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Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives.

Strickler SR, Bombarely A, Munkvold JD, York T, Menda N, Martin GB, Mueller LA - PeerJ (2015)

Bottom Line: As a result, the phylogeny in relation to its closest relatives remains uncertain.Conclusions.The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Boyce Thompson Institute for Plant Research , Ithaca, NY , USA.

ABSTRACT
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.

No MeSH data available.


Gene trees inferred from coding sequence of 8,796 Solanum species genes.Phylogenetic trees were derived using maximum likelihood and were supported in at least 75 of 100 bootstrap replicates.
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fig-3: Gene trees inferred from coding sequence of 8,796 Solanum species genes.Phylogenetic trees were derived using maximum likelihood and were supported in at least 75 of 100 bootstrap replicates.

Mentions: The coding sequence from 8,857 orthologous genes that could be aligned with confidence between YP-1, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum were analyzed to infer gene tree topology using maximum likelihood. The majority of trees (3,611) supported tree topology 1 which groups S. lycopersicum and S. galapagense, suggesting these two species may be more closely related, although two other tree topologies were also well supported, albeit to a lesser degree (2,344 and 2,037 trees) (Fig. 3). The genes were then subjected to site-branch selection tests along the S. lycopersicum lineage. Stop codons were found in at least one of the species for 288 genes and these were removed from further analysis.


Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives.

Strickler SR, Bombarely A, Munkvold JD, York T, Menda N, Martin GB, Mueller LA - PeerJ (2015)

Gene trees inferred from coding sequence of 8,796 Solanum species genes.Phylogenetic trees were derived using maximum likelihood and were supported in at least 75 of 100 bootstrap replicates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4358695&req=5

fig-3: Gene trees inferred from coding sequence of 8,796 Solanum species genes.Phylogenetic trees were derived using maximum likelihood and were supported in at least 75 of 100 bootstrap replicates.
Mentions: The coding sequence from 8,857 orthologous genes that could be aligned with confidence between YP-1, S. galapagense, S. pimpinellifolium, S. corneliomuelleri, and S. tuberosum were analyzed to infer gene tree topology using maximum likelihood. The majority of trees (3,611) supported tree topology 1 which groups S. lycopersicum and S. galapagense, suggesting these two species may be more closely related, although two other tree topologies were also well supported, albeit to a lesser degree (2,344 and 2,037 trees) (Fig. 3). The genes were then subjected to site-branch selection tests along the S. lycopersicum lineage. Stop codons were found in at least one of the species for 288 genes and these were removed from further analysis.

Bottom Line: As a result, the phylogeny in relation to its closest relatives remains uncertain.Conclusions.The use of an heirloom line is helpful in deducing true phylogenetic information of S. lycopersicum and identifying regions of introgression from wild species.

View Article: PubMed Central - HTML - PubMed

Affiliation: Boyce Thompson Institute for Plant Research , Ithaca, NY , USA.

ABSTRACT
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.

No MeSH data available.