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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.


Tree topologies across selected chromosomes of H1706.Coordinates are based on the H1706 reference genome. Posterior probabilities are shown for each tree. (A) Chromosome 4. (B) Chromosome 5. (C) Predominant tree topologies. 1 = YP; 2 = H1706; 3 = S. galapagense; 4 = S. pimpinellifolium; 5 = S. tuberosum.
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fig-4: Tree topologies across selected chromosomes of H1706.Coordinates are based on the H1706 reference genome. Posterior probabilities are shown for each tree. (A) Chromosome 4. (B) Chromosome 5. (C) Predominant tree topologies. 1 = YP; 2 = H1706; 3 = S. galapagense; 4 = S. pimpinellifolium; 5 = S. tuberosum.

Mentions: Trees for each genome partition were constructed using Bayesian phylogenetic analysis. A total of 217 loci contained gaps in the alignment and the topology could not be deduced. A total of 2,227 loci covering 27% of the H1706 genome supported topology 1 with a posterior probability of 0.9 or greater (Fig. 4, File S3, and Fig. S3) grouping S. galapagense closer to S. lycopersicum than to S. pimpinellifolium (Fig. 4, File S3, and Fig. S3). Topology 3, which clusters the two S. lycopersicum varieties more closely to S. pimpinellifolium, was found with a posterior probability of 0.9 or greater at 224 loci covering 2.8% of the H1706 genome (Fig. 4. File S3, and Fig. S3). Overall, the predominant tree topology was topology 1 which was the best supported topology at 72.9% of the genome. Topology 3 was the second most prevalent tree and supported at 19.7% while topology 2 was found at 5.6% of the genome.


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)

Tree topologies across selected chromosomes of H1706.Coordinates are based on the H1706 reference genome. Posterior probabilities are shown for each tree. (A) Chromosome 4. (B) Chromosome 5. (C) Predominant tree topologies. 1 = YP; 2 = H1706; 3 = S. galapagense; 4 = S. pimpinellifolium; 5 = S. tuberosum.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig-4: Tree topologies across selected chromosomes of H1706.Coordinates are based on the H1706 reference genome. Posterior probabilities are shown for each tree. (A) Chromosome 4. (B) Chromosome 5. (C) Predominant tree topologies. 1 = YP; 2 = H1706; 3 = S. galapagense; 4 = S. pimpinellifolium; 5 = S. tuberosum.
Mentions: Trees for each genome partition were constructed using Bayesian phylogenetic analysis. A total of 217 loci contained gaps in the alignment and the topology could not be deduced. A total of 2,227 loci covering 27% of the H1706 genome supported topology 1 with a posterior probability of 0.9 or greater (Fig. 4, File S3, and Fig. S3) grouping S. galapagense closer to S. lycopersicum than to S. pimpinellifolium (Fig. 4, File S3, and Fig. S3). Topology 3, which clusters the two S. lycopersicum varieties more closely to S. pimpinellifolium, was found with a posterior probability of 0.9 or greater at 224 loci covering 2.8% of the H1706 genome (Fig. 4. File S3, and Fig. S3). Overall, the predominant tree topology was topology 1 which was the best supported topology at 72.9% of the genome. Topology 3 was the second most prevalent tree and supported at 19.7% while topology 2 was found at 5.6% of the genome.

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.