Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass

BMC Genomics
Shaoxun YuanBingru Huang

Abstract

In recent years, dozens of Arabidopsis and rice CCCH-type zinc finger genes have been functionally studied, many of which confer important traits, such as abiotic and biotic stress tolerance, delayed leaf senescence and improved plant architecture. Switchgrass (Panicum virgatum) is an important bioenergy crop. Identification of agronomically important genes and/or loci is an important step for switchgrass molecular breeding. Annotating switchgrass CCCH genes using translational genomics methods will help further the goal of understanding switchgrass genetics and creating improved varieties. Taking advantage of the publicly-available switchgrass genomic and transcriptomic databases, we carried out a comprehensive analysis of switchgrass CCCH genes (PvC3Hs). A total of 103 PvC3Hs were identified and divided into 21 clades according to phylogenetic analysis. Genes in the same clade shared similar gene structure and conserved motifs. Chromosomal location analysis showed that most of the duplicated PvC3H gene pairs are in homeologous chromosomes. Evolution analysis of 19 selected PvC3H pairs showed that 42.1% of them were under diversifying selection. Expression atlas of the 103 PvC3Hs in 21 different organs, tissues and development...Continue Reading

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Citations

Jul 30, 2016·International Journal of Molecular Sciences·Yanjun HeGang Lu
Feb 10, 2018·Journal of Public Health·Kalpana SinghDorairaj Prabhakaran
Jan 10, 2017·Frontiers in Plant Science·Camilla B Hill, Chengdao Li
Feb 22, 2017·Frontiers in Plant Science·Pengfei WangXingjun Wang
May 17, 2019·International Journal of Genomics·Yuzhu HuoZhen Sun
Sep 4, 2021·Bioengineered·Xiaoqin WangPengcheng Feng

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Methods Mentioned

BETA
transgenic
electrophoresis
PCR

Software Mentioned

R Project
HMMER
ClustalX
JMP
Weblogo
Blast2Go
ExPASy
MapInspect
MEGA
EditPlus

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