Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton ( Gossypium
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pression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton (Gossypium hirsutum L.) Zhen Peng
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, Hua Cheng , Gaofei Sun , Zhaoe Pan , Xiao Wang , Xiaoli Geng , 1,2* 1,2* Shoupu He & Xiongming Du
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State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; 2 Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China; 3 Anyang Institute of Technology, Anyang 455000, China Received November 16, 2019; accepted January 7, 2020; published online February 24, 2020
Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization. However, the global gene pattern variation during early fiber development was unknown. In this study, through RNA-seq technology, we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton (G. hirsutum) and its diploid progenitors (G. arboreum and G. raimondii) at the fiber early development stage. In tetraploid cotton, genes showed expression level dominance (ELD) bias toward the A genome. This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor (D genome). Gene ontology (GO) enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession, and the ELD-D genes might be involved in transcription regulation and stress inducement. In addition, the number and proportion of completely A- and D-subfunctionalized gene were similar at different fiber development stages. However, for neofunctionalization, the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA. Eventually, we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process, further making the fiber property meet the human demands. Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages, providing new insights into the mechanism of cotton fiber evolution. Gossypium, fiber development, polyploid evolution, expression level dominance, sub- and neofunctionalization Citation:
Peng, Z., Cheng, H., Sun, G., Pan, Z., Wang, X., Geng, X., He, S., and Du, X. (2020). Expression patterns and functional divergence of homologous genes accompanied by polyploidization in cotton (Gossypium hirsutum L.). Sci China Life Sci 63, https://doi.org/10.1007/s11427-019-1618-7
INTRODUCTION It is generally believed that polyploidy (also called wholegenome duplication) is a driving force for plant diversification and evolution (Adams and Wendel, 2005; Otto, 2007; †Contributed equally to this work *Corres
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