Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response i
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RESEARCH ARTICLE
Open Access
Comparative transcriptome analysis reveals evolutionary divergence and shared network of cold and salt stress response in diploid D-genome cotton Yanchao Xu1,2†, Richard Odongo Magwanga1,3†, Dingsha Jin1†, Xiaoyan Cai1, Yuqing Hou1, Zheng Juyun4, Stephen Gaya Agong3, Kunbo Wang1*, Fang Liu1,5* and Zhongli Zhou1*
Abstract Background: Wild 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. Results: A 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. (Continued on next page)
* Correspondence: [email protected]; [email protected]; [email protected]; [email protected]; [email protected] † Yanchao Xu, Richard Odongo Magwanga and Dingsha Jin contributed equally to this work. 1 State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this
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