Phylogenetic analysis of phytochrome A gene from Lablab purpureus (L.) Sweet
Journal of Genetic Engineering and Biotechnology volume 20, Article number: 9 (2022)
Phytochromes are the best characterized photoreceptors that perceive Red (R)/Far-Red (FR) signals and mediate key developmental responses in plants. It is well established that photoperiodic control of flowering is regulated by PHY A (phytochrome A) gene. So far, the members of PHY A gene family remains unexplored in Lablab purpureus, and therefore, their functions are still not deciphered. PHYA3 is the homologue of phytochrome A and known to be involved in dominant suppression of flowering under long day conditions by downregulating florigens in Glycine max. The present study is the first effort to identify and characterize any photoreceptor gene (PHYA3, in this study) in Lablab purpureus and decipher its phylogeny with related legumes.
PHYA3 was amplified in Lablab purpureus cv GNIB-21 (photo-insensitive and determinate) by utilizing primers designed from GmPHYA3 locus of Glycine max. This study was successful in partially characterizing PHYA3 in Lablab purpureus (LprPHYA3) which is 2 kb longer and belongs to exon 1 region of PHYA3 gene. Phylogenetic analysis of the nucleotide and protein sequences of PHYA genes through MEGA X delineated the conservation and evolution of Lablab purpureus PHYA3 (LprPHYA3) probably from PHYA genes of Vigna unguiculata, Glycine max and Vigna angularis. A conserved basic helix-loop-helix motif bHLH69 was predicted having DNA binding property. Domain analysis of GmPHYA protein and predicted partial protein sequence corresponding to exon-1 of LprPHYA3 revealed the presence of conserved domains (GAF and PAS domains) in Lablab purpureus similar to Glycine max.
Partial characterization of LprPHYA3 would facilitate the identification of complete gene in Lablab purpureus utilizing sequence information from phylogenetically related species of Fabaceae. This would allow screening of allelic variants for LprPHYA3 locus and their role in photoperiod responsive flowering. The present study could aid in modulating photoperiod responsive flowering in Lablab purpureus and other related legumes in near future through genome editing.
Photoperiod sensitivity is an important trait as it enables crops to adapt to different latitudes. Short-day (SD) crops like Oryza sativa, Lablab purpureus, Phaseolus vulgaris and Glycine max requires photoperiod insensitivity to adapt to a high latitudinal environment . Photoperiod is governed by phytochrome genes which play critical role in responding to the light quantity, quality and periodicity in plants and make communication between different biochemicals signaling pathway for growth and development of crops . Phytochromes are Red (R)/Far-Red (FR) light receptors involving interconversion of inactive R (Pr) to active FR (Pfr) form by red light absorption which triggers its transfer to the nucleus and thus guides gene expression . Phytochrome is the best characterized photoreceptor and its apoproteins are encoded by small multigene families. In recent decade, progress has been made in characterizing the number, molecular properties and biological activity of the photoreceptors that comprise a plant R/FR detecting framework .
Legumes have been documented with vast genetic variation for flowering and photoperiod has been quite involved in governing growth habit, flowering and maturity in these crops . Legumes have been the focus of presently expanding genomics research and the availability of vast genomic resources and established synteny within the Fabaceae family has enabled the identification of candidate genes for flowering in other related species and exploring their molecular physiologies involved in downstream processes . The fundamental genes governing flowering pathway in legumes are conserved from model plant Arabidopsis that contains five PHY (phytochrome) genes (PHYA, PHYB, PHYC, PHYD and PHYE) and each of these gene have crucial role [6, 7]. Different maturity loci, i.e. E-series (E1 to E8) represent a range of allelic composition and each E locus affects flowering time and maturity in Glycine max [8,9,10,11,12,13,14]. Photoperiod sensitivity under different light conditions was found to be related to E1, E3, E4 and E7 . E3 and E4 encode GmPhyA3 and GmPhyA2, respectively, which are homologues of photoreceptor phytochrome A . GmPHYA3 and GmPHYA2 along with GmPHYA1, which is encoded by a homoeologous copy of E4, redundantly or complementarily function in floral induction and de-etiolation responses under various light conditions . E3 and E4 coordinates flowering responses to long-day (LD) conditions with different Red-to-Far-Red (R:FR) quantum ratios. E3 responds to light with high R:FR ratio; plants homozygous for the recessive e3 allele can initiate flowering under the LD conditions generated by fluorescent lamps with a high R:FR ratio . Photoperiod sensitivity and determinacy played important role in evolution of Phaseolus vulgaris . GmFT2a and GmFT5a, two homologues of FT (Flowering locus T), are reported to induce photoperiodic flowering in Glycine max  and they are regulated by E1, E3 (PHYA3) and E4 genes under different photoperiod conditions to induce or repress flowering . Photoperiodic response of PHYA3 under short day and long day conditions affects growth habit by inducing other genes that activate florigens and guides floral initiation at shoot apex .
The research on photoperiod responsive flowering is mainly anchored to few major pulse legumes viz., Glycine max, Pisum sativum, Phaseolus vulgaris, Cajanus cajan and vegetable legumes endured despite being a promising nutritional source. Indian bean [Lablab purpureus (L.) Sweet] is one such underexploited legume with wide range of uses as vegetable, forage, cover crop, split pulse, fodder and medicinal . The molecular information regarding this crop is scarce; nevertheless, it has the potential to become a model pulse crop in genomics era owing to its immense genetic diversity and adaptability . Most landraces of Lablab purpureus are photoperiod sensitive and indeterminate which flower only during short days, while few improved varieties with determinate growth and photoperiod insensitivity are available which flowers within 40 to 50 days across the year. Photoperiod responsive flowering along with growth habit might have played crucial role in domestication and evolution of this crop. Dominant nature of photoperiod sensitivity, indeterminate growth habit and purple flower was reported along with coupling phase of linkage between photoperiod insensitive flowering and determinate growth habit in Lablab purpureus . Molecular tagging of photoperiod responsive flowering in Lablab purpureus discerned that photoperiod insensitive flowering and determinate growth habit is linked and they might be governed by recessive alleles of GmPHYA3 and Dt homologs, respectively . Most recently, allelic characterization of TFL (Terminal Flowering locus) governing growth habit has been reported along with involvement of splice site single nucleotide polymorphism (SNP) for growth habit differences in Lablab purpureus . The role of PHYA3 in photoperiod responsive flowering is already reported in Glycine max and Phaseolus vulgaris, and mutations in E3/PHYA3 conferred photoperiod insensitive and early flowering [3, 26]. Lack of genome sequence data or any molecular information regarding PHYA3 gene or any marker tightly linked to it in Lablab purpureus has limited the molecular characterization of photoperiod responsive flowering in this crop. Looking to possible role of PHYA3 in photoperiod responsive flowering and lack of genome sequence information, the present work is focused on characterization of this gene in Lablab purpureus using candidate gene approach and phylogenetic analysis of legume phytochromes.
Materials and methods
The GmPHYA3 sequence from Glycine max  was obtained in FASTA format from NCBI (National Centre for Biotechnology Information) GenBank database (https://www.ncbi.nlm.nih.gov/genbank/). GmPHYA3 is 9.2kb longer, exon 1 was divided into three frames and primers for each frame were designed using web-based Primer BLAST (Basic Local Alignment Search Tool) from NCBI (Table 1). These primers were utilized for amplification of PHYA3 in Lablab purpureus cv GNIB-21 which is determinate and photoperiod insensitive.
Amplification and sequencing
Genomic DNA was isolated from young fresh trifoliate leaves of GNIB-21 using CTAB method . The DNA quality and quantity were assessed using gel electrophoresis and spectrophotometer (Nanodrop 2000, Thermo Fisher, USA). Both the stock and diluted DNA preparations were stored at −50°C until use. The target frames were amplified in GNIB-21 through Polymerase Chain Reaction (PCR) with Taq DNA polymerase (TaKaRa, Clontech, Japan). PCR mixture prepared in 200 μl contained approximately 100 ng genomic DNA, 200 μM of dNTPs, 10 pmol of forward and reverse primers, standard Taq buffer (Mg2+ plus) and 1 unit of Taq DNA polymerase in total volume of 25 μl reaction. The PCR cycle involved initial denaturation of 95°C for 7 min followed by 35 cycles of 94°C (30 s), 51–55°C (45 s) and 72°C (1 min) and a final extension of 10 min at 72°C. Amplicons giving the single discrete band when resolved on 1.5% agarose gel electrophoresis with the expected product size were purified using column purification with SLS PCR Clean-up Kit (Saffron Life science, Surat, India). Sanger sequencing reaction of purified PCR amplicon was carried out with specific primers using BDT v3.1 Cycle sequencing kit on ABI 3730xl Genetic Analyzer (Applied Biosystems). Bidirectional sequence data obtained from each amplicon were processed using BioEdit . The bidirectional sequence information obtained were processed by merging the sequences from three frames and overlapping sequences were identified in both directions to construct consensus sequence.
Sequence retrieval, alignment and phylogenetic analysis
The processed LprPHYA3 sequence was used as query for BLASTn at https://blast.ncbi.nlm.nih.gov/Blast.cgi for finding homologous sequences with reference to NCBI (National Center for Biotechnology Information) nucleotide database . Sequences showing matches with LprPHYA3 from Fabaceae family were retrieved from NCBI nucleotide database. MEGA X (Molecular Evolution Genetics Analysis) software  was used to align PHYA nucleotide sequences of 16 species from Fabaceae family in addition to Arabidopsis thaliana using the CLUSTAL W alignment algorithm . All the alignment settings were employed at default values; 2160 and 2051 positions with and without gaps were obtained, respectively. The nucleotide substitutions selected with complete deletion of gaps or missing data were used to analyse sequences. The phylogenetic tree was inferred using Maximum Likelihood method based on Tamura-Nei Model . The initial tree was inferred with default setting using Neighbour Joining method and Nearest-Neighbour Interchange was used as ML heuristic search method. The reconstructions of phylogenetic trees were conducted using Maximum Likelihood Method. Bootstraps with 1000 replicates for Poisson correction model were performed to assess node support . The best-scoring ML tree was searched simultaneously to represent the evolutionary history of the 20 specimens tested.
Prediction of conserved motifs
The detection of conserved motifs in DNA sequence of phytochrome gene was performed using online tool MEME (Multiple Em for Motif Elicitation) (https://meme-suite.org/meme/) . This online web-based analysis was performed with minimum and maximum motif width of 6 and 12 residues, respectively, which were used to identify probable motifs, keeping the rest of the parameters at default. The MEME output in HTML showed the motifs as local multiple alignments of the input sequences, as well as in several other formats. MEME HTML output were allowed one or all of the motifs to be forwarded for additional investigation. The results of the MEME analysis were applied to TOMTOM (http://memesuite.org/tools/tomtom), which is the online software performing comparison of given motifs with available databases. The output generated from TOMTOM include sequence-logo graphics on behalf of the alignment of two motifs with p and q value (a measure of false discovery rate) of the match .
Exon prediction, protein prediction and functional analysis
The identified partial sequence of LprPHYA3 was subjected to exon prediction using Eukaryotic GeneMark.hmm version 3.54 . The nucleotide sequence of exon-1 obtained in such a way was translated to protein sequence using standard codon table. This amino acid sequence obtained was further compared with GmPHYA3 sequence. The protein sequence of exon 1 from Lablab purpureus GNIB-21 was used to perform BLASTp in NCBI GenBank database and the sequences showing homology were further used to create multiple alignment using the CLUSTAL W algorithm [29, 31]. Phylogenetic analysis with amino acid sequence of PHYA in 21 different plant species was also performed using JTT model in MEGA X [30, 37]. The online web-based functional analysis tool SMART-EMBL (Simple Modular Architecture Research Tool) (http://smart.embl-heidelberg.de/) Version 9 was used for predicting domains in both GmPHYA3 and LprPHYA3 protein sequences .
LprPHYA3 characterization and phylogenetic analysis
In the present study, Lablab purpureus cv GNIB-21, which is determinate and photo-insensitive, was used for characterizing PHYA3 gene. The sequencing data after processing and analysis revealed the successful characterization of the exon-1 of PHYA3 gene in Indian bean (LprPHYA3- Lablab purpureus PHYA3) for the first time in the world. BLASTn analysis of nucleotide sequence LprPHYA3 indicated highest identity with Vigna unguiculata (95.76%) followed by Vigna angularis (95.67%) and Glycine max (90.90%), all with E-value close to zero.
Phylogenetic tree depicts formation of different clades on the basis of evolutionary changes between the sequences. LprPHYA3 nucleotide sequence was compared with the nucleotide sequences of phytochrome genes of other plant species, most of which, belonged to the Fabaceae family. Phylogenetic analysis showed that this phytochrome A gene evolved from common ancestry root but diverged into different clades during the course of evolution (Fig. 1). The PHYA sequences from Lablab purpureus, Vigna unguiculata and Glycine max form independent clade and are closest to Vigna angularis and Cajanus cajan. This indicates that LprPHYA3 has maximum closeness to Vigna unguiculata, Glycine max, Cajanus cajan and Vigna angularis PHYAs suggesting the evolutionary closeness of the gene in these species. The three outgroups depicted in the tree are Lupinus angustifolius, Lotus japonicus and Arabidopsis thaliana.
Realizing the importance of both DNA and protein sequence alignment in phylogenies, the protein sequence predicted from the exon 1 of LprPHYA3 gene was also studied along with the other sequences to delineate the amino acid changes in the sequence during the course of evolution. Alignment of the amino acid sequences from PHYA homologs was done by CLUSTAL W alignment algorithm and phylogenetic tree for protein sequences was constructed (Fig. 2). The protein alignment also depicts the most probable evolution of LprPHYA3 from common ancestral PHYA gene of Glycine max, Phaseolus vulgaris, Vigna unguiculata and Vigna angularis. This tree depicts Arabidopsis thaliana as an outgroup.
Determination of common motifs in PHYA sequence
Identification of conserved motifs in the PHY A was performed by comparing DNA sequences from these 20 PHY A sequences from different species. The analysis resulted in three conserved sites present in pool of studied sequence. The best result was a 12-nt-long motif GTGCAAAGCATG which was found in all 20 analysed sequence (Table 2). The E-value for best match discussed here was 3.4×10−45. Subsequently, the motif was compared using TOMTOM with a database of Arabidopsis thaliana DAP motifs which resulted in identification of bHLH69 basic helix-loop-helix motif containing transcription factor (p value 1.16×10−4 and E value 1.01×10−1) (Fig. 3).
Domain analysis of GmPHYA3 and LprPHYA3
Domain analysis of GmPHYA3 sequence retrieved from NCBI GenBank database after performing BLASTp search with LprPHYA3 that encodes a protein with 1130 amino acids was carried out using EMBL-SMART platform. This protein displayed normal features of Phytochrome A with five domains viz., GAF (cGMP-specific phosphodiesterase–adenylyl cyclase–FhlA), two PAS (period–ARNT–single-minded) domains and two Histidine kinase-related domains (HKRD) viz., HisKA and HATPase_c as depicted in Fig 4a. The amino acid sequence of LprPHYA3 showed two domains, i.e. GAF sand PAS (Fig 4b). This finding is in congruity with the domain analysis from GmPHYA3.
The deciphering of putative molecular pathways in legumes involving different phytochrome genes and their involvement in governing flowering time will pave way for future research. Various genetic models for this regulatory framework of photoperiod-based flowering with different known loci is available for Glycine max. It is studied in depth for photoperiod control of flowering and different E loci have been reported, out of which, E3 (GmPHYA3) is considered a strong candidate for FT3 and mutations in GmPHYA3 results in early flowering . Different mutations of E3 have been reported in Glycine max and Phaseolus vulgaris that confer significantly early flowering and photoperiod insensitivity [3, 26]. Additionally, naturally occurring E3 mutants depicted a large insertion in fourth intron and one SNP for non-synonymous amino acid substitution in third exon. Naturally occurring e3 allele carries a large deletion spanning exon 4, whereas an induced mutant e3 allele has sustained a 40-bp deletion and frameshift in the middle of exon 1 . Flowering time is a very important trait governing several other correlated functions and molecular identification of flowering networks with these E loci can be used for more efficient breeding strategies . These pathways have been more or less conserved in related legume species involving numerous loci with known or unknown functions. On the basis of available information on related genes and pathway undermining photoperiodic flowering in legumes, a theoretical model for photoperiod dependent flowering pathway is proposed (Fig. 5). In Lablab purpureus, photoperiodic response of flowering may also be governed by circadian clock as it is reported in Glycine max. CONSTANS (CO) is a circadian-regulated gene and acts as prime regulator of this pathway. It activates the expression of florigen gene FT by coordinating light and clock input to leaves. The different genes, their responses to photoperiod and their putative roles mediating this process have been proposed. It is speculated that under SD condition (low R:FR), E3 and E4 are repressed due to lack of exorbitant light condition and thus E1 is also suppressed which thus has no effect on FT2a and FT5a genes leading to early flowering phenotype. Under enriched light condition, i.e. LD condition PHYA3 (E3) and PHYA2 (E4) are expressed activating the expression of E1 which eventually leads to FT2a/FT5a downregulation, flowering repression, indeterminate growth (if TFL1 is present) and delayed maturity. The presence of TFL1 and/or tfl1 convoys indeterminate and determinate growth habit, respectively [1, 15]. Dominant TFL allele suppresses development of floral architecture at shoot apex in indeterminate types; racemes emerge from axillary bud only upon short day conditions where FTs, expressed due to favourable photoperiod condition, might be able to nullify the effect of TFL in competitive manner. Determinate growth habit results from non-functional allele (tfl) of TFL which is unable to suppress flowering in shoot apex and results into determinate growth habit and photoperiod insensitive flowering. This is unveiled by the presence of splice site SNP at third exon in Lprtfl which renders non-functional protein and is responsible for determinate growth habit and photo-insensitive flowering in Lablab purpureus cv GNIB-21 . A non-synonymous SNP in exon 4 of TFL1 locus in cowpea also resulted in determinate growth habit . However, photoperiod responsive expression of growth habit cannot be ignored .
Legumes have always been of persistent interest due to vast genetic variation for photoperiod responses mediating crucial traits like growth habit, flowering and maturity. A summary of different phytochrome A genes in some legumes along with their putative role is represented (Table 3).
Seeking the importance of GmPHYA3 (or E3) in photoperiod adaptation of short-day legumes like Glycine max and Phaseolus vulgaris, it becomes quite important to understand its role in Lablab purpureus which is also a short-day crop. Due to the lack of genome sequence database, there is very scanty information available about Lablab purpureus at molecular level. The present study was successful in characterizing exon-1 in LprPHYA3 by utilizing GmPHYA3 sequence as reference. Comparative gene mapping has been quite useful in deducing genomic structure from related plant species due to conservation of genetic content, gene order and function [25, 46]. This marks the significance of phylogenetic analysis to depict evolutionary closeness of different plant species. DNA-based phylogenies have been dominated in recent years mainly because it yields more phylogenetic information than protein. Since non-synonymous mutations do not affect amino acid sequence but do alter nucleotide sequences of a pair of homologous genes. Both DNA- and amino acid sequence-based phylogenies have been conducted in present study for validation of results obtained by phylogenetic analysis. DNA sequence phylogenies provide opportunity to the researcher for examination of both coding and non-coding regions of gene. However, the use of protein sequences in establishing evolutionary relationships cannot be ignored as amino acid sequences are more conserved than DNA sequences. The degeneracy in genetic code and difference in codon usage in different species makes it less accepted. Protein sequence gives more sensitive sequence alignment as DNA has only 4 characters, while protein has 20. The translation of DNA to protein gives a higher signal-to-noise ratio and thus sharpens up the analysis making it better for phylogenetic studies . PHYA3 gene has most probably been evolved from common ancestral PHYA gene of these species, as depicted from the tree. Previous studies have also shown closeness of Lablab purpureus to Vigna unguiculata and their predictable evolution from Glycine max in Phaseoleae clade . This study has delineated the conservation of PHYA3 among the phaseoleae clade legumes indicating evolutionary closeness with Vigna unguiculata, Vigna angularis and Glycine max employing both DNA and protein sequences for phylogenetic analysis (Figs. 1 and 2). The evolutionary relationship of Lablab purpureus to Glycine max, Vigna unguiculata and Phaseolus vulgaris among the Phaseoleae clade has been reported earlier [48,49,50]. This will aid in isolating allelic variants of PHYA3 from Lablab purpureus by utilizing model plants like Glycine max and Phaseolus vulgaris. Characterization of the full gene could pioneer the extensive photoperiodic flowering control mechanism in Lablab purpureus.
Phytochromes mediates light responses by interacting with multiple partners to modulate transcription of downstream target genes. The transcription factor (TF) containing basic helix-loop-helix (bHLH) motif interacts physically with red and far-red photoreceptor, phytochrome, called Phytochrome Interacting Factors (PIF) . The present study was also successful in identifying bHLH69 as conserved motif for PHYA gene (Fig. 3 and Table 2). The TF with bHLH motif has already been known to be involved in regulating circadian rhythm in Arabidopsis [52, 53]. Presence of DNA binding motif (bHLH) in PHYA indicates that it might compete with PIFs for DNA binding to repress flowering . The present study also deciphered the domains encoded by exon 1 of LprPHYA3 (Fig. 4) which are in congruity with the Glycine max PHYA3 . This implies to the fact that exon 1 in LprPHYA3 codes for GAF and PAS domains with chances of conserved functions. The plant phytochromes detect light via their amino-terminal photosensory module (PSM) comprising N-terminal extension (NTE), period–ARNT–single-minded (PAS), cGMP-specific phosphodiesterase–adenylyl cyclase–FhlA (GAF) and phytochrome-specific (PHY) domains with the help of a bilin chromophore. C-terminal output module (OPM) is shared by two PAS on the N-terminal side and a histidine kinase-related domain (HKRD) . NTE is related to the stability of light-activated phytochromes and interacts with the part of GAF which binds to PɸB for lyase activity and reversible Pr/Pfr photo-transformation. PAS domain represents transducer domain that mediates light signal from input photosensory domain to output module. HKRD domain plays major roles in dimerization, nuclear import and localization . LprPHYA3-Exon 1 encodes GAF and PAS domain of phytochrome genes which belongs to the photo-sensory module and is responsible for convertible Pr/Pfr transformation as well as light-signal transduction from this module to output module, respectively . Characterization of full gene sequence of PHYA3 in Lablab purpureus would unravel the different domains involved in downstreaming light-mediated response to the signaling pathway along with their putative roles.
Partial characterization of LprPHYA3 would facilitate allelic characterization in relation to photoperiod responsive flowering in Lablab purpureus. Phylogenetic analysis indicated that complete characterization of LprPHYA3 would be possible utilizing sequence information from related legumes. The presence of conserved DNA binding motif (bHLH69) in PHYA gene indicated that it might repress flowering by competing for DNA binding with bHLH containing TFs. Domain analysis of protein-encoding LprPHYA3 would unfold the signaling pathways and their interaction with different proteins from PEBP (Phosphatidyl ethanolamine-binding protein) family genes that would guide flowering response.
The continued progress in this direction would entice further questions to address in future like characterization and identification of allelic variants for LprPHYA3 and their role in modulating photoperiod responsive flowering. Additionally, qPCR studies could also be undertaken for relative expression studies of PHYA3 in LD and SD conditions. The role of LprPHYA3 may be confirmed through genome editing by utilizing partial sequence reported in the present study. These efforts would accelerate the understanding of flowering time and growth habit regulation in Lablab purpureus in response to changed photoperiod.
Availability of data and materials
The dataset supporting the conclusions of this article are included within the article. The sequencing data have been submitted as supplementary material.
- PHY :
Flowering locus T
Single nucleotide polymorphism
National Centre for Biotechnology Information
Basic Local Alignment Search Tool
Molecular Evolution Genetics Analysis
(Multiple Em for Motif Elicitation)
Cetyl trimethyl ammonium bromide
Polymerase chain reaction
Simple Modular Architecture Research Tool
N-Phosphodiesterase–adenylyl cyclase–FhlA (GAF)
Histidine kinase-related domain
Phosphatidyl ethanolamine-binding protein
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The work was supported by the funds provided by Gujarat State Government, Gandhinagar, Gujarat, India, and Indian Council of Agricultural Research, New Delhi, India
This research work was supported by Department of Genetics and Plant Breeding, Navsari Agricultural University, Gujarat, India. The research fund was utilized for purchasing reagents and conducting laboratory works.
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Krishna, S., Modha, K., Parekh, V. et al. Phylogenetic analysis of phytochrome A gene from Lablab purpureus (L.) Sweet. J Genet Eng Biotechnol 20, 9 (2022). https://doi.org/10.1186/s43141-021-00295-z