
nology and demonstrated the suitability of short-read
sequencing for de novo assembly and annotation of genes
without prior genome information. Moreover, we also
sequenced the mango chloroplast genome with the help
of a blend of Sanger and next generation sequencing. The
results provide a cost effective and efficient way to global
discovery of new functional genes in mango.
Materials and methods
Plant materials
Mangifera indica cultivar Langra used in this study was
grown in Botanical Gardens of University of Karachi,
Karachi, Pakistan. The leaf specimen of the tree used is
preserved in the Herbarium of Department of Botany, Uni-
versity of Karachi, Karachi, Pakistan. Healthy and mature
leaves from same tree were taken for RNA-seq and chloro-
plast DNA sequencing.
RNA isolation, cDNA synthesis and sequencing
Total RNA was isolated from mango leaves using RNAesy
kit (Qiagen GmbH, Hilden, Germany). RNA integrity was
confirmed using a 2100 Bioanalyzer (Agilent Inc., USA).
Beads with oligo(dT) were used to isolate poly(A) mRNA
from total RNA (Qiagen GmbH, Hilden, Germany). The
purified mRNA was fragmented into short fragments using
divalent cations under elevated temperature. The cDNA
was synthesized with random hexamer primers and mRNA
fragments as templates using Superscript®III Reverse
Transcriptase (Invitrogen, Carlsbad, CA, USA). Short
fragments were purified with the PCR extraction kit (Qia-
gen GmbH, Hilden, Germany) followed by end repair and
poly(A) addition. The short fragments were then connected
with sequencing adapters. The paired-end library (with
200 bp insert size) was prepared following the manufactur-
er’s protocol (Illumina Inc., San Diego, CA, USA). Finally,
the library was sequenced using Illumina HiSeq2000 (Illu-
mina Inc., San Diego, CA, USA). The library was linked
the flow-cell containing complementary adapters, and then
bound fragments were amplified to create ‘clusters’. The
adapters were designed to allow selective cleavage of the
forward DNA strand after resynthesis of the reverse strand
during sequencing. The copied reverse strand was then used
to sequence from the opposite end of the fragment. The raw
reads were cleaned by removing adaptor sequences, empty
read and low quality sequences.
Transcriptome de novo assembly
Transcriptome denovo assembly was carried out with short
reads assembling program—Trinity (Grabherr et al. 2011).
Plant Mol Biol
1 3
Trinity combines three independent software modules:
Inchworm, Chrysalis, and Butterfly. Trinity applies these
programs one after the other to process large volumes of
RNA-seq reads. Firstly, Inchworm assembles the RNA-
seq data into the unique sequences of transcripts, often
generating full-length transcripts for a dominant isoform,
but then reports just the unique portions of alternatively
spliced transcripts. Secondly, Chrysalis clusters the Inch-
worm ‘contigs’ into clusters and constructs complete de
Bruijn graphs for each cluster. Each cluster represents the
full transcriptional complexity for a given gene (or sets of
genes that share sequences in common). Chrysalis then par-
titions the full read set among these disjoint graphs. Finally,
Butterfly processes the individual graphs in parallel, trac-
ing the paths that reads and pairs of reads take within the
graph, ultimately reporting full-length transcripts for alter-
natively spliced isoforms, and teasing apart transcripts that
corresponds to paralogous genes. The resultant sequences
are termed as ‘unigenes’.
Annotation and classification of unigenes
Mango unigenes were analyzed by BLASTN (Zhang et al.
2000) against the NR database (NCBI non-redundant
sequence database) with an E-value cut-off of 10−5. The
coding sequences in mango unigenes were also analyzed
using BLASTN against genomic sequence datasets of Cit-
rus sinensis (sweet orange), Populus trichocarpa (black
cottonwood), Vitis vinifera (Grapevine), Ricinus communis
(castor bean), Glycine max (soya bean), Medicago trun-
catula (Barrel Medic) and Arabidopsis thaliana. Unigene
sequences were further aligned by BLASTX to protein
databases; SwissProt, KEGG (Kanehisa et al. 2008) and
COG. This step retrieved proteins with the highest sequence
similarity with the given unigenes along with their func-
tional annotations. In case of disagreement between data-
bases, a priority order of NR, Swiss-Prot, KEGG and COG
was followed. For unigenes that did not align to any of the
above databases, ESTScan software (Iseli et al. 1999) was
used to predict their coding regions and decide sequence
direction.
The Blast2GO and WEGO programs were used for GO
functional annotations, KEGG and COG analysis of mango
unigenes (Conesa et al. 2005; Ye et al. 2006). The analysis
mapped annotated unigenes to GO terms and calculated the
number of unigenes associated with every term.
Comparison with Genbank M. indica sequence entries
Six hundred and eighty four mango sequences (ESTs and
nucleotide sequences) were downloaded from the GenBank
and used for nucleotide BLAST search against 30,509 uni-
genes using an E-value cut-off of 10−5.
Mango chloroplast genome sequencing
A combination of Sanger-based and next-generation sequenc-
ing strategies were used for mango chloroplast DNA (cpDNA)
sequencing. The mango leaves (5.0 grams) were used for iso-
lation of total DNA using AxyGen multisource DNA mini-
prepration kit (Axygen Scientific, USA). Initially, a primer
walking strategy termed as “ASAP: amplification, sequenc-
ing and annotation of plastomes” (Dhingra and Folta 2005)
was used for amplification and Sanger-based sequencing of
inverted repeat (IR) and large single copy (LSC) regions of
cpDNA. Briefly, purified mango DNA was used for genera-
tion of 6.0 kb amplicons with consensus set of primers (Sup-
plementary data) (Dhingra and Folta 2005). The 6.0 kb ampli-
cons were then used for generation of 1.0 kb fragments using
internal sets of primers (Supplementary data) corresponding to
6.0 kb amplicons. Later on, gap filling primers were designed
to fill the gaps within the inverted repeat region (Supplemen-
tary data). The Sanger-based sequencing of the above men-
tioned fragments was carried out by CEQ8000 Genetic Ana-
lyzer (Beckman Coulter Inc., USA). For cycle sequencing
reactions, the DTCS kit (Beckman Coulter Inc., USA) was
used, with conditions as recommended by the suppliers. Fur-
ther mango cpDNA sequencing was carried out by next-gener-
ation sequencing technology of GS FLX System (Roche Inc.,
USA) using Titanium Mini kit and 7.0 μg of purified DNA.
The sequences obtained from Sanger-based sequenc-
ing were assembled using the Lasergene package version
7.1 (DNASTAR Inc., Madison, WI, USA). The sequencing
data from the GS FLX system was assembled using CLC
Genomics Workbench version 3.5.1 (CLCbio, Denmark).
The assembled sequences obtained from Sanger-based
and next generation sequencing were combined using
CLC Genomics Workbench (CLC bio, Denmark). Genome
annotation was performed through the DOGMA server
(Dual Organellar Genome Annotator; (Wyman et al. 2004),
ORF Finder (http://www.ncbi.nlm.nih.gov/projects/gorf/),
and BLAST (Altschul et al. 1990). Repeat analysis was
performed using the REPuter program (Kurtz et al. 2001).
A circular genome map of mango cpDNA was constructed
using the GenomeVx tool (Conant and Wolfe 2008). Con-
struction of multiple alignments and phylogenetic trees
of complete cpDNA sequences was carried out by the
mVISTA comparative genomics tool (Frazer et al. 2004).
Results and discussion
RNA-seq and de novo assembly of mango transcriptomic
sequences
To characterize the mango transcriptome, total RNAs
were isolated from leaves. After DNase treatment and
Plant Mol Biol
1 3
confirmation of RNA integrity using bioanalyzer, total
RNA was used for mRNA preparation, fragmentation and
cDNA synthesis. After cleaning and quality checks, Illu-
mina NGS sequencing generated 12,153,196 sequence
reads, encompassing 1,093,787,640 nucleotides, with each
sequence read averaging ca. 90 bp in length (Table 1). This
dataset has been submitted to the NCBI Short Read Archive
with accession number SRR947746.
Transcriptome de novo assembly was carried out with
short reads assembling program—Trinity (Grabherr et al.
2011). Using this method, initially 85,651 contigs with a
mean length of 238 were generated (Table 2). As shown
in the contig length distribution in Fig. 1, the contig count
is inversely proportional to length. Later on, the contigs
sequences were assembled into 30,509 unigenes. Mean
size of unigenes was 536 bp with lengths in the range of
300 to >3,000 bp (Fig. 2). Sum of all unigenes length was
16,354,267 nucleotides with depth of coverage of 66.8×
[depth of coverage was calculated by dividing number of
clean nucleotides i.e. 1,093,787,640 by sum of nucleo-
tides in 30,509 unigenes (16,354,267 nt)]. The unigenes
were divided into two clusters. In cluster-1, unigenes with
sequence homology >70 % were grouped (prefixed CL);
whereas cluster-2 contained singleton unigenes (prefixed
unigene). The assembled mango transcriptome sequences
have been deposited in the Genbank with Transcription
Shotgun Assembly number SUB363843.
Comparison of assembled unigenes with mango sequences
in Genbank
As of October 2013, the Genbank contained 684 sequence
entries of mango (both gene sequences and ESTs); many of
them are redundant, analyzed in the frame of phylogenetic
studies and yet unpublished. After removing the redun-
dancy, Genbank mango sequences were divided into com-
plete and partial gene sequences. Subsequently, 30 and 59
nonredundant complete and partial mango gene sequences
were found respectively (indicating 89 nonredundant
mango gene sequences in Genbank). These sequences were
submitted to the BLAST searches against 30,509 unigenes
in present mango dataset. Out of 89 nonredundant mango
gene sequences in Genbank, 76 (85.4 %) matched with
assembled unigenes with a cutoff E-value of 10−5. This
analysis provided an evaluation of the quality of unigene
sequences in present dataset. Further analysis showed that
Table 1 Output statistics of mango RNA-seq experiment
* Total clean nucleotides = total clean reads1 × read1 size + total
clean reads2 × read2 size
Total raw
reads
Total clean
reads
Total clean
nucleotides
(nt)
Q20 (%) N (%) GC (%)
15,851,736 12,153,196 1,093,787,640 91.96 0.01 44.73
Table 2 Statistics of assembly of NGS reads using Trinity
Total number Total length (nt) Mean length (nt) N50 Total consensus sequences Distinct clusters Distinct singletons
Contig 85,651 20,364,178 238 291 – – –
Unigene 30,509 16,354,267 536 687 30,509 11,403 19,106
Fig. 1 Length distribution of contigs obtained after assembly of
mango RNA-seq reads
Fig. 2 Length distribution of assembled mango Unigene sequences
Plant Mol Biol
1 3
majority of matched sequences had percent identities more
than 95 % and E-value lower than 10−40 indicating reliabil-
ity of alignment.
Recently mass spectrometry based proteomic analy-
sis identified 538 proteins in mango leaves (Renuse et al.
2012). This mango leave proteome data contained 151 non-
redundant protein sequences (length of the peptides used
for protein matching were in the range of 09–34 amino
acids; mean = 17). Comparative analysis showed that the
present mango leaf transcriptome dataset was in full agree-
ment with proteomic data. The integration of proteomic
and transcriptomic data further evaluate the quality of
assembled unigenes.
Annotation of unigenes
BLAST searching of mango unigene sequences against
nucleotide databases (NR and NT), protein database Swiss-
Prot, as well as KEGG and COG was performed with
Evalue cutoff 10−5. BLAST searches against NR database
annotated 24,593 unigenes out of total 30,509 (80 %) uni-
genes (Table 3). Sequence analyses with NR database and
several Viriplantae species genomic datasets showed that
37 % of C. sinensis coding region sequences matched with
mango sequences, followed by P. trichocarpa (22.5 %), V.
vinifera (18.3 %), R. communis (17.9 %), G. max (17.3 %),
M. truncatula (10.5 %) and Arabidopsis thaliana (6.7 %)
(Fig. 3; Table 4) (10.4 % of mango transcriptome sequences
matched with sequences of other species).
Based on sequence homology, 21,054 mango unigenes
were categorized into 57 functional groups, belonging to
three main GO ontologies: molecular function, cellular
component and biological process (Table 5). The results
showed a high percentage of genes from categories of “cel-
lular process”, “metabolic process”, “cell/cell part”, “orga-
nelle”, “catalytic”, and “binding” with only a few genes
related to “locomotion” and “nucleoid”. On the other side,
genes were not grouped in the categories of “cell killing”,
“extracellular matrix”, “metallochaperone activity”, “nutri-
ent reservoir activity”, “protein tag” and “translation regu-
lator” (Table 5).
To further evaluate the function of the assembled uni-
genes, we searched the annotated unigenes involved in
Clusters of Orthologous Groups (COG). Out of 24,593
NR Blast hits, 7,594 unigenes had a COG classification
(Fig. 4). Among the 25 COG categories, the cluster for
“general function prediction” represented the largest group,
followed by three categories related to transcription, trans-
lation and posttranslational modification (categories J, K
and O; see Fig. 4). Other most predicted gene functions
were replication, recombination, repair and signaling (cat-
egories L and T; see Fig. 4). The categories “cell motility”,
“extracellular structures” and “nuclear structure” were least
represented groups.
To identify active biochemical pathways in mango, the
unigenes were mapped to the reference canonical path-
ways in the Kyoto Encyclopedia of Genes and Genomes
(KEGG) (Kanehisa et al. 2008). The KEGG database con-
tains systematic analysis of inner-cell metabolic pathways
and functions of gene products, which aid in studying the
complex biological behaviors of genes. In total, 13,561
unigenes were assigned to 293 KEGG pathways. The path-
ways with most representation were “metabolic pathways”,
“photosynthesis”, “transcription/translation”, “DNA repair/
recombination”, “signal transduction” and “cell cycle”.
Considerable numbers of unigenes were identified as “vita-
min metabolism”, “N- and O-linked glycan biosynthesis”,
“ubiquitin mediated proteolysis/proteasome”, “endocyto-
sis” and “circadian rhythm”. KEGG analysis discovered an
array of biochemical pathways involved in biosynthesis of
secondary metabolites/natural products known to partici-
pate in plant hormonal, flavors, aromatic and other cellular
processes.
Characterization of natural products biosynthetic pathways
Annotation of mango unigenes identified many genes
involved in phenylpropanoid, flavonoid, flavone/flavonol,
isoflavonoid, terpenoid and carotenoid biosynthetic path-
ways (Pandit et al. 2010; Andrade Jde et al. 2012).
Phenylpropanoids comprise a large group of plant based
natural compounds, derived from phenylalanine (Michal
1999). First step in the phenylpropanoid biosynthesis
pathways is formation of cinnamic acid from phenylala-
nine which leads the formation of cinnamoyl-CoA, p-cou-
maroyl-CoA, feruloyl-CoA and sinapoyl-CoA. These CoA
activated compounds are starting metabolites for the syn-
thesis of lignins (the second most frequent class of com-
pounds in biosphere after cellulose), flavonoids, flavones
and flavonols (Michal 1999). KEGG analyses of mango
transcriptome sequences revealed presence of 13 genes
involved in biosynthesis of above mentioned CoA activated
Table 3 Summary of mango unigene annotation with the nucleotide and protein sequence databases NR, NT, Swiss-Prot, KEGG, COG and GO
The number of unigenes annotated with each database along with total number
NR NT Swiss-Prot KEGG COG GO ALL
24,593 21,974 14,447 13,561 7,594 21,054 25,453
Plant Mol Biol
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compounds. Analysis showed active pathways for the syn-
thesis of several lignins in mango including guaiacyl lignin,
5-hydroxyguaiacyl lignin, synringyl lignin, p-hydroxyphe-
nyl lignin.
Several phenylpropanoid and flavonoid biosynthetic
pathways genes found in the mango transcriptome dataset
were methyltransferases. Mining of mango sequence data
revealed >200 unigenes corresponding to different classes
of methyltransferases. The methyltransferases transfer a
methyl group from a donor to an acceptor. In plants, meth-
ylation occurs on nucleotide bases in DNA and amino acids
in proteins (Lam et al. 2007). This process is involved in
many cellular functions including epigenetic modification
and gene regulation. Methyltransferase are also involved in
methylation of plant secondary metabolites (such as salicy-
clic acid) that are important contributors to taste and aroma
of many fruits and flowers (Tieman et al. 2010). Identifi-
cation of >200 methyltransferases in mango provided a
wealth of data related to this important class of enzymes.
The high number of unigenes encoding methyltransferases
indicated variability in structures and functions which in
turn reflected the diversity in epigenetic mechanisms and
secondary metabolites turnover in mango.
Moreover, mango transcriptome dataset contained 12
enzymes required for the synthesis of following flavonoids
(including flavones and flavonols). Pinostrobin, pinobank-
sin, buetin, dihydrofisetin (futin), naringenin, luteolin,
afzelechin, epiafzelechin, catechin, epicatechin, homoe-
riodictyol, eriodictyol, quercetin and garbanzol (Table 6).
Several of these flavonoids are known to exhibit antioxi-
dant, anti-inflammatory, antimutagenic etc. properties (see
Table 6 for references). For instance, butein is proposed in
Fig. 3 Annotation of mango
unigenes with nonredundant
nucleotide database NR. Pie
diagram showing a E-value dis-
tribution, b percentage identity
distribution and c species distri-
bution of mango unigenes
Plant Mol Biol
1 3
the treatment of breast cancer due to its ability to inhibit
aromatase in the human body (Wang 2005). Interestingly,
two compounds in this list (i.e. homoeriodictyol, eriodic-
tyol) are bitter-masking flavonones (Ley et al. 2005).
The present dataset contained sequences encoding
enzymes for biosynthesis of precursors in Isoflavonoid
biosynthetic pathway (i.e. liquiritigenin and naringenin),
Flavone and flavonol biosynthetic pathway (i.e. apigenin
and kaemferol) and Anthocyanin biosynthetic pathway (i.e.
cyanidin).
A number of terpene and benzenoid metabolism related
genes including geranylgeranyl pyrophosphate synthase,
Farnesyl pyrophosphate synthase and isochorismate hydro-
lase were also found in mango unigenes. Terpenoids and
benzenoids are important natural products in mango. These
genes are reported to involve in fruit ripening process (Pan-
dit et al. 2010; Kulkarni et al. 2013). However, they are not
limited to tissues of fruit ripening and transcribe in leaf tis-
sues as well. Since most these genes are comprised of large
families, most likely different genes would be expressed in
leaf and fruit tissues.
Twenty-two enzyme sequences involved in terpenoid
backbone biosynthetic pathways were present in mango
unigenes. Mevalonate pathway for the synthesis of Isopen-
tenyl-pyrophosphate was found active in mango. Moreover,
enzymes required for syntheses of other key intermedi-
ates i.e. geranyl-pyrophosphate, farnesyl-pyrophosphate
and geranyl-geranyl-pyrophosphate were also present. The
farnesal biosynthetic pathway from farnesyl-pyrophosphate
was also found active as all required enzymes were pre-
sent. Moreover, enzymes for the synthesis of dehydrodeli-
chol-pyrophosphate from farnesyl-pyrophosphate; phy-
tyl-pyrophosphate and nona-prenyl-pyrophosphate from
greanyl-geranyl-pyrophosphate were also present. Among
several monoterpenoid biosynthetic pathways, enzyme for
production of Linalool from geranyl-pyrophosphate was
found. As a terpene alcohol, Linalool has a pleasant scent
and found in many flowering and spice plants (Lewinshon
et al. 2001). Triterpenoid biosynthetic pathway from farn-
eyl-pyrophosphate was found active in mango. However,
enzymes needed for sesqui terpenoid biosynthesis was not
detected in present dataset.
Plant hormone signal transduction pathways in mango
The subsystem based gene annotation identified active
presence of a number of plant hormone signal transduc-
tion pathways in the present dataset. These plant hormones
included auxin, cytokinin, gibberillin, abscisic acid, ethyl-
ene, brassinosteroid, jasmonic acid, salicylic acid. Genes
encoding receptors, enzymes and others proteins of these
signaling pathways and found in the present mango dataset
are given in Table 7.
Table 4 Summary of BLASTN searches of mango coding region sequences (n = 24,642) with the coding sequences of seven Viridiplantae species
Name of plant species Citrus sinensis
(sweet orange)
Populus trichocarpa
(black cottonwood)
Vitis vinifera (Grape-
vine)
Ricinus communis
(Castor beans)
Glycine max (soya
bean)
Medicago truncatula
(Barrel Medic)
Arabidopsis thaliana
Source Citrus Genome DB
(www.citrusgenome
db.org)
Plant Genome DB
(www.plantgdb.org)
www.genoscope.fr)J. Craig Ventor
Institute
(castorbean.jcvi.org/
index.php)
Plant Genome DB
(www.plantgdb.org)
J. Craig Ventor
Institute, Castor
(castorbean.jcvi.org/
index.php)
Plant Genome DB
(www.plantgdb.org)
No. of transcript/
coding region
sequences
46,147 45,033 26,346 31,225 55,787 62,319 41,671
No. of mango coding
sequences matched
(%)
9,141 (37.0) 5,568 (22.5) 4,529 (18.3) 4,427 (17.9) 3,634 (17.3) 2,606 (10.5) 1,663 (6.7)
Plant Mol Biol
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From work in model plants, it is known that the ethyl-
ene receptors (ER) are negative modulators of the plant
hormone ethylene, and therefore likely to play an impor-
tant part in plant cell physiology. In Arabidopsis, ER is
perceived by a family of 05 receptors, divided into two
subfamilies (Bleecker et al. 1998). The type-I subfamily
include ETR1 and ERS1 and the type-II subfamily recep-
tors include ETR2, ERS2 and EIN4. Mining of mango
transcriptome dataset identified a total of five receptor
genes. Multiple alignment and phylogenetic comparisons
of mango ER sequences with representative ER sequences
from other fruit species identified two ETR1 genes
(CL3814 and CL5014), one ETR2 gene (CL3814), ETR2-
like gene (Unigene15424) and EIN4 gene (Unigene2479)
each (Fig. 5). Hence the analysis showed that both ER sub-
family members were present in mango. This study demon-
strates the potential for the whole genome sequence to be
used as a resource for characterization of large multi-gene
families in mango.
Proteolytic enzymes in mango
Proteases or peptidases are involved in myriad important
cellular functions. Few studies have been reported on pro-
teolytic enzymes in mango (Mehrnoush et al. 2012). The
current mango transcriptome analysis revealed 235 uni-
genes (0.8 % of all unigenes) corresponding to proteases.
These unigenes were grouped in five catalytic classes of
peptidases/proteases. Number of unigenes related to dif-
ferent classes of peptidases were as follows; serine pepti-
dases (n = 89), metallo peptidases (n = 72), cysteine pepti-
dases (n = 25), aspartic peptidases (n = 40) and threonine
peptidases (n = 09) (Table 8). This list contains several
plant-specific proteases including Xylem serine protease,
Table 5 Gene ontology (GO) classification of mango transcriptome unigenes
No. Functional class Unigenes No. Functional class Unigenes No. Functional class Unigenes
GO ontology: biological_process GO ontology: cellular_component GO ontology: molecular_function
01 Biological adhesion 195 26 Cell 17,541 43 Antioxidant activity 109
02 Biological regulation 5,891 27 Cell junction 1,183 44 Binding 10,722
03 Carbon utilization 08 28 Cell part 17,541 45 Catalytic activity 10,009
04 Cell killing 01 29 Extracellular matrix 19 46 Electron carrier activity 353
05 Cell proliferation 206 30 Extracellular matrix part 03 47 Enzyme regulator activity 227
06 Cellular component organiza-
tion or biogenesis
4,265 31 Extracellular region 1,056 48 Metallochaperone activity 03
07 Cellular process 14,285 33 Extracellular region part 20 49 Molecular transducer activity 329
08 Death 592 34 Macromolecular complex 2,844 50 Nucleic acid binding transcrip-
tion factor activity
670
09 Developmental process 4,286 34 Membrane 7,249 51 Nutrient reservoir activity 13
10 Establishment of localization 4,334 35 Membrane part 2,698 52 Protein binding transcription
factor activity
102
11 Growth 1,053 36 Membrane-enclosed lumen 1,076 53 Protein tag 04
12 Immune system process 1,090 37 Nucleoid 38 54 Receptor activity 142
13 Localization 4,561 38 Organelle 14,293 55 Structural molecule activity 581
14 Locomotion 31 39 Organelle part 4,393 56 Translation regulator activity 07
15 Metabolic process 13,425 40 Symplast 1,175 57 Transporter activity 1,631
16 Multi-organism process 2,054 41 Virion 03
17 Multicellular organismal proc. 4,285 42 Virion part 03
18 −ve regulation of biological
proc.
1,445
19 +ve regulation of biological
proc.
1,276
20 Regulation of biological
process
5,403
21 Reproduction 2,552
22 Reproductive process 2,548
23 Response to stimulus 7,526
24 Signaling 2,265
25 Single-organism process 5,756
Plant Mol Biol
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thalakoidal processing peptidase, Chloroplast process-
ing peptidase, and Germination-specific cysteine protease.
Highest number of unigenes for a specific protease was
estimated for ATP dependent protease ClpAP (n = 36).
The ClpAP is a two component system energy depend-
ent protease system composed of ClpP, the peptidase and
ClpA, the ATPase. ClpAP is involved in intracellular pro-
teolysis. We found 25 unigene sequences of ClpP (both
cytosolic and chloroplast) which indicated presence of sev-
eral isoforms of ClpP probably due to alternative splicing.
The ClpP isoforms would be responsible for degradation
of different proteins due to variation in substrate specific-
ity as a result of sequence variation at the substrate bind-
ing cleft of ClpP. Mango contained several unigenes related
to papain-like cysteine proteases. These include actinidin
homologues with >65 % sequence similarity (CL3299 and
Unigene4699) and cathepsins L/H homologues with 40 %
sequence similarity (CL3398, CL3842 and CL4516).
Stress response genes
Several stress response genes identified in mango uni-
gene sequences included metallothionein (04 unigenes),
Ubiquitin-protein ligase (03 unigenes), cysteine proteinase
inhibitor (03 unigenes), FtsJ-like methyltransferase (several
unigenes), 14-3-3 protein (12 unigenes), small heat shock
protein (04 unigenes) and chitinase (13 unigenes). Two out
of four metalothionin (MTH) sequences (i.e. Unigene10572
and Unigene12274) were classified as plant MTH type 1.
Sequence motif analysis showed that Unigene12272 codes
for MTH type-2 and Unigene10535 codes for MTH type-3
protein. Therefore present data provided evidence of pres-
ence of type-1, -2 and -3 MTH in mango.
Fig. 4 COG functional classification of mango Unigene sequences.
A RNA processing and modification; B Chromatin structure and
dynamics; C Energy production and conversion; D Cell cycle control,
cell division, chromosome partitioning; E Amino acid transport and
metabolism; F Nucleotide transport and metabolism; G Carbohydrate
transport and metabolism; H Coenzyme transport and metalbolism; I
Lipid transport and metabolism; J Translation, ribosomal structure and
biogenesis; K Transcription; L Replication, recombination and repair;
M Cell wall/membrane/envelope biogenesis; N Cell motility; O Post-
translational modification, protein turnover, chaperones; P Inorganic
ion transport and metabolism; Q Secondary metabolites biosynthesis,
transport and catabolism; R General function prediction only; S Func-
tion unknown; T Signal transduction mechanisms; U Intracellular traf-
ficking, secretion, and vesicular transport; V Defense mechanisms; W
Extracellular structures; Y Nuclear structure; Z Cytoskeleton
Table 6 Analysis of mango transcriptome sequences revealed active biosynthetic pathways for bioactive flavonoids mentioned in the table
No. Name of flavonoid compounds Known bioactivities
1 Pinostrobin, Pinobanksin Antioxidant flavonoids that inhibit peroxidation of low density lipoprotein (Fahey and Stephenson
2002)
2 Homoeriodictyol, eriodictyol Bitter-masking flavanones (Ley et al. 2005)
3 Afzelechin A flavan-3ol, a type of flavonoids, found in Bergenia ligulata (aka Paashaanbhed in Ayurveda tradi-
tional Indian medicine) (en.wikidepia.org/wiki/afzelechin)
4 Garbanzol Antimutagenic flavonoid (Park et al. 2004)
5 Butein A chalconoid with antioxidative, aldose reductase and advanced glycation endproducts inhibitory
effects. (Lee et al. 2008; Wang 2005)
6 Catechin, epicatechain, gallocatechin Flavan-3-ol compounds with antioxidant and number of other health benefits
(en.wikidepia.org/wiki/catechin)
7 Dihydrofisetin (also known as fustin) A flavanonol, a type of flavonoid; showed protective effects on 6-hydroxydopamine-induced neu-
ronal cell death (Park et al. 2007)
8 Quercetin Antioxidant (Edwards et al. 2007)
9 Naringenin A flavanone, a type of flavonoid. It has antioxidant, free radical scavenging, anti-inflammatory,
carbohydrate metabolism promoting, and immune system modulating activities (Mulvihill et al.
2009)
10 Luteolin A flavones with antioxidant and anti-inflammatory activities (López-Lázaro 2009)
Plant Mol Biol
1 3
Mango chloroplast genome
We carried out chloroplast genome sequencing of mango
using Sanger-based and next-generation sequencing
methods. Chloroplast genome contains a pair of inverted
repeat (IR) regions separated by small and large sin-
gle copy regions (SSC and LSC). Initially, 22,918 bp of
the inverted repeat (IR) region were sequenced using the
ASAP protocol (Dhingra and Folta 2005). For this, primers
reported by Dhingra and Folta (2005) were used. Addition-
ally, gap filling primers was designed. Consequently, com-
plete IR region of mango cpDNA was sequenced with size
of 27,093 bp. Furthermore, 5,783 bp of LSC region was
also sequenced using same strategy. Therefore, collectively
32,876 bp of complete IR region and partial LSC region
of mango chloroplast genome was obtained using Sanger-
based sequencing.
To get more sequence coverage, the mango cpDNA
was subjected to pyrosequencing based 454 technology
adopted in GS FLX genome sequencer. The raw data of
GS FLX was analyzed to get finished sequences. GS FLX
sequencer generated sequence data of 10.573 megabases
containing 26,988 reads with average length of 400
nucleotides. This data along with the 32,876 bp sequence
obtained from Sanger sequencing was used to generate
a circular map of mango chloroplast genome contain-
ing 151,173 base pairs. However, a complete cpDNA
Table 7 List of genes involved in plant hormone signaling found in mango mango transcriptome dataset
No. Plant hormone Plant hormone signal transduction pathways genes found in mango transcriptome dataset
1 Auxin auxin influx carrier (AUX1 LAX family),
auxin response factor,
auxin responsive GH3 gene family,
SAUR family protein
2 Cytokinin histidine-containing phosphotransfer protein,
two-component response regulator ARR-A family protein,
two-component response regulator ARR-B family protein
3 Gibberillin gibberellin receptor GID1,
DELLA protein
4 Abscisic acid abscisic acid receptor PYR/PYL family,
protein phosphatase 2C [EC:3.1.3.16],
serine/threonine-protein kinase SRK2 [EC:2.7.11.1],
ABA responsive element binding factor
5 Ethylene ethylene receptor,
serine/threonine-protein kinase CTR1 [2.7.11.1],
mitogen-activated protein kinase 6 [2.7.11.24],
ethylene-insensitive protein 2,
EIN3-binding F-box protein,
ethylene-insensitive protein 3
6 Brassinosteroid protein brassinosteroid insensitive 1,
BR-signaling kinase [2.7.11.1],
brassinosteroid resistant 1/2
7 Jasmonic acid jasmonic acid-amino synthetase,
coronatine-insensitive protein 1,
jasmonate ZIM domain-containing protein,
transcription factor MYC2
8 Salicylic acid regulatory protein NPR1,
transcription factor TGA,
pathogenesis-related protein 1
Fig. 5 Phylogenetic tree generated based on multiple alignment of
12 representative ethylene receptor (ER) sequences and five mango
ER sequences found in present RNA-seq dataset
Plant Mol Biol
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sequence could not be obtained as the 151,173 bp mango
cpDNA sequence contained 30 gaps when compared to
Citrus cpDNA (17 gaps located in intergenic homopoly-
mer repeat regions whereas 13 intragenic gaps). Prelimi-
nary sequence comparison revealed close relationship of
mango and C. sinensis cpDNA sequences. The chloroplast
genome size of C. sinensis is 160,129 base pairs. This
comparison indicated that 95 % of mango chloroplast
genome sequences have been obtained resulting from the
current study. The draft sequence of mango chloroplast
genome was submitted in GenBank with accession num-
ber FJ212316.
Table 8 Proteolytic enzymes found in mango transcriptome dataset
No. Protease Unigenes No. Protease Unigenes
Metallo-peptidases Serine peptidases
1 Zn metallopeptidase (endoproteinase) 12 19 ATP dependent protease Clp; proteolytic subunit (18),
proteolytic subunit (chloroplast) (7), ATPase subunit
(5)
36
2 FTSH4 (2), FTSH9 (3), FTSH2 (1), FTSH6 (2),
FTSH10 (2), FTSH (Chloroplast) (1)
11 20 ATP-dependent protease La (Lon) 9
3 Methionine aminopeptidase (6) Methionine amin-
opeptidase 1A-like (2)
8 21 Serine carboxypeptidase (6), carboxypeptidase type
III (2),
8
4Oligopeptidase A 7 22 Subtilisin like 5
5 Xaa-Pro aminopeptidase 6 23 Protease Do-like 7-like (2), Protease Do-like 2-like
(1), Protease Do-like 9-like (1)
4
6 Mitochondrial processing peptidase 6 24 Thalakoidal processing peptidase 2 4
7 Aminopeptidase (2), Aminopeptidase N-like (2) 4 25 Xylem serine proteinase1 3
8Carboxypeptidase A2-like 3 26 Proline iminopeptidase 3
9 Puromycin-sensitive aminopeptidase 3 27 Mitochondrial inner membrane protease 3
10 Glutamate pro-X carboxypeptidase 2-like 3 28 Site-1 protease 2
11 Caax prenyl protease ste24 2 29 Serine endopeptidase depp2 2
12 Zinc metaloprotesae SLR1821-like isoform 2 1 30 Prolyl oligopeptidase like 2
13 Protease ecfe (RseP peptidase) 1 31 Dipeptidyl peptidase 8-like 2
14 Zinc protease PQQL-like protease 1 32 Ubiquitin-specific protease 21(ESD4-like) serine
protease HtrA 2
1
15 Membrane-bound transcription factor protease Site-2 1 33 Serine endopeptidase II-2 1
16 Endoplasmic reticulum metallopeptidase1 1 34 Leucine endopeptidase 1
17 Aspartyl aminopeptidase-like 1 35 Lysosomal pro-X carboxypeptidase 1
18 Chloroplast processing peptidase 1 36 Glutamyl endopeptidase (choloplastic) 1
37 Protease 4-like 1
Cysteine proteases Aspartic proteases
38 Cysteine peptidase-like 7 49 Aspartic proteinase-nepenthesin-1 (7), aspartic
proteinase-nepenthesin-2 (4)
11
39 Cysteine protease (5), Cysteine protease like (3),
Cysteine protease ATG4B (2),
5 50 Aspartic proteinase-like protein2-like 7
40 Sentrin/sumo-specific protease (2), sentrin-specific
protease (1)
2 51 Signal peptide peptidase-like 2B 6
41 UFM1-specific protease-like 2 52 d-Alanyl-d-alanine endopeptidase 6
42 Cysteine protease 2
43 pyrrolidone-carboxylate peptidase 2 53 Aspartic proteinase (2), Aspartic proteinase 1 (1),
Aspartic proteinase 2 (1)
4
44 Germination-specific cysteine protease 1-like 1 54 Aspartic proteinase-Asp1 3
45 Cysteine proteinase 15A-like 1 55 Aspartic Proteinase-like protein1-like 3
46 Legumain-like proteinase 1 Threonine proteases
47 PPPDE peptidase domain-containing protein2 like 1 56 26S proteasome regulatory subunits 6A, S10B, 6B, 7 7
48 Asparaginyl endopeptidase 1 57 Isoarpartyl peptidase/L-aspargenase2 1
58 Gamma-glutamyltranspeptidase1 1
Plant Mol Biol
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The available sequence of mango cpDNA (151,173 bp;
GC 38.18 %) contains a pair of inverted repeats (IRA and
IRB) of 27,093 bp separated by small and large single copy
(SSC, LSC) regions, respectively (Fig. 6). The inverted
repeat of mango chloroplast is larger as compared to sev-
eral previously reported angiosperms for example length of
cpDNA inverted repeat of A. thaliana is 26,264 bp (Sato
et al. 1999), Solanum tuberosum is 25,595 bp (Chung et al.
2006), Nicotiana tabacum is 25,339 bp (Shinozaki et al.
1986) and Gossypium barbadense is 25,591 bp (Ibrahim
et al. 2006). The length of mango cpDNA IR region is only
97 base pairs larger compared to its closest neighbour C.
sinensis which has 26,996 bp (Bausher et al. 2006). This
finding support the previous observations that contraction
and expansion of IR region of chloroplast DNA is a major
source of size variation of cpDNA among angiosperms
(Chung, et al. 2006).
A total of 139 genes were detected in mango cpDNA
sequence (119 single copy genes while 20 duplicated genes
in inverted repeat regions). 91 genes code for proteins,
including nine duplicated genes in the inverted repeats.
There were four rRNA genes and 29 distinct tRNAs, 7
of which are duplicated in the inverted repeat. Notably,
M. indica cpDNA contains the infA gene which code for
a translation initiation factor and not present in its clos-
est neighbour Citrus genome (Bausher et al. 2006). The
detailed list of gene contents is present in Table 9.
Chloroplast genome-wide comparative analysis was
carried by multiple alignment of cp DNA sequence
from mango and 16 representatives of land plants and 2
Fig. 6 Circular map of mango
chloroplast DNA indicating
LSC, SSC and IR regions and
the color scheme for gene indi-
cation. The map has been con-
structed by GenomeVx at http://
wolfe.gen.tcd.ie/GenomeVx/
(Conant and Wolfe 2008)
Plant Mol Biol
1 3
representatives of Chlorophyta using VISTA web server
(Asif et al. 2013; Khan et al. 2012; Frazer et al. 2004). The
phylogenetic tree also indicated grouping of mango cpDNA
sequences with C. sinensis (citrus sp.), Gossypium hirsu-
tum (cotton) and V. vinifera (red grape). However, the most
closely related sequence is C. sinensis cpDNA (Fig. 7).
Repeats in M. indica chloroplast genome
Along with two large inverted repeats in chloroplast
genome sequences i.e. IRA and IRB, a large number of rel-
atively small repeats have been recently observed (Haberle
et al. 2008). In mango chloroplast genome 51 direct repeats
(Supplementary data) could be found using RePuter
server http://bibiserv.techfak.uni-ielefeld.de/reputer/
submission.html (Kurtz et al. 2001). The RePuter pro-
gram provides software solutions to compute and visual-
ize repeats in whole genomes or chromosomes. It provides
interactive as well as static images of the results. Figure 8
indicates the position of repeats along with their sizes and
orientation. RePuter analysis of mango cpDNA revealed
15 repeats of size >50 bp while rest were less than 50 bp.
These repeats occur as the part of genes as well as inter-
genic spacers. It is interesting to note that presence of
hundreds of repeats in Trachelium caeruleum chloroplast
genome is supposed to be associated with extensive rear-
rangements (Haberle et al. 2008).
Conclusion
Mango genomic research lags that of other crops of eco-
nomic importance. To facilitate biochemical and molecular
biological research in mango, we characterized mango leaf
transcriptome and cpDNA. Most of the resultant unigenes
Table 9 Genes encoded by mango chloroplast DNA
a Partial gene sequences due to gaps in respective regions of mango chloroplast genome
transfer RNA trnH-GUG, trnK-UUU, trnQ-UUG, trnR-UCU, trnC-GCA, trnD-GUC, trnY-GUA, trnE-UUC, trnT-
GGU, trnM-CAU, trnS-UGA, trnG-UCC, trnfM-CAU, trnS-GGA, trnT-UGU, trnL-UAA, trnF-GAA,
trnV-UAC, trnM-CAU, trnT-GGU, trnW-CCA, trnP-UGG, trnI-CAU, trnL-CAA, trnV-GAC, trnI-GAU,
trnI-GAU, trnA-UGC, trnR-ACG, trnA-UGC, trnI-GAU, trnI-GAU, trnV-GAC, trnL-CAA, trnL-UAGa,
trnI-CAU
Photosystem I psa Aa, psa B, psa C, psaJ, psaI
Photosystem II psb A, psb B, psb C, psb D, psb E, psb F,psb H,psb I,psb J, psb L, psb M, psb N, psb T
Assembly stability of photosystem I Ycf3a, ycf4
Ribosomal proteins rps 2, rps 3, rps 4, rps 7, rps 8, rps 11, rps12, rps14, rps15, rps16, rps18, rps19, rpl14, rpl16, rpl20,
rpl22, rpl23, rpl32, rpl33, rpl36
ATP synthase subunits atpA,atpB,atpE, atpF, atpH, atpI
Unknown function YCF Ycf1a, ycf2, ycf15
Ribosomal RNA rrn23, rrn16, rrn5, rrn4.5
NAHD dehydrogenase ndhAa, ndhB, ndhC, ndhD, ndhE, ndhF, ndhGa, ndhH,ndhI, ndhJ, ndhK
Rubisco subunit rbcL
cytochrome related PetA, PetBa, PetD, PetG, PetL, PetN,ccsA
Plastid encoded RNA polymerase rpo Aa,rpo B,rpo C1a, rpo C2
Maturase matKa
Acetyl-CoA carboxylase subunit accD
ATP dependnt protease subunit clpP
Gene for inorganic carbon uptake cemAa
Fig. 7 Phylogenetic tree of cpDNA from 19 plant species (includ-
ing mango) using VISTA comparative genomics server (http://
genome.lbl.gov/vista/mvista/submit.shtml)
Plant Mol Biol
1 3
were aligned with mango sequences deposited in the
Genbank, whereas all of coding regions in unigenes were
matched with proteins sequences identified in mango pro-
teomic dataset. Subsystem based gene annotation provided
information for the production of a number of bioactive fla-
vonoids, carotenoids and terpenoids in mango. These bio-
active natural products are known to have a range of health
beneficial properties. The large number of unigenes identi-
fied in this study provides an important resource for future
studies on mango biology. The advancements in transcrip-
tomic, genomic, epigenomic, proteomic resources of non-
model plants would greatly facilitate research in plant
biology.
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Supplementary resources
May 2014
- ... To our knowledge, there is only one transcriptome report about heat stress in the peel of mango "Shelly" ( Luria et al., 2014). However, there are other transcriptome studies in Mangifera indica L. ( Azim et al., 2014;Wu et al., 2014;Dautt-Castro et al., 2015;Sherman et al., 2015;Srivastava et al., 2016). These works have increased the knowledge about the transcriptional regulation of fruit development and ripening. ...
- ... For the cellular component, transcripts with the most frequent GO terms being " cell " , " cell part " , and " organelle ". Accordingly, the annotated sequences involved in the main GO classification regulate the basic biological and metabolic processes, which were consistent with the most representative GO terms in the mango leaf and fruit transcriptome[19,46]. Since a portion of our transcriptome assembly was generated from plants under salt treatment, stress-and signaling-linked annotation were frequently found in this dataset. ...
- ... Madison metabolomics http://mmcd.nmrfam.wisc.edu/ NMR and MS The genome sequences of 27 fruit and nut crops have been published to date; these include grape ( Jaillon et al., 2007), papaya ( Ming et al., 2008), cucumber ( Huang et al., 2009), apple ( Velasco et al., 2010), strawberry ( Shulaev et al., 2011), tomato (Tomato Genome Consortium, 2012), melon ( Garcia-Mas et al., 2012), banana (D' Hont et al., 2012), Chinese plum ( Zhang et al., 2012), pear ( Wu et al., 2013), watermelon ( Guo et al., 2013), peach ( Verde et al., 2013), kiwifruit ( Huang et al., 2013), orange ( Xu et al., 2013a), mandarin ( Wang et al., 2015), jujube ( Liu et al., 2014), mulberry ( He et al., 2013), pineapple ( Zhang et al., 2014), blueberry ( Gupta et al., 2015), raspberry ( VanBuren et al., 2016), mango ( Azim et al., 2014), macadamia nut ( Nock et al., 2014), cocoa ( Motamayor et al., 2013), coffee ( Denoeud et al., 2014), hazelnut ( Hampson et al., 1996), aubergine ( Hirakawa et al., 2014) and pepper ( Qin et al., 2014). Nevertheless, the additional development of physical and functional annotation and improved genome assembly is required. ...
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