1. Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton
- Author
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Zhongli Zhou, Yangyang Wei, Kunbo Wang, Zhang Zhenmei, Dingsha Jin, Xinlei Guo, Fang Liu, Yanchao Xu, Xiaoyan Cai, Yuhong Wang, Xingxing Wang, Richard Odongo Magwanga, and Li Zhenqing
- Subjects
0106 biological sciences ,0301 basic medicine ,abiotic stress ,fiber development ,RNA-Seq ,transcription analysis ,Biology ,Gossypium ,01 natural sciences ,Genome ,Catalysis ,Article ,Inorganic Chemistry ,Transcriptome ,lcsh:Chemistry ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Stress, Physiological ,Physical and Theoretical Chemistry ,ROS genes ,Molecular Biology ,Gene ,lcsh:QH301-705.5 ,Spectroscopy ,Phylogeny ,Genetics ,Abiotic stress ,Gene Expression Profiling ,Organic Chemistry ,General Medicine ,biology.organism_classification ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,lcsh:QD1-999 ,Synonymous substitution ,Reactive Oxygen Species ,Orthologous Gene ,Genome, Plant ,010606 plant biology & botany - Abstract
Reactive oxygen species (ROS) are important molecules in the plant, which are involved in many biological processes, including fiber development and adaptation to abiotic stress in cotton. We carried out transcription analysis to determine the evolution of the ROS genes and analyzed their expression levels in various tissues of cotton plant under abiotic stress conditions. There were 515, 260, and 261 genes of ROS network that were identified in Gossypium hirsutum (AD1 genome), G. arboreum (A genome), and G. raimondii (D genome), respectively. The ROS network genes were found to be distributed in all the cotton chromosomes, but with a tendency of aggregating on either the lower or upper arms of the chromosomes. Moreover, all the cotton ROS network genes were grouped into 17 families as per the phylogenetic tress analysis. A total of 243 gene pairs were orthologous in G. arboreum and G. raimondii. There were 240 gene pairs that were orthologous in G. arboreum, G. raimondii, and G. hirsutum. The synonymous substitution value (Ks) peaks of orthologous gene pairs between the At subgenome and the A progenitor genome (G. arboreum), D subgenome and D progenitor genome (G. raimondii) were 0.004 and 0.015, respectively. The Ks peaks of ROS network orthologous gene pairs between the two progenitor genomes (A and D genomes) and two subgenomes (At and Dt subgenome) were 0.045. The majority of Ka/Ks value of orthologous gene pairs between the A, D genomes and two subgenomes of TM-1 were lower than 1.0. RNA seq. analysis and RT-qPCR validation, showed that, CSD1,2,3,5,6, FSD1,2, MSD1,2, APX3,11, FRO5.6, and RBOH6 played a major role in fiber development while CSD1, APX1, APX2, MDAR1, GPX4-6-7, FER2, RBOH6, RBOH11, and FRO5 were integral for enhancing salt stress in cotton. ROS network-mediated signal pathway enhances the mechanism of fiber development and regulation of abiotic stress in Gossypium. This study will enhance the understanding of ROS network and form the basic foundation in exploring the mechanism of ROS network-involving the fiber development and regulation of abiotic stress in cotton.
- Published
- 2019