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

BMC Genomics
Shefali GuptaSabhyata Bhatia

Abstract

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. 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 Arabidopsi...Continue Reading

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Citations

Apr 19, 2017·International Journal of Molecular Sciences·Qi JiaHon-Ming Lam
Sep 22, 2019·International Journal of Molecular Sciences·Dong XueHan Xing
Feb 20, 2020·Planta·Nur-Athirah Abd-HamidIsmanizan Ismail
Mar 25, 2021·Journal, Genetic Engineering & Biotechnology·Md Abu SadatMd Shahidul Islam
Nov 2, 2021·Frontiers in Plant Science·Claudio CropanoBruno Studer

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Datasets Mentioned

BETA
SRX048834
SRX125162

Methods Mentioned

BETA
RNA seq
PCR
transgenic

Software Mentioned

Pfam
Cufflinks
SMART
TopHat
Primer Express
WoLF PSORT
MEME
MEGA5
MEME ( Multiple Expectation Maximization for Motif Elicitation
Bioedit

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