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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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Related in: MedlinePlus

Heat map showing digital expression profiles of F-box genes (based on RPKM values) in chickpea root and shoot under stress. The three abiotic stress conditions were- desiccation, salinity and cold. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.
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Fig8: Heat map showing digital expression profiles of F-box genes (based on RPKM values) in chickpea root and shoot under stress. The three abiotic stress conditions were- desiccation, salinity and cold. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.

Mentions: Chickpea F-box genes were also analysed for their in-silico expression profiles using the available root and shoot transcriptomes of chickpea under three abiotic stress conditions- desiccation, salinity and cold [31]. Out of 265 genes for which RPKM values could be calculated, 220 were found to have RPKM values ≥ 1.0 in at least one tissue [see Additional file 7: Table S7B]. Many of 220 F-box genes, for which RPKM values could be retrieved, exhibited differential transcript accumulation in one or more of the stress conditions. The k-means clustering resulted in clusters showing genes expressing high in one or few stresses. For example 16 genes were found to be expressing at high levels in root tissue under various stress conditions as compared to shoot. Whereas 30 genes showed high expression in root under salinity stress. Moreover 14 genes showed high expression in shoot under desiccation and salinity stress (Figure 8; Additional file 8: Table S8B).Figure 8


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

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

Heat map showing digital expression profiles of F-box genes (based on RPKM values) in chickpea root and shoot under stress. The three abiotic stress conditions were- desiccation, salinity and cold. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig8: Heat map showing digital expression profiles of F-box genes (based on RPKM values) in chickpea root and shoot under stress. The three abiotic stress conditions were- desiccation, salinity and cold. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.
Mentions: Chickpea F-box genes were also analysed for their in-silico expression profiles using the available root and shoot transcriptomes of chickpea under three abiotic stress conditions- desiccation, salinity and cold [31]. Out of 265 genes for which RPKM values could be calculated, 220 were found to have RPKM values ≥ 1.0 in at least one tissue [see Additional file 7: Table S7B]. Many of 220 F-box genes, for which RPKM values could be retrieved, exhibited differential transcript accumulation in one or more of the stress conditions. The k-means clustering resulted in clusters showing genes expressing high in one or few stresses. For example 16 genes were found to be expressing at high levels in root tissue under various stress conditions as compared to shoot. Whereas 30 genes showed high expression in root under salinity stress. Moreover 14 genes showed high expression in shoot under desiccation and salinity stress (Figure 8; Additional file 8: Table S8B).Figure 8

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
Related in: MedlinePlus