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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.


Putative deletion size distribution in combined assemblies.
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fig-2: Putative deletion size distribution in combined assemblies.

Mentions: To determine the nature of regions where reads from YP-1, S. galapagense, or S. pimpinellifolium could not map to the H1706 genome, but H1706 reads could map, these regions were further analyzed for each species. Regions lacking coverage in the H1706 mapping are mainly scaffolding gaps in the H1706 reference genome. Gap size distribution was similar between S. galapagense and S. pimpinellifolium with less gaps found in YP-1 (Fig. 2), with all genotypes having a peak at 90 bp. Since gaps could be missing regions or divergent regions where short reads cannot map, de novo contigs assembled from the wild and heirloom species reads were mapped to the reference genome to determine if they covered gap regions. Approximately 3.3% of YP-1, 3.7% of S. galapagense, and 6.0% of S. pimpinellifolium contigs did not map with greater than 90% id. A small number of these contigs contained many repeats or matched plastid, mitochondrial, or vector DNA (Table S5). After removal of gaps covered by de novo contigs, a total of 2.4 Mbp of YP-1, 13.8 Mbp of S. galapagense, and 21.6 Mbp of S. pimpinellifolium was putatively deleted relative to H1706. The largest gap in each species was 12.7 kbp on chromosome 12 for YP-1, 41 kb on chromosome 12 of S. galapagense, and 38.7 kbp on chromosome 10 of S. pimpinellifolium (File S1). Deleted genes were determined as genes that were at least 90% contained in putative gaps and had no matches in de novo contig assemblies. A total of 13 genes from YP-1, 87 genes in S. galapagense, and 157 in S. pimpinellifolium were found to have no coverage in either the small read mapping or contig mapping (Table S6). Many of these genes were classified as disease resistance-related proteins or lacked a predicted function (Table S6).


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)

Putative deletion size distribution in combined assemblies.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig-2: Putative deletion size distribution in combined assemblies.
Mentions: To determine the nature of regions where reads from YP-1, S. galapagense, or S. pimpinellifolium could not map to the H1706 genome, but H1706 reads could map, these regions were further analyzed for each species. Regions lacking coverage in the H1706 mapping are mainly scaffolding gaps in the H1706 reference genome. Gap size distribution was similar between S. galapagense and S. pimpinellifolium with less gaps found in YP-1 (Fig. 2), with all genotypes having a peak at 90 bp. Since gaps could be missing regions or divergent regions where short reads cannot map, de novo contigs assembled from the wild and heirloom species reads were mapped to the reference genome to determine if they covered gap regions. Approximately 3.3% of YP-1, 3.7% of S. galapagense, and 6.0% of S. pimpinellifolium contigs did not map with greater than 90% id. A small number of these contigs contained many repeats or matched plastid, mitochondrial, or vector DNA (Table S5). After removal of gaps covered by de novo contigs, a total of 2.4 Mbp of YP-1, 13.8 Mbp of S. galapagense, and 21.6 Mbp of S. pimpinellifolium was putatively deleted relative to H1706. The largest gap in each species was 12.7 kbp on chromosome 12 for YP-1, 41 kb on chromosome 12 of S. galapagense, and 38.7 kbp on chromosome 10 of S. pimpinellifolium (File S1). Deleted genes were determined as genes that were at least 90% contained in putative gaps and had no matches in de novo contig assemblies. A total of 13 genes from YP-1, 87 genes in S. galapagense, and 157 in S. pimpinellifolium were found to have no coverage in either the small read mapping or contig mapping (Table S6). Many of these genes were classified as disease resistance-related proteins or lacked a predicted function (Table S6).

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.