A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.).
The RNA editing occurring in plant organellar genomes mainly involves the change of cytidine to uridine. This process involves a deamination reaction, with cytidine deaminase as the catalyst. Pentatricopeptide repeat (PPR) proteins with a C-terminal DYW domain are reportedly associated with cytidine deamination, similar to members of the deaminase superfamily. PPR genes are involved in many cellular functions and biological processes including fertility restoration to cytoplasmic male sterility (CMS) in plants. In this study, we identified 227 and 211 DYW deaminase-coding PPR genes for the cultivated tetraploid cotton species G. hirsutum and G. barbadense (2n = 4x = 52), respectively, as well as 126 and 97 DYW deaminase-coding PPR genes in the ancestral diploid species G. raimondii and G. arboreum (2n = 26), respectively. The 227 G. hirsutum PPR genes were predicted to encode 52-2016 amino acids, 203 of which were mapped onto 26 chromosomes. Most DYW deaminase genes lacked introns, and their proteins were predicted to target the mitochondria or chloroplasts. Additionally, the DYW domain differed from the complete DYW deaminase domain, which contained part of the E domain and the entire E+ domain. The types and number of DYW tripeptides may have been influenced by evolutionary processes, with some tripeptides being lost. Furthermore, a gene ontology analysis revealed that DYW deaminase functions were mainly related to binding as well as hydrolase and transferase activities. The G. hirsutum DYW deaminase expression profiles varied among different cotton tissues and developmental stages, and no differentially expressed DYW deaminase-coding PPRs were directly associated with the male sterility and restoration in the CMS-D2 system. Our current study provides an important piece of information regarding the structural and evolutionary characteristics of Gossypium DYW-containing PPR genes coding for deaminases and will be useful for characterizing the DYW deaminase gene family in cotton biology and breeding.
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Bingbing
http://orcid.org/0000-0001-9811-6770
B
Zhang
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Guoyuan
G
Liu
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Xue
X
Li
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Liping
L
Guo
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Xuexian
X
Zhang
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Tingxiang
T
Qi
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Hailin
H
Wang
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Huini
H
Tang
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Xiuqin
X
Qiao
Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, New Mexico, United States of America.
Jinfa
J
Zhang
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Chaozhu
C
Xing
State Key Laboratory of Cotton Biology (China)/Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.
Jianyong
J
Wu
D003564:Cytidine Deaminase / Q000235:genetics*; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D017393:RNA Editing
D010940:Plant Proteins; D003564:Cytidine Deaminase