The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance
Solanum 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 o...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-10-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01402/full |
| _version_ | 1818978803769147392 |
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| author | Rozaimi Razali Salim Bougouffa Mitchell J. L. Morton Damien J. Lightfoot Intikhab Alam Intikhab Alam Magbubah Essack Stefan T. Arold Stefan T. Arold Allan A. Kamau Allan A. Kamau Sandra M. Schmöckel Yveline Pailles Mohammed Shahid Craig T. Michell Salim Al-Babili Yung Shwen Ho Mark Tester Vladimir B. Bajic Vladimir B. Bajic Sónia Negrão |
| author_facet | Rozaimi Razali Salim Bougouffa Mitchell J. L. Morton Damien J. Lightfoot Intikhab Alam Intikhab Alam Magbubah Essack Stefan T. Arold Stefan T. Arold Allan A. Kamau Allan A. Kamau Sandra M. Schmöckel Yveline Pailles Mohammed Shahid Craig T. Michell Salim Al-Babili Yung Shwen Ho Mark Tester Vladimir B. Bajic Vladimir B. Bajic Sónia Negrão |
| author_sort | Rozaimi Razali |
| collection | DOAJ |
| description | Solanum 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. |
| first_indexed | 2024-12-20T16:49:27Z |
| format | Article |
| id | doaj.art-32c82866d88d497195fd6c6302d83926 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-20T16:49:27Z |
| publishDate | 2018-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-32c82866d88d497195fd6c6302d839262022-12-21T19:32:52ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-10-01910.3389/fpls.2018.01402390082The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity ToleranceRozaimi Razali0Salim Bougouffa1Mitchell J. L. Morton2Damien J. Lightfoot3Intikhab Alam4Intikhab Alam5Magbubah Essack6Stefan T. Arold7Stefan T. Arold8Allan A. Kamau9Allan A. Kamau10Sandra M. Schmöckel11Yveline Pailles12Mohammed Shahid13Craig T. Michell14Salim Al-Babili15Yung Shwen Ho16Mark Tester17Vladimir B. Bajic18Vladimir B. Bajic19Sónia Negrão20Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaInternational Center for Biosaline Agriculture, Dubai, United Arab EmiratesRed Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaDivision of Biological and Environmental Sciences and Engineering, The Bioactives Lab, King Abdullah University of Science and Technology, Thuwal, Saudi ArabiaSolanum 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.https://www.frontiersin.org/article/10.3389/fpls.2018.01402/fullwild tomatoSolanum pimpinellifoliumgenome analysissalinity toleranceinositol 3-phosphate synthase |
| spellingShingle | Rozaimi Razali Salim Bougouffa Mitchell J. L. Morton Damien J. Lightfoot Intikhab Alam Intikhab Alam Magbubah Essack Stefan T. Arold Stefan T. Arold Allan A. Kamau Allan A. Kamau Sandra M. Schmöckel Yveline Pailles Mohammed Shahid Craig T. Michell Salim Al-Babili Yung Shwen Ho Mark Tester Vladimir B. Bajic Vladimir B. Bajic Sónia Negrão The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance Frontiers in Plant Science wild tomato Solanum pimpinellifolium genome analysis salinity tolerance inositol 3-phosphate synthase |
| title | The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance |
| title_full | The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance |
| title_fullStr | The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance |
| title_full_unstemmed | The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance |
| title_short | The Genome Sequence of the Wild Tomato Solanum pimpinellifolium Provides Insights Into Salinity Tolerance |
| title_sort | genome sequence of the wild tomato solanum pimpinellifolium provides insights into salinity tolerance |
| topic | wild tomato Solanum pimpinellifolium genome analysis salinity tolerance inositol 3-phosphate synthase |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01402/full |
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