Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton.

Xu Xu,Guo Guo,Cai Cai,Zhou Zhou,Zhang Zhang,Wei Wei,Magwanga Magwanga,Li Li,Liu Liu,Jin Jin,Wang Wang

doi:10.3390/ijms20081863

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.

Highlights

Gossypium is one of the largest and most widely distributed genus with more than 50 species [1,2]
In all the Reactive oxygen species (ROS) proteins obtained from the three cotton species, they were further subdivided into different classes or sub families, in which the highest ROS proteins were observed for peroxidase (PER) with 279 proteins encoding the ROS genes, accounting for 26.9% of all the ROS proteins in the three cotton species
We found that the activity of POD, CAT, ascorbate peroxidase (APX), and glutathione reductase (GR) was not significantly changed in roots of marie-galante 85 (M85), suggesting that ROS production and removal was balanced in roots of M85

Summary

Introduction

Gossypium is one of the largest and most widely distributed genus with more than 50 species [1,2]. Cotton has a long evolution and domestication history. The allopolyploid cottons emerged about 1–2 MYA due to an intergenomic hybridization event between A and D genomes [3,4], and were domesticated at least 4000 to 5000 years ago [5]. Both G. arboreum and G. hirsutum have a natural long spinable fiber, G. raimondii generates fiber, its fibers are short and not spinable [6]. During human domestication history of cotton, the central focus was on the fiber quality and quantity [7]. Increasing number of genome sequencing and resequencing, mRNA sequencing and phenotype assessment of cotton [8] provided an important resource for studying potential biological mechanism related to abiotic stress tolerance in cotton

Methods

Results

Conclusion