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

Handle URI:
http://hdl.handle.net/10754/626165
Title:
The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance
Authors:
Razali, Rozaimi; Bougouffa, Salim ( 0000-0001-9218-6452 ) ; Morton, Mitchell J. L.; Lightfoot, Damien ( 0000-0003-3824-8856 ) ; Alam, Intikhab; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Arold, Stefan T. ( 0000-0001-5278-0668 ) ; Kamau, Allan; Schmöckel, Sandra M.; Pailles, Yveline; Shahid, Mohammed; Michell, Craig; Al-Babili, Salim ( 0000-0003-4823-2882 ) ; Ho, Yung Shwen; Tester, Mark A. ( 0000-0002-5085-8801 ) ; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Negrão, Sónia ( 0000-0001-8059-5240 )
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.
KAUST Department:
Computational 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)
Citation:
Razali 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.
Publisher:
Cold Spring Harbor Laboratory
KAUST Grant Number:
2302; 1976-02; BAS/1/1606-01-01
Issue Date:
14-Nov-2017
DOI:
10.1101/215517
Type:
Preprint
Sponsors:
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, 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.
Additional Links:
https://www.biorxiv.org/content/early/2017/11/08/215517
Appears in Collections:
Red Sea Research Center (RSRC); Other/General Submission; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division; Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRazali, Rozaimien
dc.contributor.authorBougouffa, Salimen
dc.contributor.authorMorton, Mitchell J. L.en
dc.contributor.authorLightfoot, Damienen
dc.contributor.authorAlam, Intikhaben
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorArold, Stefan T.en
dc.contributor.authorKamau, Allanen
dc.contributor.authorSchmöckel, Sandra M.en
dc.contributor.authorPailles, Yvelineen
dc.contributor.authorShahid, Mohammeden
dc.contributor.authorMichell, Craigen
dc.contributor.authorAl-Babili, Salimen
dc.contributor.authorHo, Yung Shwenen
dc.contributor.authorTester, Mark A.en
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorNegrão, Sóniaen
dc.date.accessioned2017-11-15T10:58:19Z-
dc.date.available2017-11-15T10:58:19Z-
dc.date.issued2017-11-14en
dc.identifier.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.en
dc.identifier.doi10.1101/215517en
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 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.en
dc.description.sponsorshipThis 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.en
dc.publisherCold Spring Harbor Laboratoryen
dc.relation.urlhttps://www.biorxiv.org/content/early/2017/11/08/215517en
dc.rightsThe copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectwild tomatoen
dc.subjectSolanum pimpinellifoliumen
dc.subjectgenome analysisen
dc.subjectsalinity toleranceen
dc.subjectinositol 3-phosphate synthaseen
dc.titleThe genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity toleranceen
dc.typePreprinten
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentKAUST Environmental Epigenetics Research Program (KEEP)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.eprint.versionPre-printen
dc.contributor.institutionInternational Center for Biosaline Agriculture (ICBA), PO Box 14660, Dubai, United Arab Emiratesen
dc.contributor.institutionDepartment of Environmental and Biological Sciences, University of Eastern Finland, Yliopistokatu 7, FI-80101, Joensuu, Finlanden
kaust.authorRazali, Rozaimien
kaust.authorBougouffa, Salimen
kaust.authorMorton, Mitchell J. L.en
kaust.authorLightfoot, Damienen
kaust.authorAlam, Intikhaben
kaust.authorEssack, Magbubahen
kaust.authorArold, Stefan T.en
kaust.authorKamau, Allanen
kaust.authorSchmöckel, Sandra M.en
kaust.authorPailles, Yvelineen
kaust.authorMichell, Craigen
kaust.authorAl-Babili, Salimen
kaust.authorHo, Yung Shwenen
kaust.authorTester, Mark A.en
kaust.authorBajic, Vladimir B.en
kaust.authorNegrão, Sóniaen
kaust.grant.number2302en
kaust.grant.number1976-02en
kaust.grant.numberBAS/1/1606-01-01en
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