title: Genome-wide analysis of the RNA helicase gene family in Gossypium raimondii.
abstract: The RNA helicases, which help to unwind stable RNA duplexes, and have important roles in RNA metabolism, belong to a class of motor proteins that play important roles in plant development and responses to stress. Although this family of genes has been the subject of systematic investigation in Arabidopsis, rice, and tomato, it has not yet been characterized in cotton. In this study, we identified 161 putative RNA helicase genes in the genome of the diploid cotton species Gossypium raimondii. We classified these genes into three subfamilies, based on the presence of either a DEAD-box (51 genes), DEAH-box (52 genes), or DExD/H-box (58 genes) in their coding regions. Chromosome location analysis showed that the genes that encode RNA helicases are distributed across all 13 chromosomes of G. raimondii. Syntenic analysis revealed that 62 of the 161 G. raimondii helicase genes (38.5%) are within the identified syntenic blocks. Sixty-six (40.99%) helicase genes from G. raimondii have one or several putative orthologs in tomato. Additionally, GrDEADs have more conserved gene structures and more simple domains than GrDEAHs and GrDExD/Hs. Transcriptome sequencing data demonstrated that many of these helicases, especially GrDEADs, are highly expressed at the fiber initiation stage and in mature leaves. To our knowledge, this is the first report of a genome-wide analysis of the RNA helicase gene family in cotton.
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. chenj_19@163.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. Zhangj_19@163.com.
authors.forename: Yujuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. liujubo2014@163.com.
authors.forename: Jubo
authors.initials: J
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. Xiaj_19@163.com.
authors.forename: Minxuan
authors.initials: M
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. sdauww@126.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, Shandong, China. ffshen@sdau.edu.cn.
authors.forename: Fafu
authors.initials: F
authors.lastname: Shen
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D032561:Cotton Fiber; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000201:enzymology / Q000235:genetics*; D018551:Solanum lycopersicum / Q000201:enzymology / Q000235:genetics; D005810:Multigene Family; D010802:Phylogeny; D018515:Plant Leaves / Q000201:enzymology / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D020365:RNA Helicases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D026801:Synteny; D059467:Transcriptome / Q000235:genetics
chemical_list: D010940:Plant Proteins; D020365:RNA Helicases