Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress

Wencai Yu; Guanghong Kong; Jinquan Chao; Tuo Yin; Hai Tian; Huajin Ya; Ligang He; Hanyao Zhang

doi:10.7717/peerj.14251

Genome-wide identification of the rubber tree superoxide dismutase (SOD) gene family and analysis of its expression under abiotic stress

PeerJ. 2022 Oct 24:10:e14251. doi: 10.7717/peerj.14251. eCollection 2022.

Authors

Wencai Yu^#^{1

2}, Guanghong Kong^#², Jinquan Chao³, Tuo Yin¹, Hai Tian², Huajin Ya², Ligang He², Hanyao Zhang¹

Affiliations

¹ Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan Province, China.
² Yunnan Institute of Tropical Crops, Jinghong, Yunnan Province, China.
³ Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan Province, China.

^# Contributed equally.

Abstract

Background: The rubber tree (Hevea brasiliensis) is the only species capable of producing high-quality natural rubber for commercial use, and is often subjected to various abiotic stresses in non-traditional rubber plantation areas. Superoxide dismutase (SOD) is a vital metalloenzyme translated by a SOD gene family member and acts as a first-line of protection in plant cells by catalysing the disproportionation of reactive oxygen species (ROS) to produce H₂O₂ and O₂. However, the SOD gene family is not reported in rubber trees.

Methods: Here, we used hidden markov model (HMM) and BLASTP methods to identify SOD genes in the H. brasiliensis genome. Phylogenetic tree, conserved motifs, gene structures, cis elements, and gene ontology annotation (GO) analyses were performed using MEGA 6.0, MEME, TBtools, PlantCARE, and eggNOG database, respectively. HbSOD gene expression profiles were analysed using quantitative reverse transcription polymerase chain reaction (qRT-PCR).

Results: We identified nine HbSOD genes in the rubber tree genome, including five HbCSDs, two HbFSDs, and two HbMSDs. Phylogenetic relationship analysis classified the SOD proteins from the rubber tree and other related species into three subfamilies. The results of gene structure and conserved motif analysis illustrated that most HbSOD genes have similar exon-intron numbers and conserved motifs in the same evolutionary branch. Five hormone-related, four stress-related, and light-responsive elements were detected in the HbSODs' promoters. HbSODs were expressed in different tissues, gradually increased with leaf development, and were abundantly expressed in mature leaves. HbCSD2 and HbCSD4 was significantly upregulated under low and high temperatures, and salt stress, except for HbCSD2, by heat. Furthermore, most HbSOD genes were significantly upregulated by drought, except HbMSD2. These findings imply that these genes may play vital roles in rubber tree stress resistance. Our results provide a basis for further studies on the functions of HbSOD genes in rubber trees and stress response mechanisms.

Keywords: Abiotic stress; Cis-elements; Gene expression; Gene ontology; Gene structure; Hevea brasiliensis; ROS; Superoxide dismutase (SOD).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Hevea* / genetics
Hydrogen Peroxide
Phylogeny
Stress, Physiological / genetics
Superoxide Dismutase / genetics

Substances

Hydrogen Peroxide
Superoxide Dismutase

Grants and funding

This work was supported by the Youth Growth Foundation of Yunnan Institute of Tropical Crops (Grant No. QNCZ2020-2), the National Key R&D Program of China (Grant No. 2019YFD1001102-02). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.