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Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)

  • Steven Dodsworth
    ,
  • Tae-Soo Jang
    ,
  • Monika Struebig
    ,
  • Mark W. Chase
    ,
  • Hanna Weiss-Schneeweiss
    ,
  • Andrew R. Leitch
  • Queen Mary University of London
    ,
  • University of Western Australia
    ,
  • Royal Botanic Gardens, Kew
    ,
  • University of Vienna
Research Output: Contribution to journal Article Peer-review

Open access

Abstract

Nicotiana sect. Repandae is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of N. nudicaulis as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing (N. nudicaulis) from those with genome upsizing (N. repanda, N. nesophila, N. stocktonii). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between N. nudicaulis and the Revillagigedo Island taxa (N. nesophila and N. stocktonii), thereby placing N. repanda as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for N. nudicaulis as sister to the rest of the section, with N. repanda sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original (N. nudicaulis (N. repanda (N. nesophila ? N. stocktonii))) hypothesis. Furthermore, overall repeat dynamics in the island species N. nesophila and N. stocktonii confirm their similarity to N. repanda and the distinctive patterns between these three species and N. nudicaulis. Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.

Publication Information

Output type

Research Output: Contribution to journal Article Peer-review

Original language

English

Pages from-to (Number of pages)

Pages 1013-1020

Journal (Volume, Issue Number)

Plant Systematics and Evolution (Volume 303, Issue 8)

Publication milestones

  • Published - 01/11/2016

Publication status

Published - 01/11/2016

ISSN

0378-2697

External Publication IDs

  • handle.net: 10547/623143
  • Scopus: 84994113153

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