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Lupins, like other legumes, have a unique biosynthesis scheme of 5-deoxy-type flavonoids and isoflavonoids. A key enzyme in this pathway is chalcone isomerase (CHI), a member of CHI-fold protein family, encompassing subfamilies of CHI1, CHI2, CHI-like (CHIL), and fatty acid-binding (FAP) proteins. Here, two Lupinus angustifolius (narrow-leafed lupi...
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... on the recently published data ( Ngaki et al., 2012;Chu et al., 2014;Dastmalchi and Dhaubhadel, 2015;Liu et al., 2015) the reference set of 172 CHI-fold protein sequences has been selected (Supplementary Table 2). These sequences were aligned to the sequence of the narrow-leafed lupin genome (PRJNA179231) and transcriptomes of L. angustifolius (PRJNA248164, GBRP00000000.1), ...
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... group assignment according to Kroc et al. (2014). 8), CHIL1 marker was mapped in linkage group NLL-03 of the L. angustifolius genetic map, whereas CHIL2 was localized in NLL-15 ( Table 2). ...
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... narrow-leafed lupin genome and transcriptome were screened with 172 CHI-fold reference protein sequences (Supplementary Table 2) belonging to six main subfamilies (CHI1, AtCHI/TT5/CHI2, AtFAPb/CHI3A, ATFAPa1/CHI3B, AtFAPa2/CHI3C, AtCHIL/CHI4). Mining of the L. albus tran- scriptome resulted in identification of 20 CHI-fold like sequences but multiple alignment survey revealed that 5 were redundant and 4 truncated. ...
Citations
... However, it is important to note that at least two stem representatives of polyploid crown genera, including Stenochlaena (Blechnaceae) [80,81] and Cyclocarya (Juglandaceae) [82], are known to have emerged immediately above the K/Pg boundary in the strata of western North America [29,34,83]. Examples of duplicated genes retained across the K/Pg boundary in both Fabaceae and Stenochlaena include chalcone isomerase (chi1/2) genes, which also function in seed coat traits and other stress-related factors [84][85][86][87]. Clearly, this is a topic worth further investigation. ...
These authors contributed equally to this work. Abstract: Physical dormancy (PY) due to a water-impermeable seed/fruit coat is one of the characteristic features of many species of Fabaceae; however, the timing and context of the evolution of this trait are poorly understood. In this investigation, fossil and molecular data are used to constrain the timing of the evolution of PY. The phylogenetic reconstruction programs GB-to-TNT and BEAUTi/BEAST are used to create chloroplast gene-based (rbcL and matK) phylogenies of taxa with well-represented fossil records. PY and non-dormancy are mapped to the terminals of the phylogeny, and ancestral states are reconstructed using parsimony. The initial evolution of PY in Fabaceae is reconstructed to have occurred sometime in the interval between divergence from Polygalaceae (late Campanian) to the diversification of crown-group Fabaceae (late Paleocene) when Fabaceae is known to have undergone multiple whole genome duplication (WGD) events across the Cretaceous/Paleogene (K/Pg) boundary. As in Nelumbo, another taxon with PY, Fabaceae may have developed PY in association with climatic change and WGD across the K/Pg boundary. The evolution of PY in association with WGD at the K/Pg boundary is an intriguing hypothesis that requires further investigation.
... Of these, type I and type II CHIs are catalytically active and represent bona fide CHIs, while the catalytic activity is lost in type III and type IV CHIs. Type I CHIs are ubiquitous in vascular plants and catalyze the conversion of 6′-hydroxychalcone into 5-hydroxyflavanone, while type II CHIs are primarily found in leguminous plants and have a broader substrate specificity [1,13]. In addition to catalyzing the conversion of 6′-hydroxychalcone to 5hydroxyflavanone, type II CHIs catalyze the conversion of 6′-deoxychalcone to 5deoxyflavanone [14,15]. ...
... It has been reported that the expression patterns of CHI genes differ across plant tissues owing to distinct functions in the different tissues. The CHI genes of Scutellaria lateriflora are mostly expressed in the roots [41], which is similar to the expression patterns observed in leguminous plants and could be attributed to the interactions between signal molecules and rhizobia [11,13,42]. The expression levels of the CHI genes of Fagopyrum dibotrys are high in petals and low in stems [43]. ...
... Previous studies on other plants have demonstrated that CHIs partake in the formation of pericarp color and influence the bulb color in onion [44] and seed coat color in A. thaliana. [13]. The high content of flavonoids in the leaves of C. nitidissima could be correlated to the high expression levels of CnCHI1/4 [27]. ...
Camellia nitidissima is a woody plant with high ornamental value, and its golden-yellow flowers are rich in a variety of bioactive substances, especially flavonoids, that are beneficial to human health. Chalcone isomerases (CHIs) are key enzymes in the flavonoid biosynthesis pathway; however, there is a scarcity of information regarding the CHI family genes of C. nitidissima. In this study, seven CHI genes of C. nitidissima were identified and divided into three subfamilies by phylogenetic analysis. The results of multiple sequence alignment revealed that, unlike CnCHI1/5/6/7, CnCHI2/3/4 are bona fide CHIs that contain all the active site and critical catalytic residues. Analysis of the expression patterns of CnCHIs and the total flavonoid content of the flowers at different developmental stages revealed that CnCHI4 might play an essential role in the flavonoid biosynthesis pathway of C. nitidissima. CnCHI4 overexpression significantly increased flavonoid production in Nicotiana tabacum and C. nitidissima. The results of the dual-luciferase reporter assay and yeast one-hybrid system revealed that CnMYB7 was the key transcription factor that governed the transcription of CnCHI4. The study provides a comprehensive understanding of the CHI family genes of C. nitidissima and performed a preliminary analysis of their functions and regulatory mechanisms.
... The CHI-fold protein family in A. fistulosum has been identified in this study. In previous studies, CHI-fold family protein was encoded by a small gene family, which varies from species to species (Ngaki et al., 2012;Przysiecka et al., 2015;Zhu et al., 2021). Four CHI-fold family protein genes have been isolated from A. fistulosum. ...
Naringenin is an essential precursor for all flavonoids, and effectively promoting naringenin production is crucial in metabolic engineering. The interaction between plant metabolic enzymes ensures metabolic flux. The effect can effectively improve the natural product synthesis of engineering microbial systems. In this study, chalcone isomerase genes in Allium fistulosum have been identified. The expression of AfCHIL is closely related to the accumulation of anthocyanins, and the expression of AfCHIL and AfCHS was highly synchronized. Yeast two-hybrid and firefly luciferase complementation imaging assay further confirmed AfCHIL physically interacted with AfCHS/AfCHI. The bioconversion experiment confirmed that AfCHIL reduced the derailment produced by AfCHS and increased the yield of naringenin. In addition, a system of biosynthesis naringenin involved in AfCHS was constructed, and these results suggested that the potential function between CHS with CHIL advanced naringenin production effectively. In conclusion, this study illustrated the function of AfCHIs in Allium fistulosum and provided new insight into improving the synthesis efficiency of naringenin.
... angustifolius) have been trailed as potential normalizing genes. [77][78][79] Yet, we only considered testing the three best candidate reference genes previously considered in blue lupin by Taylor et al. as this was the only study addressing several experimental conditions, organ types, and cultivars in the expression stability of the candidate genes, which strongly justified their validation for RT-qPCR analysis in Andean lupin. 46 Our results are comparable with those of Taylor et al., where the LmUBC gene was the best candidate reference gene. ...
BACKGROUND
Andean lupin (Lupinus mutabilis Sweet) is an important leguminous crop from South America with a high protein content. In Ecuador, lupin yields are severely affected by the infestation of Delia platura larvae on germinating seeds. The application of elicitor molecules with activity against herbivorous insects to control D. platura infestation constitutes an unexplored and promising alternative for chemical insecticides. In this study, methyl jasmonate (MeJA), hexanoic acid, menadione sodium bisulfite, and DL‐β‐aminobutyric acid were evaluated for their ability to induce resistance against D. platura in three commercial lupin cultivars.
RESULTS
Only seeds pretreated with MeJA significantly impaired insect performance during choice and no‐choice assays. Additionally, fitness indicators such as seed germination and growth were not affected by MeJA treatment. To investigate the molecular mechanisms behind the MeJA‐mediated resistance, RT‐qPCR assays were performed. First, RT‐qPCR reference genes were validated, showing that LmUBC was the most stable reference gene. Next, expression analysis over time revealed that MeJA application up‐regulated the activity of the jasmonic acid biosynthetic genes LmLOX2 and LmAOS, together with other jasmonate‐related defense genes, such as LmTPS1, LmTPS4, LmPI2, LmMBL, LmL/ODC, LmCSD1, and LmPOD.
CONCLUSION
This study indicates that MeJA can be used as an environmentally friendly elicitor molecule to protect Andean lupin from D. platura attack without fitness cost. MeJA application induces plant defense responses to insects in Andean lupin that may be modulated by the onset of terpenoid biosynthesis, proteinase inhibitors, lectins, polyamines, and antioxidative enzymes. © 2021 Society of Chemical Industry.
... Online BLAST results revealed a 22%-98% homology between the CHI folding proteins. We renamed the gene ID of A. thaliana and G. max according to the literature (Przysiecka et al. 2015). Fagaceae species were renamed according to the size of the gene ID because the genomic annotation information was incomplete (Supplementary Table S1). ...
Chalcone Isomerase (CHI) catalyzes the biosynthesis of flavonoids and secondary metabolism in plants. Currently, there is no systematic analysis of CHIs gene family in Fagaceae which is available. In this study, twenty-two CHI proteins were identified in five species of the Fagaceae family. The CHI superfamily in Fagaceae can be classified into three subfamilies and five groups using phylogenetic analysis, analysis of physicochemical properties, and structural prediction. Results indicated that serine (Ser) and isoleucine (Ile) residues determine the substrate preferred by active Type I Fagaceae CHI, and the chalcone isomerase-like (CHIL) of Fagaceae had active site residues. Adaptive analysis of CHIs showed that CHIs are subject to selection pressure. The active CHI gene of Fagaceae was located in the cytoplasm, and it had the typical gene structure of CHI and contains four exons. All the twenty-two identified CHIs had the conserved domain motif 3, and the different groups had their own structural characteristics. In the process of fatty acid binding protein (FAP) evolution to CHIL and CHI, the physical and chemical properties of proteins also had significant differences in addition to changes in protein functions.
... They are known to participate in a large number of physiological and biochemical processes including photosynthesis, respiration, growth and development, and plant defense against various stresses (Przysiecka et al., 2015). Moreover, flavonoids have multiple pharmacological activities and play important roles in human health and diet (Przysiecka et al., 2015;Borovaya and Klykov, 2020). ...
... They are known to participate in a large number of physiological and biochemical processes including photosynthesis, respiration, growth and development, and plant defense against various stresses (Przysiecka et al., 2015). Moreover, flavonoids have multiple pharmacological activities and play important roles in human health and diet (Przysiecka et al., 2015;Borovaya and Klykov, 2020). Chalcone isomerase (CHI, EC5.5.1.6.) is a key enzyme involved in the flavonoid biosynthesis, which catalyzes the conversion of chalcones to flavanones leading to the different subgroups of flavonoid compounds (Yin et al., 2019;Nabavi et al., 2020). ...
... Identification and Sequence Analysis of CHI Gene Family CHI genes from Arabidopsis and soybean (Dastmalchi and Dhaubhadel, 2015;Przysiecka et al., 2015) were used as queries in a BLASTx to search against transcriptome and genome sequence of D. cambodiana (Zhu et al., 2016Ding et al., 2018). Candidate DcCHI sequences were further validated their putative protein domain signatures based on database searches PFAM 1 and CDD. 2 The calculated theoretical molecular weight and isoelectric point of proteins were calculated using ExPASy. ...
Dragon’s blood is a traditional medicine in which flavonoids are the main bioactive compounds; however, the underlying formation mechanism of dragon’s blood remains largely poorly understood. Chalcone isomerase (CHI) is the key enzyme in the flavonoid biosynthesis pathway. However, CHI family genes are not well understood in Dracaena cambodiana Pierre ex Gagnep, an important source plant of dragon’s blood. In this study, 11 CHI family genes were identified from D. cambodiana, and they were classified into three types. Evolutionary and transcriptional profiling analysis revealed that DcCHI1 and DcCHI4 might be involved in flavonoid production. Both DcCHI1 and DcCHI4 displayed low expression levels in stem under normal growth conditions and were induced by methyl jasmonate (MeJA), 6-benzyl aminopurine (6-BA, synthetic cytokinin), ultraviolet-B (UV-B), and wounding. The recombinant proteins DcCHI1 and DcCHI4 were expressed in Escherichia coli and purified by His-Bind resin chromatography. Enzyme activity assay indicated that DcCHI1 catalyzed the formation of naringenin from naringenin chalcone, while DcCHI4 lacked this catalytic activity. Overexpression of DcCHI1 or DcCHI4 enhanced the flavonoid production in D. cambodiana and tobacco. These findings implied that DcCHI1 and DcCHI4 play important roles in flavonoid production. Thus, our study will not only contribute to better understand the function and expression regulation of CHI family genes involved in flavonoid production in D. cambodiana but also lay the foundation for developing the effective inducer of dragon’s blood.
... L. angustifolius genome contains two FTa and two FTc genes, which putatively arose from single copies by lineage-specific duplication, whereas the whole FTb subclade is absent . Indeed, L. angustifolius was recently used as a reference species in several phylogenetic studies addressing the influence of wholegenome and local duplications on the evolutionary fate of selected legume-specific and plant-wide gene clades (Przysiecka et al., 2015;Narożna et al., 2017;Szczepaniak et al., 2018;Czyż et al., 2020). The differences in the expression profiles for FTa and FTc genes, as established in the present study, provided novel evidence supporting the hypothesis on a functional divergence of particular duplicates. ...
Narrow-leafed lupin (Lupinus angustifolius L.) is a moderate-yielding legume crop known for its high grain protein content and contribution to soil improvement. It is cultivated under photoperiods ranging from 9 to 17 h, as a spring-sown (in colder locations) or as an autumn-sown crop (in warmer regions). Wild populations require a prolonged cold period, called vernalization, to induce flowering. The key achievement of L. angustifolius domestication was the discovery of two natural mutations (named Ku and Jul) conferring vernalization independence. These mutations are overlapping deletion variants in the promoter of LanFTc1, a homolog of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene. The third deletion, named here as Pal, was recently found in primitive germplasm. In this study, we genotyped L. angustifolius germplasm that differs in domestication status and geographical origin for LanFTc1 alleles, which we then phenotyped to establish flowering time and vernalization responsiveness. The Ku and Jul lines were vernalization-independent and early flowering, wild (ku) lines were vernalization-dependent and late flowering, whereas the Pal line conferred intermediate phenotype. Three lines representing ku, Pal, and Ku alleles were subjected to gene expression surveys under 8- and 16-h photoperiods. FT homologs (LanFTa1, LanFTa2, LanFTc1, and LanFTc2) and some genes selected by recent expression quantitative trait loci mapping were analyzed. Expression profiles of LanFTc1 and LanAGL8 (AGAMOUS-like 8) matched observed differences in flowering time between genotypes, highlighted by high induction after vernalization in the ku line. Moreover, these genes revealed altered circadian clock control in Pal line under short days. LanFD (FD) and LanCRLK1 (CALCIUM/CALMODULIN-REGULATED RECEPTOR-LIKE KINASE 1) were negatively responsive to vernalization in Ku and Pal lines but positively responsive or variable in ku, whereas LanUGT85A2 (UDP-GLUCOSYL TRANSFERASE 85A2) was significantly suppressed by vernalization in all lines. Such a pattern suggests the opposite regulation of these gene pairs in the vernalization pathway. LanCRLK1 and LanUGT85A2 are homologs of A. thaliana genes involved in the FLOWERING LOCUS C (FLC) vernalization pathway. Lupins, like many other legumes, do not have any FLC homologs. Therefore, candidate genes surveyed in this study, namely LanFTc1, LanAGL8, LanCRLK1, and LanUGT85A2, may constitute anchors for further elucidation of molecular components contributing to vernalization response in legumes.
... Table S1: Candidate genes identified in regions of the P. vulgaris (2.0) genome where high nucleotide diversity (π) was discovered in landrace genotypes compared to PPB genotypes [5,32,33,35,[37][38][39]46,63,67,[111][112][113][114][115]. Table S2: Candidate genes identified in regions of the P. vulgaris (2.0) genome where SNPs with significantly high weighted FST values (>0.5) were found [40,[42][43][44]46,116,117]. Table S3: F-test of fixed and Pearson's χ 2 test of random effects in the combined GLIMMIX mixed model analysis of the Honduran panel genotypes tested in multiple field locations in Ontario, Canada and Yorito, Honduras, 2014-2015. ...
Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.
... Hane et al. estimated the Papilionoideae radiation at 58 mya with genistoid lineage separation from the other Papilionoideae legumes at 54.6 mya, followed by whole-genome triplication in the genistoid lineage at 24.6 mya [11]. Additionally, the ancient polyploidy event has been confirmed based on an analysis of several genes, such as chalcone isomerases (CHI) [62], phosphatidylethanolamine binding proteins (PEBP) [30], isoflavone synthetases (IFS) [63], and cytosolic and plastid acetyl-coenzyme A carboxylases (ACCase) [64]. All listed genes are present in the narrow-leafed lupin genome in multiple variants and evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. ...
... During the early divergence of some downstream lineages, dated to roughly~30-55 mya, additional independent WGD events probably occurred, affecting Mimosoideae-Cassiinae-Caesalpinieae, Detarieae, Cercideae, and Lupinus clades [75]. Large-scale duplication and/or triplication in the L. angustifolius genome has been well-evidenced by recent studies involving linkage and comparative mapping [17,36] and microsynteny analysis of selected gene families [30,31,34,62,63]. These WGD events apparently contributed to multiplication of the gene copy number of L. angustifolius GS and PEPC genes because hypothetical duplicates were found in sister branches of the phylogenetic tree and the genome regions harboring these genes shared common collinearity links. ...
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
... Later, more chromosome markers were generated as part of research whose goal was to characterise the important processes or metabolic pathways in L. angustifolius, and these markers were introduced into the genome map. The BACs analysed were carrying sequences connected with Phomopsis stem blight resistance (Ksiazkiewicz et al. 2013), sequences of genes of flowering induction Nelson et al. 2017) and genes of chalcone isomerase (Przysiecka et al. 2015). ...
Lupins are a group within Genisteae interesting from the point of view of their complex evolutionary history, which is the result of their paleoploid origin (Atkins et al in Lupins as crop plants: biology, production, and utilization. CAB International, pp 67–92, 1998; Gladstones in Lupins as crop plants: biology, production, and utilization. CAB International, pp. 1–36, 1998). Contemporary species are characterised by a striking diversity of chromosome numbers. Their genomes vary in size and consist of many small and similar length chromosomes. The Old World lupins and New World lupins are different in their cytological traits such as the basic and somatic chromosome numbers. Here, we summarise the cytogenetic research on genome size estimation, chromosome number identification and integrative genetic and cytogenetic mapping. The importance of narrow-leafed lupin as a crop and the relative wealth of data concerning its cytogenetic and genetic characterisation have led to its role as a useful model species within the genus Lupinus and a reference for better understanding of legume genome evolution. Cytogenetic comparative mapping, using L. angustifolius-derived markers, has revealed the karyotype variation in lupins. Insight into chromosome rearrangements has led to a hypothetic model of lupin karyotype evolution. This research has established a starting point for the further analysis of the structure and diversity of lupin karyotypes in the facet of evolution.
