J Integr Plant Biol. ›› 2019, Vol. 61 ›› Issue (1): 45-59.DOI: 10.1111/jipb.12763

• Research Articles • Previous Articles     Next Articles

Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors

Hua Cheng1,2, Gaofei Sun1, Shoupu He1, Wenfang Gong1, Zhen Peng1, Ruiping Wang3, Zhongxu Lin2 and Xiongming Du1*   

  1. 1Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, the Chinese Academy of Agricultural Science, Anyang 455000, China
    2College of Plant Science & Technology of Huazhong Agricultural University, Wuhan 430070, China
    3Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang 455000, China

    *Correspondence:

    Email: Xiongming Du (dujeffrey8848@hotmail.com)
  • Received:2018-08-23 Accepted:2018-12-15 Online:2018-12-19 Published:2019-01-01

Abstract: An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements (TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes. Gypsy was the most abundant TE type and most TEs were located ~500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs (siRNAs) that targeted TEs. TEs, particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

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