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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 ProfileSónia Negrão
doi: https://doi.org/10.1101/215517
Rozaimi Razali
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Salim Bougouffa
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Mitchell J. L. Morton
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Damien J. Lightfoot
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
3King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences & Engineering, KAUST Environmental Epigenetic Program (KEEP), Thuwal 23955-6900, Kingdom of Saudi Arabia (present address).
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Intikhab Alam
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
4King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Magbubah Essack
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Stefan T. Arold
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Allan Kamau
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
4King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Sandra M. Schmöckel
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Yveline Pailles
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Mohammed Shahid
5International Center for Biosaline Agriculture (ICBA), PO Box 14660, Dubai, United Arab Emirates.
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Craig T. Michell
6King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, 23955-6900, Kingdom of Saudi Arabia
7Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 7, FI-80101, Joensuu, Finland (present address)
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Salim Al-Babili
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Yung Shwen Ho
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Mark Tester
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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Vladimir B. Bajic
1King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia
4King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia
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  • For correspondence: vladimir.bajic@kaust.edu.sa snegrao@kaust.edu.sa
Sónia Negrão
2King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Kingdom of Saudi Arabia
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  • For correspondence: vladimir.bajic@kaust.edu.sa snegrao@kaust.edu.sa
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SUMMARY

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, Sónia 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, Sónia Negrão
bioRxiv 215517; doi: https://doi.org/10.1101/215517

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