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dc.contributor.authorDodsworth, Stevenen
dc.contributor.authorJang, Tae-Sooen
dc.contributor.authorStruebig, Monikaen
dc.contributor.authorChase, Mark W.en
dc.contributor.authorWeiss-Schneeweiss, Hannaen
dc.contributor.authorLeitch, Andrew R.en
dc.date.accessioned2019-02-11T14:23:50Z
dc.date.available2019-02-11T14:23:50Z
dc.date.issued2016-11-01
dc.identifier.citationDodsworth 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.en
dc.identifier.issn0378-2697
dc.identifier.doi10.1007/s00606-016-1356-9
dc.identifier.urihttp://hdl.handle.net/10547/623143
dc.description.abstractNicotiana 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.
dc.language.isoenen
dc.publisherSpringer-Verlag Wienen
dc.relation.urlhttps://link.springer.com/article/10.1007/s00606-016-1356-9en
dc.rightsGreen - can archive pre-print and post-print or publisher's version/PDF
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/*
dc.subjectrepetitive DNAen
dc.subjectTy-3 Gypsyen
dc.subjectgraph-based clusteringen
dc.subjectphylogeneticsen
dc.subjecthigh-throughput sequencingen
dc.subjectchromovirusesen
dc.subjectC400 Geneticsen
dc.titleGenome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)en
dc.typeArticleen
dc.contributor.departmentQueen Mary University of Londonen
dc.contributor.departmentRoyal Botanic Gardens, Kewen
dc.contributor.departmentUniversity of Viennaen
dc.contributor.departmentUniversity of Western Australiaen
dc.identifier.journalPlant Systematics and Evolutionen
dc.date.updated2019-02-11T12:04:49Z
dc.description.noteOA article Creative Commons Attribution 4.0 International License
html.description.abstractNicotiana 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.


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