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dc.contributor.authorRazali, Rozaimi
dc.contributor.authorBougouffa, Salim
dc.contributor.authorMorton, Mitchell J. L.
dc.contributor.authorLightfoot, Damien
dc.contributor.authorAlam, Intikhab
dc.contributor.authorEssack, Magbubah
dc.contributor.authorArold, Stefan T.
dc.contributor.authorKamau, Allan
dc.contributor.authorSchmöckel, Sandra M.
dc.contributor.authorPailles, Yveline
dc.contributor.authorShahid, Mohammed
dc.contributor.authorMichell, Craig
dc.contributor.authorAl-Babili, Salim
dc.contributor.authorShwen, Ho
dc.contributor.authorTester, Mark A.
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorNegrão, Sónia
dc.date.accessioned2018-11-25T07:47:27Z
dc.date.available2017-11-15T10:58:19Z
dc.date.available2018-11-25T07:47:27Z
dc.date.issued2018-10-04
dc.identifier.citationRazali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, et al. (2018) The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance. Frontiers in Plant Science 9. Available: http://dx.doi.org/10.3389/fpls.2018.01402.
dc.identifier.issn1664-462X
dc.identifier.doi10.3389/fpls.2018.01402
dc.identifier.doi10.1101/215517
dc.identifier.urihttp://hdl.handle.net/10754/626165
dc.description.abstractSolanum 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.
dc.description.sponsorshipWe thank John Hanks and Craig Kapfer for the great assistance with the computational resources and the installation of the many bioinformatics tools. 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 also thank Hajime Ohyanagi for his comments on the phylogenetic analysis. Funding. This publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. 2302-01-01 and KAUST Base Research Funds to VB Grant No. BAS/1/1606-01-01 and to MT Grant No. BAS/1/1038-01-01.
dc.publisherFrontiers Media SA
dc.relation.urlhttps://www.frontiersin.org/articles/10.3389/fpls.2018.01402/full
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectGenome analysis
dc.subjectInositol 3-phosphate synthase
dc.subjectSalinity tolerance
dc.subjectSolanum pimpinellifolium
dc.subjectWild tomato
dc.titleThe Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentRed Sea Research Center (RSRC)
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBioinformatics
dc.contributor.departmentPublication Srvcs and Researcher Support
dc.contributor.departmentPlant Science
dc.identifier.journalFrontiers in Plant Science
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionInternational Center for Biosaline Agriculture, Dubai, , United Arab Emirates
kaust.personRazali, Rozaimi
kaust.personBougouffa, Salim
kaust.personMorton, Mitchell J. L.
kaust.personLightfoot, Damien
kaust.personAlam, Intikhab
kaust.personEssack, Magbubah
kaust.personArold, Stefan T.
kaust.personKamau, Allan
kaust.personSchmöckel, Sandra M.
kaust.personPailles, Yveline
kaust.personMichell, Craig
kaust.personAl-Babili, Salim
kaust.personShwen, Ho
kaust.personTester, Mark A.
kaust.personBajic, Vladimir B.
kaust.personNegrão, Sónia
kaust.grant.number2302-01-01
kaust.grant.numberBAS/1/1606-01-01
kaust.grant.numberBAS/1/1038-01-01
refterms.dateFOA2018-06-13T10:24:29Z


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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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