Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives
Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycop...
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PeerJ Inc.
2015-02-01
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| Online Access: | https://peerj.com/articles/793.pdf |
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| author | Susan R. Strickler Aureliano Bombarely Jesse D. Munkvold Thomas York Naama Menda Gregory B. Martin Lukas A. Mueller |
| author_facet | Susan R. Strickler Aureliano Bombarely Jesse D. Munkvold Thomas York Naama Menda Gregory B. Martin Lukas A. Mueller |
| author_sort | Susan R. Strickler |
| collection | DOAJ |
| description | Background. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato.Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported.Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species. |
| first_indexed | 2024-03-09T06:53:19Z |
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| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:53:19Z |
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| spelling | doaj.art-8f1241af3f544c2c96b689e2259073012023-12-03T10:16:09ZengPeerJ Inc.PeerJ2167-83592015-02-013e79310.7717/peerj.793793Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relativesSusan R. Strickler0Aureliano Bombarely1Jesse D. Munkvold2Thomas York3Naama Menda4Gregory B. Martin5Lukas A. Mueller6Boyce Thompson Institute for Plant Research, Ithaca, NY, USADepartment of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, USABoyce Thompson Institute for Plant Research, Ithaca, NY, USABoyce Thompson Institute for Plant Research, Ithaca, NY, USABoyce Thompson Institute for Plant Research, Ithaca, NY, USABoyce Thompson Institute for Plant Research, Ithaca, NY, USABoyce Thompson Institute for Plant Research, Ithaca, NY, USABackground. Studies of ancestry are difficult in the tomato because it crosses with many wild relatives and species in the tomato clade that have diverged very recently. As a result, the phylogeny in relation to its closest relatives remains uncertain. By using the coding sequence from Solanum lycopersicum, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum and the genomic sequence from S. lycopersicum ‘Heinz’, an heirloom line, S. lycopersicum ‘Yellow Pear’, and two of cultivated tomato’s closest relatives, S. galapagense and S. pimpinellifolium, we have aimed to resolve the phylogenies of these closely related species as well as identify phylogenetic discordance in the reference cultivated tomato.Results. Divergence date estimates suggest that the divergence of S. lycopersicum, S. galapagense, and S. pimpinellifolium happened less than 0.5 MYA. Phylogenies based on 8,857 coding sequences support grouping of S. lycopersicum and S. galapagense, although two secondary trees are also highly represented. A total of 25 genes in our analysis had sites with evidence of positive selection along the S. lycopersicum lineage. Whole genome phylogenies showed that while incongruence is prevalent in genomic comparisons between these genotypes, likely as a result of introgression and incomplete lineage sorting, a primary phylogenetic history was strongly supported.Conclusions. Based on analysis of these genotypes, S. galapagense appears to be closely related to S. lycopersicum, suggesting they had a common ancestor prior to the arrival of an S. galapagense ancestor to the Galápagos Islands, but after divergence of the sequenced S. pimpinellifolium. Genes showing selection along the S. lycopersicum lineage may be important in domestication or selection occurring post-domestication. Further analysis of intraspecific data in these species will help to establish the evolutionary history of cultivated tomato. The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.https://peerj.com/articles/793.pdfTomatoPhylogenySolanumGenomeIncomplete lineage sortingIntrogression |
| spellingShingle | Susan R. Strickler Aureliano Bombarely Jesse D. Munkvold Thomas York Naama Menda Gregory B. Martin Lukas A. Mueller Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives PeerJ Tomato Phylogeny Solanum Genome Incomplete lineage sorting Introgression |
| title | Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| title_full | Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| title_fullStr | Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| title_full_unstemmed | Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| title_short | Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| title_sort | comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives |
| topic | Tomato Phylogeny Solanum Genome Incomplete lineage sorting Introgression |
| url | https://peerj.com/articles/793.pdf |
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