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.
Highlights
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
92.1% of the S. lycopersicum H1706 reads, 93.5% of the YP-1 reads, 89% of the S. galapagense, 88% of the S. pimpinellifolium reads mapped to the S. lycopersicum version 2.40 genome assembly giving 39x, 45x, 32x, and 25x coverage and covering 99.2%, 99.3%, 95.4%, and 95% of the tomato genome respectively, after mapping quality filtering and duplicate read removal (Table S1)
Gaps were calculated as regions without read coverage that were not gaps in the S. lycopersicum H1706 scaffolds
Summary
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. 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. Identifying and exploiting diversity present in wild tomato species has been crucial for the improvement of production traits in cultivated tomato (Grandillo et al, 2011). Most wild species are green-fruited except for three: S. pimpinellifolium, S. galapagense, and S. cheesmaniae These species are thought to be the closest relatives to cultivated tomato (Darwin, Knapp & Peralta, 2003; The Tomato Genome Consortium, 2012)
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