Genome-wide analysis of superoxide dismutase gene family in Gossypium raimondii and G. arboreum

Superoxide dismutases (SODs) convert highly reactive superoxide radicals to hydrogen peroxide and molecular oxygen, and belong to a class of proteins with important roles in plant responses to stress. Genome-wide analysis was performed in cotton species Gossypium raimondii and Gossypium arboreum to characterize SOD genes and proteins. From the two genomes, 18 SOD genes were identified with several bioinformatics tools, and classified into two subfamilies: Cu/Zn-SODs (ten genes) and Mn/Fe-SODs (eight genes). The highest number of SOD genes was on chromosome 13 with two genes in G. raimondii, and on chromosomes 9, 10 and 13 with two genes on each in G. arboreum. Four (50%) SOD genes from Arabidopsis thaliana had one putative ortholog in G. raimondii, and three (37.5%) had one putative ortholog in G. arboreum; and eight (88.89%) from G. arboreum had one putative ortholog in G. raimondii. There were 4–8 introns in SOD genes of G. raimondii and 5–8 of G. arboreum. Phylogenetic analysis revealed that Cu/Zn-SODs (92%) and Mn/Fe-SODs (100%) were separated by high bootstrap value. Tissue-specific expressions of cotton SOD genes showed that 9, 10, 9, 8 and 18 of a total of 18 putative SOD genes were expressed in root, stem, leaf, flower and ovule, respectively. Stage-specific expression patterns in ovule showed that expressions of GaFSD1, GaMSD2, GrMSD1 and GrMSD2 peaked during the elongation stage and declined coincident with the initiation of secondary cell wall synthesis, and had similar patterns to genes expressed primarily during cell elongation in fiber development. Three-dimensional structures were determined and compared within each cotton SOD protein. These results will improve understanding of SOD genes and proteins in these cotton species, and especially in Gossypium hirsutum.