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

PeerJ
Susan R StricklerLukas A Mueller

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 comparis...Continue Reading

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Citations

Apr 29, 2020·The New Phytologist·Kyungyong SeongBrian Staskawicz
Sep 11, 2019·BMC Genomics·Xing WuStephen L Dellaporta
Mar 7, 2017·Frontiers in Plant Science·Yveline PaillesSandra M Schmöckel
Oct 8, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jian LiSamuel F Hutton

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Datasets Mentioned

BETA
SRX520161
SRX521582

Methods Mentioned

BETA
454 sequencing

Software Mentioned

BLAT
Breakdancer
ClustalW
Bedtools
MrBayes
BLAST
PhygOmics
BEAST
Mega
Samtools

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