Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton

BMC Plant Biology

Zheng Juyun¹  Stephen Gaya Agong²  Dingsha Jin³  Zhongli Zhou³  Xiaoyan Cai³  Yuqing Hou³  Kunbo Wang³  Yanchao Xu⁴  Fang Liu⁵  Richard Odongo Magwanga⁶ 

[1] Economic Crops Research Institute of Xinjiang Academy of Agricultural Science, Urumqi, Xinjiang province, China;School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya;State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;College of Plant Science and Technology, Huazhong Agricultural University, 40070, Wuhan, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;School of Agricultural Sciences, Zhengzhou University, 450001, Zhengzhou, Henan, China;State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, 455000, Anyang, China;School of Biological, Physical, Mathematics and Actuarial sciences (SBPMAS), Main campus, Jaramogi Oginga Odinga University of Science and Technology (JOOUST), P.O Box 210-40601, Bondo, Kenya;

关键词: Diploid D-genome cotton;    Co-expression;    Comparative transcriptome;    Evolutionary divergence;    Shared network;   

DOI  :  10.1186/s12870-020-02726-4

来源: Springer

【 摘 要 】

BackgroundWild species of cotton are excellent resistance to abiotic stress. Diploid D-genome cotton showed abundant phenotypic diversity and was the putative donor species of allotetraploid cotton which produce the largest textile natural fiber.ResultsA total of 41,053 genes were expressed in all samples by mapping RNA-seq Illumina reads of G. thurberi (D1), G. klotzschianum (D3-k), G. raimondii (D5) and G. trilobum (D8) to reference genome. The numbers of differently expressed genes (DEGs) were significantly higher under cold stress than salt stress. However, 34.1% DEGs under salt stress were overlapped with cold stress in four species. Notably, a potential shared network (cold and salt response, including 16 genes) was mined out by gene co-expression analysis. A total of 47,180–55,548 unique genes were identified in four diploid species by De novo assembly. Furthermore, 163, 344, 330, and 161 positively selected genes (PSGs) were detected in thurberi, G. klotzschianum, G. raimondii and G. trilobum by evolutionary analysis, respectively, and 9.5–17% PSGs of four species were DEGs in corresponding species under cold or salt stress. What’s more, most of PSGs were enriched GO term related to response to stimulation. G. klotzschianum showed the best tolerance under both cold and salt stress. Interestingly, we found that a RALF-like protein coding gene not only is PSGs of G. klotzschianum, but also belongs to the potential shared network.ConclusionOur study provided new evidence that gene expression variations of evolution by natural selection were essential drivers of the morphological variations related to environmental adaptation during evolution. Additionally, there exist shared regulated networks under cold and salt stress, such as Ca2+ signal transduction and oxidation-reduction mechanisms. Our work establishes a transcriptomic selection mechanism for altering gene expression of the four diploid D-genome cotton and provides available gene resource underlying multi-abiotic resistant cotton breeding strategy.

【 授权许可】

CC BY