Data_Sheet_1_The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance.docx

Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome assembly and annotation of S. pimpinellifolium ‘LA0480.’ Moreover, we present phenotypic data from one field experiment that demonstrate a greater salinity tolerance for fruit- and yield-related traits in S. pimpinellifolium compared with cultivated tomato. The ‘LA0480’ genome assembly size (811 Mb) and the number of annotated genes (25,970) are within the range observed for other sequenced tomato species. We developed and utilized the Dragon Eukaryotic Analyses Platform (DEAP) to functionally annotate the ‘LA0480’ protein-coding genes. Additionally, we used DEAP to compare protein function between S. pimpinellifolium and cultivated tomato. Our data suggest enrichment in genes involved in biotic and abiotic stress responses. To understand the genomic basis for these differences in S. pimpinellifolium and S. lycopersicum, we analyzed 15 genes that have previously been shown to mediate salinity tolerance in plants. We show that S. pimpinellifolium has a higher copy number of the inositol-3-phosphate synthase and phosphatase genes, which are both key enzymes in the production of inositol and its derivatives. Moreover, our analysis indicates that changes occurring in the inositol phosphate pathway may contribute to the observed higher salinity tolerance in ‘LA0480.’ Altogether, our work provides essential resources to understand and unlock the genetic and breeding potential of S. pimpinellifolium, and to discover the genomic basis underlying its environmental robustness.

醋栗番茄（Solanum pimpinellifolium）是栽培番茄的野生近缘物种，具备诸多优良抗逆性状的育种潜力，包括对非生物胁迫与生物胁迫的耐受性。本研究报道了醋栗番茄‘LA0480’的基因组组装与注释结果。此外，本研究提供了一项田间试验的表型数据，结果显示相较于栽培番茄，醋栗番茄的果实及产量相关性状具有更显著的盐胁迫耐受性。‘LA0480’的基因组组装规模为811 Mb，注释基因数量为25970个，处于已测序番茄物种的正常范围内。我们开发并使用了龙真核分析平台（Dragon Eukaryotic Analyses Platform，DEAP）对‘LA0480’的蛋白编码基因进行功能注释。同时，我们借助DEAP平台对比了醋栗番茄与栽培番茄的蛋白功能差异，数据表明参与生物与非生物胁迫响应的基因存在显著富集现象。为解析醋栗番茄与栽培番茄（Solanum lycopersicum）之间性状差异的基因组基础，本研究分析了15个已被证实可介导植物盐胁迫耐受性的基因。研究结果显示，醋栗番茄中肌醇-3-磷酸合酶与肌醇-3-磷酸磷酸酶基因的拷贝数更高，这两类酶均为肌醇及其衍生物合成过程中的关键酶。进一步分析表明，肌醇磷酸通路的相关变化可能是‘LA0480’表现出更高盐胁迫耐受性的潜在原因。综上，本研究为解析并挖掘醋栗番茄的遗传与育种潜力，以及揭示其环境鲁棒性的基因组基础提供了关键的研究资源。