The Catalase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis

Abstract

Catalases (CATs), which were coded by the catalase gene family, were a type notably distinguished ROS-metabolizing proteins implicated to perform various physiological functions in plant growth, development and stress responses. However, no systematical study has been performed in cotton. In the present study, we identified 7 and 7 CAT genes in the genome of Gossypium hirsutum L. Additionally, G. barbadense L., respectively. The results of the phylogenetic and synteny analysis showed that the CAT genes were divided into two groups, and whole-genome duplication (WGD) or polyploidy events contributed to the expansion of the Gossypium CAT gene family. Expression patterns analysis showed that the CAT gene family possessed temporal and spatial specificity and was induced by the Verticillium dahliae infection. In addition, we predicted the putative molecular regulatory mechanisms of the CAT gene family. Based on the analysis and preliminary verification results, we hypothesized that the CAT gene family, which might be regulated by transcription factors (TFs), alternative splicing (AS) events and miRNAs at different levels, played roles in cotton development and stress tolerance through modulating the reactive oxygen species (ROS) metabolism. This is the first report on the genome-scale analysis of the cotton CAT gene family, and these data will help further study the roles of CAT genes during stress responses, leading to crop improvement.

Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6

“…This result is possibly because only one or two miRNAs regulated the isoforms of the GhCIPKs or only part of the isoforms transcribed from GhCIPK genes were detected from our mRNA-seq data. Similar phenomena could also be detected in the cotton CAT gene family in Figure S6 [39].…”

“…A total of 80 and 78 CIPK genes were identified in G. hirsutum and G. barbadense, respectively (Tables S2 and S3). The number of CIPK genes in each of the G. hirsutum and G. barbadense genome was greater than that in Arabidopsis (26) and rice (34), and was basically equal to the total sum of G. raimondii (41) and G. arboretum (39), suggesting that the CIPK gene family expands during evolution. G. raimondii and G. arboretum underwent a Gossypium-specific whole-genome duplication (WGD) [27,30,31], and the CIPK gene family of G. raimondii and G. arboretum may expand by an ancient WGD event.…”

“…Two genomes of allotetraploid cotton species (G. hirsutum and G. barbadense) underwent a diploidization following the divergence of G. arboreum (A genome) and G. raimondii (D genome). Based on the genome scans of two diploid cotton species, the CIPK gene family was investigated in G. raimondii (41) and G. arboreum (39) [19]. To clarify the divergence during cotton evolution, we analyzed the orthologous CIPK genes between G. raimondii, G. arboreum, and the A and D subgenomes of the two allotetraploid species (G. hirsutum and G. barbadense) (Table S5, Figure S1).…”

“…Here, the putative stress-related and hormone-related cis-elements were scanned in the 1.5 kb upstream of the start codons of 80 GhCIPKs using the PlantCARE database. In total, 12 stress-related and hormone-related cis-elements were predicted in the promoters of 80 GhCIPKs (Table S8) It is well known that TFs regulate the transcription of their target genes by binding certain upstream elements [39]. To explore the regulatory interactions between TFs and GhCIPKs, we further searched highly conserved transcription factor binding sites (TFBSs) in 1.5 kb promoter regions of the 80 GhCIPKs.…”

Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt

“…In the present study, we identified 151 Pkinase genes in three cotton species, G. raimondii, G. arboreum and G. hirsutum, which were found to have 41, 35 and 75 genes, respectively. The number identified in upland cotton (G. hirsutum) was relatively higher (more than double) than in G. arboreum and G. raimondii, which indicates that whole genome duplication (WGD) or polyploidy events played a major role in Pkinase gene family expansion [67]. Allotetraploid cotton possibly emerged from the polyploidization of the A and D genomes, suggesting that the expansion of Pkinase family genes from diploid to allotetraploid cotton is mainly a consequence of gene duplication and the conservation of the Pkinase genes during the polyploidization process.…”