The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance

Abstract

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.

Keywords: Solanum pimpinellifolium; genome analysis; inositol 3-phosphate synthase; salinity tolerance; wild tomato.

FIGURE 1

Comparison of S. pimpinellifolium and S. lycopersicum salinity tolerance (ST) indices across various traits measured in the field (log₂ ratio). Traits for which the ST index is higher in S. pimpinellifolium and S. lycopersicum are in green and gray, respectively.

FIGURE 2

Identification of orthologous gene clusters in S. pimpinellifolium, S. pennellii, S. lycopersicum, and S. tuberosum. The Venn diagram represents the number of protein-coding genes and gene clusters shared between, or distinct to, the indicated species. The number in each sector of the diagram indicates the number of homologous clusters and the numbers in parentheses indicate the total number of genes contained within the associated clusters. The numbers in parentheses below the species names indicate the number of species-specific singletons (genes with no homologs).

FIGURE 3

Circular representation of S. pimpinellifolium genome structure in comparison with S. lycopersicum. From the outside to the inside: The outer layer represents the 12 chromosomes of S. lycopersicum, with the axis scale in Mb. The second layer (blue/red) represents the scatter plot of copy number variant (CNVs) regions with blue and red circles denoting high and low copy variants, respectively in S. pimpinellifolium relative to S. lycopersicum. The size of the circles is proportional to the absolute value of the log₂ CNV. The y-axis scale on the second layer corresponds to the log₂ CNV ranging from –10 to 10. The innermost layer represents the histogram of SNPs in 1 Mb bins. The y-axis scale on the innermost layer represents the SNP distribution between the two species, which ranges from 0 to 19,095 SNPs.

FIGURE 4

Comparison of KO term frequency in S. pimpinellifolium (KO_Spi) and S. lycopersicum (KO_Sly) genomes, presented as the ratio on a log₂ scale. Bars are color-coded based on the P-values from a Fisher’s exact test-based enrichment analysis (corrected for multiplicity using the Bonferroni method); the top 20 entries with the highest P values are presented. Entries are ordered based on log₂ values.

FIGURE 5

Phylogenetic analysis of the inositol-3-phosphate synthase (I3PS) gene family in the Solanaceae family. Node values represent the percentage of 100 bootstrap replicates that support the topology. The I3PSa and I3PSb genes are encircled in red and blue, respectively. A. thaliana MIPS genes were used as outgroups.

FIGURE 6

Structural evaluation of the catalytic activity of S. pimpinellifolium I3PS proteins. (A) Multiple sequence alignment. Yeast MIP protein. Asterisks label residues involved in binding to NAD (green), DG6 (cyan) and NH₄ (magenta). (B) Overall view of the MIP tetramer (PDB: 1jki); individual monomers are shown in gray and yellow (dimer A) and orange and black (dimer B). Red: regions deleted in SpiI3PSc. Blue: homology model of SpiI3PSa superposed. NAD is shown as stick model with green carbons, and DG6 as stick model with cyan carbons, and NH₄ as magenta sphere; (C) Detail of the binding site. Colors as in (B). Side chains discussed in the text are shown.

FIGURE 7

The inositol metabolism pathway in S. pimpinellifolium and S. lycopersicum. The pathway was adapted from the KEGG inositol metabolism pathway (map00562- http://www.genome.jp/kegg/pathway/map/map00562.html). Compounds are represented with diamonds, myo-inositol is shown in a blue diamond whereas phytate and Ins(1,3,4,5)P₄ are represented by a gray diamond. Enzymes are represented with their EC numbers placed directly on arrows. Enzymes with gene copy numbers higher in S. pimpinellifolium than in S. lycopersicum are underlined and colored in red (Supplementary Table S18). Compound abbreviations were taken from the ChEBI database (Hastings et al., 2013): Ins(1)P: Inositol 1-phosphate; PtdIns: Phosphatidyl-1D-myo-inositol; PtdIns3P: 1-Phosphatidyl-1D-myo-Inositol-3P; PtsIns(3,5)P₂: 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate; PtdIns5P: 1-phosphatidyl-1D-myo-inositol 5-phosphate; PtsIns(3,4,5)P₃: 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate; PtsIns(4,5)P₂: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate; Ins(1,4,5)P₃: 1D-myo-inositol 1,4,5-trisphosphate; Ins(1,3,4,5)P₄: 1D-myo-inositol 1,3,4,5-P₄; Ins(1,4,5,6)P₄: 1D-myo-inositol 1,3,4,5-P₄; Ins(1,3,4,5,6)P₅: 1D-myo-inositol 1,3,4,5,6-P₅.

FIGURE 8

Schematic overview of the main tools used for the genome sequence assembly and annotation of S. pimpinellifolium ‘LA0480’. The diagram outlines the workflow and the main tools that were used in the different stages of assembly, gene model annotation and functional annotation.