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Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

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Classification of chickpea F-box genes. The number of F-box genes in each group are shown.
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Fig1: Classification of chickpea F-box genes. The number of F-box genes in each group are shown.

Mentions: Using the SMART and Pfam databases, the C-terminal domains in chickpea F-box genes were identified, based on which, the F-box genes were classified into 10 subfamilies (Figure 1). The most abundant F-box genes (86) were those that did not have any known functional domain other than the F-box domain and were classified as the FBX subfamily. The other 199 genes displayed the presence of one or more known functional domains at their C-terminals and were classified as FBD (39) which contained FBD domain, FBK (34) having kelch repeats, FBL (32) containing LRRs (leucine rich repeats), FBA (25) having F-box associated domain (FBA), FBDUF (16) having domain of unknown function (DUF), FBT (10) containing TUB domain, FBP (8) containing PP2 (phloem protein 2) domain, FBW (4) with WD40 repeats, and FBO (31) containing other domains such as LysM, PAS, PAH, Sel1, Actin, Cupin, PPR, Zf-MyND, SNF2, SNO among others (Figure 1). Further, the unknown motifs in F-box genes of the FBX subfamily, that were found to have no known functional domain other than the F-box, were investigated using MEME. Out of the 50 motifs identified, thirteen were found to be conserved in at least five of the F-box genes [see Additional file 3: Table S3]. Two of these motifs (motifs 3 and 32) were conserved in more than 20 chickpea F-box genes and three motifs (motifs 1, 3 and 4) were found to be statistically significant (e value less than e-100).Figure 1


Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Classification of chickpea F-box genes. The number of F-box genes in each group are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340835&req=5

Fig1: Classification of chickpea F-box genes. The number of F-box genes in each group are shown.
Mentions: Using the SMART and Pfam databases, the C-terminal domains in chickpea F-box genes were identified, based on which, the F-box genes were classified into 10 subfamilies (Figure 1). The most abundant F-box genes (86) were those that did not have any known functional domain other than the F-box domain and were classified as the FBX subfamily. The other 199 genes displayed the presence of one or more known functional domains at their C-terminals and were classified as FBD (39) which contained FBD domain, FBK (34) having kelch repeats, FBL (32) containing LRRs (leucine rich repeats), FBA (25) having F-box associated domain (FBA), FBDUF (16) having domain of unknown function (DUF), FBT (10) containing TUB domain, FBP (8) containing PP2 (phloem protein 2) domain, FBW (4) with WD40 repeats, and FBO (31) containing other domains such as LysM, PAS, PAH, Sel1, Actin, Cupin, PPR, Zf-MyND, SNF2, SNO among others (Figure 1). Further, the unknown motifs in F-box genes of the FBX subfamily, that were found to have no known functional domain other than the F-box, were investigated using MEME. Out of the 50 motifs identified, thirteen were found to be conserved in at least five of the F-box genes [see Additional file 3: Table S3]. Two of these motifs (motifs 3 and 32) were conserved in more than 20 chickpea F-box genes and three motifs (motifs 1, 3 and 4) were found to be statistically significant (e value less than e-100).Figure 1

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Show MeSH