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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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Gene ontology terms enriched in chickpea F-box genes. Enrichment of GO terms was determined by Fisher’s exact test.
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Fig2: Gene ontology terms enriched in chickpea F-box genes. Enrichment of GO terms was determined by Fisher’s exact test.

Mentions: A Gene Ontology (GO) analysis was also performed using Blast2GO to predict the putative functions of the identified chickpea F-box genes. Most of the F-box genes were predicted to be involved in cellular processes (47) followed by metabolic process (39). Others were found to be involved in essential processes such as response to stimulus, developmental processes, biological regulation, reproduction and signalling. A Fisher’s exact test showed the enrichment of several GO categories such as multicellular organismal development (GO:0007275), primary metabolic process (GO:0044238), response to external stimulus (GO:0009605), protein metabolic process (GO:0019538) and response to biotic stimulus (GO:0009607), followed by catabolic process (GO:0009056) and post-embryonic development (GO:0009791) (Figure 2, Additional file 4: Table S4). Moreover, several homologs of well characterized Arabidopsis F-box genes such as FKF1 [39], UFO [40], TIR1 [41], SLOMO [42], AFB [43], among others were observed in chickpea F-box genes sharing 42% to 79% amino acid identity.Figure 2


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

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

Gene ontology terms enriched in chickpea F-box genes. Enrichment of GO terms was determined by Fisher’s exact test.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Gene ontology terms enriched in chickpea F-box genes. Enrichment of GO terms was determined by Fisher’s exact test.
Mentions: A Gene Ontology (GO) analysis was also performed using Blast2GO to predict the putative functions of the identified chickpea F-box genes. Most of the F-box genes were predicted to be involved in cellular processes (47) followed by metabolic process (39). Others were found to be involved in essential processes such as response to stimulus, developmental processes, biological regulation, reproduction and signalling. A Fisher’s exact test showed the enrichment of several GO categories such as multicellular organismal development (GO:0007275), primary metabolic process (GO:0044238), response to external stimulus (GO:0009605), protein metabolic process (GO:0019538) and response to biotic stimulus (GO:0009607), followed by catabolic process (GO:0009056) and post-embryonic development (GO:0009791) (Figure 2, Additional file 4: Table S4). Moreover, several homologs of well characterized Arabidopsis F-box genes such as FKF1 [39], UFO [40], TIR1 [41], SLOMO [42], AFB [43], among others were observed in chickpea F-box genes sharing 42% to 79% amino acid identity.Figure 2

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