AUTHOR=Feng Kun , Yu Jiahong , Cheng Yuan , Ruan Meiying , Wang Rongqing , Ye Qingjing , Zhou Guozhi , Li Zhimiao , Yao Zhuping , Yang Yuejian , Zheng Qingsong , Wan Hongjian 

TITLE=The SOD Gene Family in Tomato: Identification, Phylogenetic Relationships, and Expression Patterns

JOURNAL=Frontiers in Plant Science

VOLUME=7

YEAR=2016

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2016.01279

DOI=10.3389/fpls.2016.01279

ISSN=1664-462X

ABSTRACT=<p>Superoxide dismutases (SODs) are critical antioxidant enzymes that protect organisms from reactive oxygen species (ROS) caused by adverse conditions, and have been widely found in the cytoplasm, chloroplasts, and mitochondria of eukaryotic and prokaryotic cells. Tomato (<italic>Solanum lycopersicum</italic> L.) is an important economic crop and is cultivated worldwide. However, abiotic and biotic stresses severely hinder growth and development of the plant, which affects the production and quality of the crop. To reveal the potential roles of <italic>SOD</italic> genes under various stresses, we performed a systematic analysis of the tomato <italic>SOD</italic> gene family and analyzed the expression patterns of <italic>SlSOD</italic> genes in response to abiotic stresses at the whole-genome level. The characteristics of the <italic>SlSOD</italic> gene family were determined by analyzing gene structure, conserved motifs, chromosomal distribution, phylogenetic relationships, and expression patterns. We determined that there are at least nine <italic>SOD</italic> genes in tomato, including four Cu/ZnSODs, three FeSODs, and one MnSOD, and they are unevenly distributed on 12 chromosomes. Phylogenetic analyses of <italic>SOD</italic> genes from tomato and other plant species were separated into two groups with a high bootstrap value, indicating that these <italic>SOD</italic> genes were present before the monocot-dicot split. Additionally, many <italic>cis</italic>-elements that respond to different stresses were found in the promoters of nine <italic>SlSOD</italic> genes. Gene expression analysis based on RNA-seq data showed that most genes were expressed in all tested tissues, with the exception of <italic>SlSOD6</italic> and <italic>SlSOD8</italic>, which were only expressed in young fruits. Microarray data analysis showed that most members of the <italic>SlSOD</italic> gene family were altered under salt- and drought-stress conditions. This genome-wide analysis of <italic>SlSOD</italic> genes helps to clarify the function of <italic>SlSOD</italic> genes under different stress conditions and provides information to aid in further understanding the evolutionary relationships of <italic>SOD</italic> genes in plants.</p>