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Int. J. Mol. Sci. 2014, 15(3), 4635-4656; doi:10.3390/ijms15034635
Article

Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii

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Received: 12 January 2014; in revised form: 25 February 2014 / Accepted: 27 February 2014 / Published: 17 March 2014
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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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.
Keywords: cotton; RNA helicase; gene expansion; structure; fiber cotton; RNA helicase; gene expansion; structure; fiber
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Chen, J.; Zhang, Y.; Liu, J.; Xia, M.; Wang, W.; Shen, F. Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii . Int. J. Mol. Sci. 2014, 15, 4635-4656.

AMA Style

Chen J, Zhang Y, Liu J, Xia M, Wang W, Shen F. Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii . International Journal of Molecular Sciences. 2014; 15(3):4635-4656.

Chicago/Turabian Style

Chen, Jie; Zhang, Yujuan; Liu, Jubo; Xia, Minxuan; Wang, Wei; Shen, Fafu. 2014. "Genome-Wide Analysis of the RNA Helicase Gene Family in Gossypium raimondii ." Int. J. Mol. Sci. 15, no. 3: 4635-4656.


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