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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

Chromosomal locations and gene duplication events of F-box genes. Respective chromosome numbers are indicated at the top of each bar. Numbers in brackets next to each chromosome name represent the number of F-box genes in each chromosome. The scale on the left is in megabases (Mb). Tandemly duplicated genes are shown in orange boxes. Segmental duplications are shown in coloured blocks.
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Fig4: Chromosomal locations and gene duplication events of F-box genes. Respective chromosome numbers are indicated at the top of each bar. Numbers in brackets next to each chromosome name represent the number of F-box genes in each chromosome. The scale on the left is in megabases (Mb). Tandemly duplicated genes are shown in orange boxes. Segmental duplications are shown in coloured blocks.

Mentions: Chromosomal locations of the F-box genes were identified using the draft genome sequences of the desi [13] and the kabuli genomes [14]. Map positions of 88 F-box protein-encoding genes identified from desi chickpea genome could be found, others being present in the scaffolds. Whereas, in case of F-box genes identified from kabuli chickpea genome, the chromosomal locations of 192 F-box genes were obtained and hence were considered for mapping of genes on chromosomes as well as for synteny analysis. The F-box genes were found to be almost evenly distributed on all the chromosomes of chickpea except chromosome 8, on which the density of F-box genes was significantly lower (Figure 4). The densities of the genes were relatively higher in specific chromosomal regions, such as the upper arms of chromosome 1, 4 and 6, and the lower arms of chromosome 5 and 7. In contrast, a large middle region on chromosome 4 was devoid of F-box genes. Chromosome 3 was densely populated with F-box genes which had the maximum number of F-box genes (37), followed by 29 genes on chromosome 4.Figure 4


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

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

Chromosomal locations and gene duplication events of F-box genes. Respective chromosome numbers are indicated at the top of each bar. Numbers in brackets next to each chromosome name represent the number of F-box genes in each chromosome. The scale on the left is in megabases (Mb). Tandemly duplicated genes are shown in orange boxes. Segmental duplications are shown in coloured blocks.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig4: Chromosomal locations and gene duplication events of F-box genes. Respective chromosome numbers are indicated at the top of each bar. Numbers in brackets next to each chromosome name represent the number of F-box genes in each chromosome. The scale on the left is in megabases (Mb). Tandemly duplicated genes are shown in orange boxes. Segmental duplications are shown in coloured blocks.
Mentions: Chromosomal locations of the F-box genes were identified using the draft genome sequences of the desi [13] and the kabuli genomes [14]. Map positions of 88 F-box protein-encoding genes identified from desi chickpea genome could be found, others being present in the scaffolds. Whereas, in case of F-box genes identified from kabuli chickpea genome, the chromosomal locations of 192 F-box genes were obtained and hence were considered for mapping of genes on chromosomes as well as for synteny analysis. The F-box genes were found to be almost evenly distributed on all the chromosomes of chickpea except chromosome 8, on which the density of F-box genes was significantly lower (Figure 4). The densities of the genes were relatively higher in specific chromosomal regions, such as the upper arms of chromosome 1, 4 and 6, and the lower arms of chromosome 5 and 7. In contrast, a large middle region on chromosome 4 was devoid of F-box genes. Chromosome 3 was densely populated with F-box genes which had the maximum number of F-box genes (37), followed by 29 genes on chromosome 4.Figure 4

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