A genome-wide identification and analysis of the DYW-deaminase genes in the pentatricopeptide repeat gene family in cotton (Gossypium spp.)

Abstract

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.

Fig 1

a: The Logo of DYW domain in G. hirsutum. The higher the letter, the higher the conservation; b: The comparison of DYW domain consensus sequence in upland cotton, tomato and Arabidopsis. The capital letters represent highly conserved, lowercase letters indicate lower conservative.

Fig 2

a: The alignment of the DYW deaminase domain in G. hirsutum; b: The Logo of DYW deaminase domain in G. hirsutum; c: The consensus sequence in G. hirsutum and comparison of DYW deaminase domain in Gossypium. The capital letters represent highly conserved, lowercase letters indicate lower conservative.

Fig 3. Mapping of the DYW deaminase genes in the chromosomes.

Partial DYW deaminase genes localized in scaffolds.

Fig 4. Genome wide synteny analysis of DYW deaminase genes.

a: Synteny analysis between G. hirsutum and two diploid cotton species; b: Synteny analysis between G. barbadense and two diploid cotton species; Blue lines indicate syntenic regions between G. arboretum and tetraploid cotton species, red lines between G. raimondii and tetraploid cotton species.

Fig 5. The GO analysis of DYW deaminase proteins in G. hirsutum.

Fig 6. Phylogenetic tree of DYW deaminase genes in Gossypium.

Fig 7. Expression profiles of DYW deaminase genes during fiber development and in different tissues.

The color bar represents the expression values.

Fig 8. Expression analysis of 16 selected DYW deaminase genes in different tissues through qRT-PCR.

a: High expression in the flower; b: Expression peaks in the leaf; c: High expression in the stem; d: High expression in the root.

Fig 9. Sequence alignment of the 14 repeats of Gh_D05G3392.

The residues at 2, 5 and 35 positions were predicted to be the molecular determinants for RNA binding specificity are red. The RNA sequences recognized are listed on the right, 5’ to 3’ from top to bottom.