Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling

PloS One
Annapurna BhattacharjeeMukesh Jain

Abstract

Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and...Continue Reading

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Citations

Mar 29, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Asuka ArimotoEiichi Shoguchi
Jan 10, 2018·Plant, Cell & Environment·Mostafa AbdelrahmanLam-Son Phan Tran
Oct 21, 2016·Journal of Cancer Research and Clinical Oncology·Wen-Jin DingChun-Ying Qu

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Datasets Mentioned

BETA
GSE40627

Methods Mentioned

BETA
RNA-seq
PCR

Software Mentioned

R programming
CLUSTALX
MultiExperiment Viewer ( MeV )
PAML package
MAST ( Motif Alignment and Search Tool )
R
HMMER
PLINC
BLASTN
Circos

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