Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Abstract

SRO (SIMILAR TO RCD ONE) is a family of plant-specific small molecule proteins that play an important role in plant growth and development and environmental responses. However, SROs still lack systematic characterization in tomato. Based on bioinformatics methods, SRO family genes were identified and characterized from cultivated tomatoes and several wild tomatoes. qRT-PCR was used to study the expression of SRO gene in cultivated tomatoes. Phylogenetic and evolutionary analyses showed that SRO genes in angiosperms share a common ancestor and that the number of SRO family members changed as plants diverged and evolved. Cultivated tomato had six SRO members, five of which still shared some degree of identity with the ancestral SRO genes. Genetic structure and physicochemical properties showed that tomato SRO genes were highly conserved with chromosomal distribution. They could be divided into three groups based on exon-intron structure, and cultivated tomato contained only two of these subclades. A number of hormonal, light and abiotic stress-responsive cis-regulatory elements were identified from the promoter of the tomato SRO gene, and they also interacted with a variety of stress-responsive proteins and microRNAs. RNA-seq analysis showed that SRO genes were widely expressed in different tissues and developmental stages of tomato, with significant tissue-specific features. Expression analysis also showed that SRO genes respond significantly to high temperature and salt stress and mediate the tomato hormone regulatory network. These results provide a theoretical basis for further investigation of the functional expression of tomato SRO genes and provide potential genetic resources for tomato resistance breeding.

Comprehensive Analysis of SRO Gene Family in Sesamum indicum (L.) Reveals Its Association with Abiotic Stress Responses

“…Over-expression of IcSRO1 conferred salt and drought tolerance in transgenic Arabidopsis [ 4 ]. In this study, the cis elements analysis of SiSRO genes suggested that SiSROs are widely involved in response to abiotic stresses and phytohormone treatments, which is consistent with the results reported in maize, wheat, tomato, and banana [ 23 , 25 , 26 , 29 ]. Subsequently, the expression levels of SiSRO genes under various abiotic stresses (osmotic, salt, cold, heat, and submerge) and different hormone (ABA, ACC, JA and SA) treatments were analyzed by qRT-PCR.…”

“…Group II SiSROs, SiSRO2a, and SiSRO2b, only have the PARP domain and RST domain, lacking the WWE domain. Gene duplication events of the SRO family have been reported in tomato and wheat [ 25 , 26 ], but not detected in SiSROs.…”

“…In rice, OsSRO1d and OsSRO1e showed constitutive expression in various tissues, while the expression of OsSRO1c in developing endosperm is much higher than other tissues [ 6 ]. The tissue-specific and ubiquitously expressed of SROs were also identified in tomato [ 26 ]. The results of the transcriptome data in this study showed that Group I SiSROs showed ubiquitously expressed in all detected tissues, suggesting they may function in the development of various tissues in sesame.…”

“…In recent years, a total of 5, 6, 6, 6, 12, and 30 SRO family genes have been identified in rice [ 6 , 21 ], apple [ 19 ], maize [ 22 ], banana [ 23 ], Chinese cabbage [ 24 ], wheat [ 25 ], and tomato [ 26 ], respectively. However, no relevant systematic study about the expression and possible roles of SRO genes in sesame, which has high nutritional quality, but its production is severely threatened by adverse environmental stresses [ 27 , 28 ].…”

Genome-wide identification and expression analysis of serine hydroxymethyltransferase (SHMT) gene family in tomato (Solanum lycopersicum)

“…Tomato is favoured by consumers worldwide due to its abundant nutrients ( Wang & Liu., 2021 ). What’s more, tomato is an important model plant in horticultural research, including the study concerning the tolerance of adverse stress ( Guo et al, 2021 ; Li et al, 2021 ). Hitherto, SHMT genes have been identified and characterized in pea, A. thaliana , soybean and poplar ( Turner et al, 1992 ; McClung et al, 2000 ; Wu et al, 2016 ; Li & Cheng, 2020 ).…”