Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

Abstract

BackgroundSuperoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies have shown that the gene family are involved in plant growth and developmental processes and biotic and abiotic stress responses, little is known about its functional role in upland cotton.ResultsIn the present study, we comprehensively analyzed the characteristics of the SOD gene family in upland cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified and phylogenetically classified into five subgroups which corroborated their classifications based on gene-structure patterns and subcellular localizations. The GhSOD sequences were distributed at different densities across 12 of the 26 chromosomes. The conserved domains, gene family evolution cis-acting elements of promoter regions and miRNA-mediated posttranscriptional regulation were predicted and analyzed. In addition, the expression pattern of 18 GhSOD genes were tested in different tissues/organs and developmental stages, and different abiotic stresses and abscisic acid, which indicated that the SOD gene family possessed temporal and spatial specificity expression specificity and may play important roles in reactive oxygen species scavenging caused by various stresses in upland cotton.ConclusionsThis study describes the first genome-wide analysis of the upland cotton SOD gene family, and the results will help establish a foundation for the further cloning and functional verification of the GhSOD gene family during stress responses, leading to crop improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3768-5) contains supplementary material, which is available to authorized users.

Genome-wide identification and characterization of the soybean SOD family during alkaline stress

“…Thirdly, the conserved motifs further revealed the varied widely from different subfamilies, especially MnSODs and Cu/ZnSODs subfamily (Fig. 3), which consistent with previous study (Wang et al, 2017).…”

MicroRNA414c affects salt tolerance of cotton by regulating reactive oxygen species metabolism under salinity stress

“…miRNAs are ubiquitous transcriptional and/or post-transcriptional regulators in plants, and previous studies had shown that cotton miRNAs were involved in the regulation of plant response to salt stress [29][30][31]. In our previous study, we had predicted that ghr-miR414c matched the CDS of GhFSD1 [23]. Previous reports had suggested that a functional miRNA and its target can contain up to five mismatches [32], and our analysis showed that there were two mismatches within the predicted complementary region between ghr-miR414c and GhFSD1.…”

“…Iron superoxide dismutase (Fe-SOD) was thought to be the most ancient SOD of the metalloenzymes and is an important component of the primary enzymatic antioxidant system controlling ROS accumulation in plants; they are most abundantly localized inside plant chloroplasts, to which they are indigenous [22]. In our previous study, we found that the expression of an upland cotton (Gossypium hirsutum L.) iron superoxide dismutase 1 (GhFSD1) gene was regulated by salinity stress, and that the coding sequence (CDS) of GhFSD1 harbored a potential ghr-miR414c targeting site [23]. Previous sequencing data showed that ghr-miR414c belongs to a member of the large miR414 miRNA family, which contains seven members in cotton, from ghr-miR414a to ghr-miR414g, the mature sequences of which are identical [24].…”

“…Cotyledons, hypocotyls, roots, and stems were harvested from 10-day-old seedlings; leaves and flowers were harvested from field-grown plants for expression profiling analysis. For salt stress treatments, three-week-old seedlings were treated with NaCl or water (control) as described in our previous report [23]. The leaves of treated plantlets were harvested at 0, 3, 6, 12 and 24 h. All samples were frozen immediately in liquid nitrogen and stored at −80°C until to analysis.…”

Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family

“…Genes may be duplicated by some mechanisms, such as WGD or polyploidy, tandem, proximal and/or dispersed duplication [27]. It is generally known that WGD or polyploidy are important processes throughout the history of plant evolution, and have long been recognized as fundamental mechanisms of diversification and gene family expansion in plants [39][40][41][42]. Throughout plant history, there have been some common WGD or polyploidy events, such as occurred at the appearance of the seed plants approximately 310 MYA and another paleohexaploidization event at the evolution of the eudicots 130~190 MYA, as well as some lineage-specific WGD or polyploidy events, such as the WGD series of the ρ-σ-τ in the cereal grass Fig.…”