Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress.

Yu Zang,Shuai Shang,Ruoxi Li,Jun Chen,Xuexi Tang

doi:10.7717/peerj.9063

Yu Zang, Shuai Shang + Show 3 more

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https://doi.org/10.7717/peerj.9063

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Abstract

Superoxide dismutases (SODs) serve as the first line of defense in the plant antioxidant enzyme system, and play a primary role in the removal of reactive oxygen species (ROS). However, our understanding of the functions of the SOD family in Zostera marina is limited. In this study, a systematic analysis was conducted on the characteristics of the SOD genes in Z. marina at the whole-genome level. Five SOD genes were identified, consisting of two Cu/ZnSODs, two FeSODs, and one MnSOD. Phylogenetic analysis showed that ZmSOD proteins could be divided into two major categories (Cu/ZnSODs and Fe-MnSODs). Sequence motifs, gene structure, and the 3D-modeled protein structures further supported the phylogenetic analysis, with each subgroup having similar motifs, exon-intron structures, and protein structures. Additionally, several cis-elements were identified that may respond to biotic and abiotic stresses. Transcriptome analysis revealed expression diversity of ZmSODs in various tissues. Moreover, qRT-PCR analysis showed that the expression level of most ZmSOD genes trended to decreased expression with the increase of temperature, indicating that heat stress inhibits expression of ZmSODs and may result in reduced ability of ZmSODs to scavenge ROS. Our results provide a basis for further functional research on the SOD gene family in Z. marina, which will help to determine the molecular mechanism of ZmSOD genes in response to environmental stress.

Highlights

Seagrasses are marine angiosperms that have adapted to live and grow fully submersed in the sea (Orth et al, 2006; Papenbrock, 2012)
Sequence acquisition The whole genome sequence of Z. marina and Spirodela polyrhiza were downloaded from phytozome, and that of Z. muelleri was obtained from Applied Bioinformatics Group
Identification of the superoxide dismutase (SOD) genes in Z. marina Five putative ZmSOD genes were identified in the Z. marina genome, including two Fe-SOD, three Cu/Zn-SOD, and one Mn-SOD (Table 1)

Summary

Introduction

Seagrasses are marine angiosperms that have adapted to live and grow fully submersed in the sea (Orth et al, 2006; Papenbrock, 2012). Seagrasses play important roles in trophodynamics, habitat provision, substrate stability, and biogeochemical cycling, and can sequester about 27.4 million tons of CO2 annually, twice. Genome-wide analysis of the superoxide dismutase (SOD) gene family in Zostera marina and expression profile analysis under temperature stress. Zostera marina is an important representative seagrass and provides key ecological services to the marine environment in north-temperate coastal areas (Fourqurean et al, 2012; Hemminga & Duarte, 2000). Increasing evidence indicates that extreme summer heat waves may lead to significant losses of several seagrass species (Collier et al, 2017; Moore & Jarvis, 2008; Thomson et al, 2015)

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