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

2.50
Hdl Handle:
http://hdl.handle.net/10547/623143
Title:
Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid Nicotiana (Solanaceae)
Authors:
Dodsworth, Steven ( 0000-0001-6531-3540 ) ; Jang, Tae-Soo ( 0000-0002-5527-1137 ) ; Struebig, Monika; Chase, Mark W. ( 0000-0002-9927-4938 ) ; Weiss-Schneeweiss, Hanna; Leitch, Andrew R. ( 0000-0001-8574-302X )
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.
Affiliation:
Queen Mary University of London; Royal Botanic Gardens, Kew; University of Vienna; University of Western Australia
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 Wien
Journal:
Plant Systematics and Evolution
Issue Date:
1-Nov-2016
URI:
http://hdl.handle.net/10547/623143
DOI:
10.1007/s00606-016-1356-9
Additional Links:
https://link.springer.com/article/10.1007/s00606-016-1356-9
Type:
Article
Language:
en
ISSN:
0378-2697
Appears in Collections:
Biomedical and biological science

Full metadata record

DC FieldValue Language
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.en
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-
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