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

Abstract

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 (Solanum lycopersicum 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 SOD genes under various stresses, we performed a systematic analysis of the tomato SOD gene family and analyzed the expression patterns of SlSOD genes in response to abiotic stresses at the whole-genome level. The characteristics of the SlSOD 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 SOD genes in tomato, including four Cu/ZnSODs, three FeSODs, and one MnSOD, and they are unevenly distributed on 12 chromosomes. Phylogenetic analyses of SOD genes from tomato and other plant species were separated into two groups with a high bootstrap value, indicating that these SOD genes were present before the monocot-dicot split. Additionally, many cis-elements that respond to different stresses were found in the promoters of nine SlSOD genes. Gene expression analysis based on RNA-seq data showed that most genes were expressed in all tested tissues, with the exception of SlSOD6 and SlSOD8, which were only expressed in young fruits. Microarray data analysis showed that most members of the SlSOD gene family were altered under salt- and drought-stress conditions. This genome-wide analysis of SlSOD genes helps to clarify the function of SlSOD genes under different stress conditions and provides information to aid in further understanding the evolutionary relationships of SOD genes in plants.

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

“…The results revealed that four and six of soybean SOD genes were significantly induced under alkaline and salt stresses, respectively. Similarly, studies have reported that SOD genes played positive roles in other plants (Feng et al, 2016). Whereas, almost all the expression levels of soybean SOD genes displayed no significant change under cold stress, except for a slightly up-regulation (|Log 2 fold change| > 1) of GmFSD2.…”

“…Antioxidant enzymes SOD play significantly roles in plant response to abiotic stresses by reducing the molecular oxygen and hydrogen peroxide in plant cells. The plant SOD family genes have been identified and characterized in some species at the genome-wide level (Feng et al, 2016;Verma, Lakhanpal & Singh, 2019). However, the roles of soybean SOD family genes in regulating various abiotic stresses, especially alkaline stress, are rarely reported.…”

“…Hence, our research conducted a comprehensive exploration of soybean SOD family, and mainly identified potential roles of soybean SOD genes in response to alkaline stress. The SOD family genes were reported to be divided into three subfamilies, and each subfamily genes frequently located in different cellular compartments (Feng et al, 2016). This indicated that SOD family genes may display evolutionarily divergence.…”

Concomitant phytonutrient and transcriptome analysis of mature fruit and leaf tissues of tomato (Solanum lycopersicum L. cv. Oregon Spring) grown using organic and conventional fertilizer

“…Under such conditions, plants attempt to decrease photosystem II activity by activating the Mehler peroxidase reaction (reviewed in [70]), which results in an increase in superoxide radicals. Increased oxygen radicals stimulate SOD production [71,72], and APX and catalase expression activity during tomato fruit ripening [73]. Increased level of APX expression was also observed in Lactuca sativa L. cv Romaine leaves when Mehler reaction was initiated by potassium cyanide (KCN)mediated inhibition of the electron transport chain [74].…”

Dissecting the proteome dynamics of the salt stress induced changes in the leaf of diploid and autotetraploid Paulownia fortunei

“…High-throughput genomic and transcriptomic sequencing techniques are powerful tools that have been used to gain comprehensive genomic information of the novelty and plasticity underlying the adaptation response of plants under salt stress. Many studies have focused on the transcriptional reprogramming of the related biological processes [ 11 – 13 ]. However, because most biological functions are carried out by proteins, and posttranscriptional regulation and posttranslational modifications can influence a system, quantitation of the proteins in a system is mandatory to understand the biological process and functions involved [ 14 , 15 ].…”