The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance
Morton, Mitchell J. L.
Arold, Stefan T.
Schmöckel, Sandra M.
Ho, Yung Shwen
Tester, Mark A.
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Biological and Environmental Sciences and Engineering (BESE) Division
KAUST Environmental Epigenetics Research Program (KEEP)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Red Sea Research Center (RSRC)
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AbstractSolanum 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.
CitationRazali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, et al. (2017) The genome sequence of the wild tomatoSolanum pimpinellifoliumprovides insights into salinity tolerance. Available: http://dx.doi.org/10.1101/215517.
SponsorsThis publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. 2302, No. 1976-02 and KAUST Base Research Funds to VBB grant No. BAS/1/1606-01-01. Genome sequencing was performed at the biological core laboratories of KAUST. All the computational analyses were performed on Dragon and Snapdragon computer clusters of the Computational Bioscience Research Center (CBRC) at King Abdullah University of Science and Technology (KAUST). We thank Gabriele Fiene (KAUST) for her assistance with the field trial and phenotypic data collection. We thank Hajime Ohyanagi for his comments on the phylogenetic analysis.
PublisherCold Spring Harbor Laboratory
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