Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae)

Steven Dodsworth*, Mark W. Chase, Tiina Särkinen, Sandra Knapp, Andrew R. Leitch

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Abstract

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.

Original languageEnglish
Pages (from-to)96-105
Number of pages10
JournalBiological Journal of the Linnean Society
Volume117
Issue number1
DOIs
Publication statusPublished - 1 Jan 2016

Keywords

  • genome skimming
  • high-throughput sequencing
  • molecular systematics
  • next-generation sequencing
  • phylogenetic signal
  • phylogenetics
  • repetitive elements
  • UKRI
  • NERC

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