Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)
Authors
Dodsworth, StevenJang, Tae-Soo
Struebig, Monika
Chase, Mark W.
Weiss-Schneeweiss, Hanna
Leitch, Andrew R.
Affiliation
Queen Mary University of LondonRoyal Botanic Gardens, Kew
University of Vienna
University of Western Australia
Issue Date
2016-11-01Subjects
repetitive DNATy-3 Gypsy
graph-based clustering
phylogenetics
high-throughput sequencing
chromoviruses
C400 Genetics
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Show full item recordAbstract
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.Citation
Dodsworth S., Jang T., Struebig M., Chase M., Weiss-Schneeweiss H., Leitch A. (2017) 'Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)', Plant Systematics and Evolution, 303 (8), pp.1013-1020.Publisher
Springer-Verlag WienJournal
Plant Systematics and EvolutionAdditional Links
https://link.springer.com/article/10.1007/s00606-016-1356-9Type
ArticleLanguage
enISSN
0378-2697ae974a485f413a2113503eed53cd6c53
10.1007/s00606-016-1356-9
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