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The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance

Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell, Salim Al-Babili, Yung Shwen Ho, View ORCID ProfileMark Tester, View ORCID ProfileVladimir B. Bajic, View ORCID ProfileSonia Negrão
doi: https://doi.org/10.1101/215517
Rozaimi Razali
King Abdullah University of Science and Technology;
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Salim Bougouffa
King Abdullah University of Science and Technology;
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Mitchell J. L. Morton
King Abdullah University of Science and Technology;
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Damien J. Lightfoot
King Abdullah University of Science and Technology;
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Intikhab Alam
King Abdullah University of Science and Technology;
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Magbubah Essack
King Abdullah University of Science and Technology;
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Stefan T. Arold
King Abdullah University of Science and Technology;
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Allan Kamau
King Abdullah University of Science and Technology;
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Sandra M. Schmöckel
King Abdullah University of Science and Technology;
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Yveline Pailles
King Abdullah University of Science and Technology;
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Mohammed Shahid
International Center for Biosaline Agriculture;
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Craig T. Michell
University of Eastern Finland
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Salim Al-Babili
King Abdullah University of Science and Technology;
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Yung Shwen Ho
King Abdullah University of Science and Technology;
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Mark Tester
King Abdullah University of Science and Technology;
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Vladimir B. Bajic
King Abdullah University of Science and Technology;
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Sonia Negrão
King Abdullah University of Science and Technology;
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  • For correspondence: snegrao@kaust.edu.sa
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Abstract

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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 08, 2017.
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The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance
Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell, Salim Al-Babili, Yung Shwen Ho, Mark Tester, Vladimir B. Bajic, Sonia Negrão
bioRxiv 215517; doi: https://doi.org/10.1101/215517
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The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance
Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell, Salim Al-Babili, Yung Shwen Ho, Mark Tester, Vladimir B. Bajic, Sonia Negrão
bioRxiv 215517; doi: https://doi.org/10.1101/215517

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