PT  - JOURNAL ARTICLE
AU  - Rozaimi Razali
AU  - Salim Bougouffa
AU  - Mitchell J. L. Morton
AU  - Damien J. Lightfoot
AU  - Intikhab Alam
AU  - Magbubah Essack
AU  - Stefan T. Arold
AU  - Allan Kamau
AU  - Sandra M. Schmöckel
AU  - Yveline Pailles
AU  - Mohammed Shahid
AU  - Craig T. Michell
AU  - Salim Al-Babili
AU  - Yung Shwen Ho
AU  - Mark Tester
AU  - Vladimir B. Bajic
AU  - Sónia Negrão
TI  - The genome sequence of the wild tomato <em>Solanum pimpinellifolium</em> provides insights into salinity tolerance
AID  - 10.1101/215517
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 215517
4099  - http://biorxiv.org/content/early/2017/11/08/215517.short
4100  - http://biorxiv.org/content/early/2017/11/08/215517.full
AB  - Solanum pimpinellifolium, a wild relative of cultivated tomato, offers a wealth of breeding potential for several desirable traits such as tolerance to abiotic and biotic stresses. Here, we report the genome and annotation of S. pimpinellifolium ‘LA0480’. The ‘LA0480’ genome 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. 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. 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.