Using genomic repeats for phylogenomics: A case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae)
Issue Date
2015-07-17Subjects
genome skimmingrepetitive elements
phylogenetic signal
phylogenetics
high-throughput sequencing
next-generation sequencing
molecular systematics
C400 Genetics
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High-throughput sequencing data have transformed molecular phylogenetics and a plethora of phylogenomic approaches are now readily available. Shotgun sequencing at low genome coverage is a common approach for isolating high-copy DNA, such as the plastid or mitochondrial genomes, and ribosomal DNA. These sequence data, however, are also rich in repetitive elements that are often discarded. Such data include a variety of repeats present throughout the nuclear genome in high copy number. It has recently been shown that the abundance of repetitive elements has phylogenetic signal and can be used as a continuous character to infer tree topologies. In the present study, we evaluate repetitive DNA data in tomatoes (Solanum section Lycopersicon) to explore how they perform at the inter- and intraspecific levels, utilizing the available data from the 100 Tomato Genome Sequencing Consortium. The results add to previous examples from angiosperms where genomic repeats have been used to resolve phylogenetic relationships at varying taxonomic levels. Future prospects now include the use of genomic repeats for population-level analyses and phylogeography, as well as potentially for DNA barcoding.Citation
Dodsworth S., Chase M., Särkinen T., Knapp S., Leitch A. (2016) 'Using genomic repeats for phylogenomics: A case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae)', Biological Journal of the Linnean Society, 117 (1), pp.96-105.Publisher
Blackwell Publishing LtdAdditional Links
https://onlinelibrary.wiley.com/doi/full/10.1111/bij.12612Type
ArticleLanguage
enISSN
0024-4066ae974a485f413a2113503eed53cd6c53
10.1111/bij.12612
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