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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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Heat map showing digital expression profiles of F-box genes in various tissues of chickpea based on RPKM values. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.
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Fig6: Heat map showing digital expression profiles of F-box genes in various tissues of chickpea based on RPKM values. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.

Mentions: Since tissue specific transcriptomes of chickpea were available for flower bud, pod, leaf, root in SRA database [30] and for seed and nodule, it was possible to investigate the in-silico expression profiles of F-box genes in various chickpea tissues. Mapping of the available transcriptome reads revealed expression patterns of 265 F-box genes out of 285 which were retrieved in terms of RPKM values. Out of 265 genes, 258 were found to have RPKM ≥1.0 in at least one of the tissues and were considered as expressed genes [see Additional file 7: Table S7A]. Hierarchical clustering of the expression profiles showed that several F-box genes exhibited preferential expression in one or more of the chickpea tissues. Moreover, tissue specific F-box genes could also be identified. Analysis using k-means clustering resulted in identification of several clusters of which 4 major clusters with genes showing high expression in different tissues are represented in Figure 6. The maximum number of F-box genes (46) were found to have high expression in flower bud followed by 23 in seed, 16 in root and 15 in nodule [see Additional file 8: Table S8A]. Moreover F-box genes having tissue specific expression varied from 15 in flower bud, 13 in seed, 6 in nodule, 2 in leaf and 1 in pod. Several chickpea F-box genes showing tissue specific expression profiles exhibited high similarity with well documented F-box genes in Arabidopsis. For example, Ca_05121 sharing 62.88% homology with UFO [40] was observed to be flower bud specific. Moreover other F-box genes exhibiting high expression levels in flower bud included genes such as Ca_07787 that showed homology with FBL17 [44] (60.7%) and Ca_10410 with FKF1 [39] (78.68%). Ca_10433 which showed predominant transcript accumulation in seed was distantly related to MEE11 [45] F-box gene (42.86% homology). Ca_16962 chickpea F-box gene which shared 73.88% amino acid identity with ARABIDILLO1 [46] F-box gene of Arabidopsis accumulated preferentially in root.Figure 6


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 in various tissues of chickpea based on RPKM values. 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

Fig6: Heat map showing digital expression profiles of F-box genes in various tissues of chickpea based on RPKM values. Color key represents RPKM values. Tissue samples are indicated at the top of each lane.
Mentions: Since tissue specific transcriptomes of chickpea were available for flower bud, pod, leaf, root in SRA database [30] and for seed and nodule, it was possible to investigate the in-silico expression profiles of F-box genes in various chickpea tissues. Mapping of the available transcriptome reads revealed expression patterns of 265 F-box genes out of 285 which were retrieved in terms of RPKM values. Out of 265 genes, 258 were found to have RPKM ≥1.0 in at least one of the tissues and were considered as expressed genes [see Additional file 7: Table S7A]. Hierarchical clustering of the expression profiles showed that several F-box genes exhibited preferential expression in one or more of the chickpea tissues. Moreover, tissue specific F-box genes could also be identified. Analysis using k-means clustering resulted in identification of several clusters of which 4 major clusters with genes showing high expression in different tissues are represented in Figure 6. The maximum number of F-box genes (46) were found to have high expression in flower bud followed by 23 in seed, 16 in root and 15 in nodule [see Additional file 8: Table S8A]. Moreover F-box genes having tissue specific expression varied from 15 in flower bud, 13 in seed, 6 in nodule, 2 in leaf and 1 in pod. Several chickpea F-box genes showing tissue specific expression profiles exhibited high similarity with well documented F-box genes in Arabidopsis. For example, Ca_05121 sharing 62.88% homology with UFO [40] was observed to be flower bud specific. Moreover other F-box genes exhibiting high expression levels in flower bud included genes such as Ca_07787 that showed homology with FBL17 [44] (60.7%) and Ca_10410 with FKF1 [39] (78.68%). Ca_10433 which showed predominant transcript accumulation in seed was distantly related to MEE11 [45] F-box gene (42.86% homology). Ca_16962 chickpea F-box gene which shared 73.88% amino acid identity with ARABIDILLO1 [46] F-box gene of Arabidopsis accumulated preferentially in root.Figure 6

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