Dodsworth, Steven and Chase, M.W. and Kelly, L.J. and Leitch, I.J. and Macas, J. and Novák, P. and Piednoël, M. and Weiss-Schneeweiss, H. and Leitch, A.R. (2015) Genomic repeat abundances contain phylogenetic signal. Systematic Biology 64 (1), pp. 112-126. ISSN 1063-5157.
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Abstract
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Herewedemonstrate the usefulness of this repetitive fraction inphylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution.
Metadata
| Item Type: | Article |
|---|---|
| Additional Information: | Funding Information: This work was supported by the Natural Environment Research Council (grant number NE/G01724/1) and the Czech Science Foundation (grant number P501/12/G090 to JM). Sequencing of Fritillaria and Lilium was conducted as part of a NERC-funded project |
| Keyword(s) / Subject(s): | continuous characters, genomics, molecular systematics, next-generation sequencing, phylogenetics, repetitive DNA, UKRI, NERC, NE/G01724/1 |
| School: | Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences |
| Research Centres and Institutes: | Structural Molecular Biology, Institute of (ISMB) |
| Depositing User: | Steven Dodsworth |
| Date Deposited: | 20 Sep 2024 15:49 |
| Last Modified: | 20 Sep 2024 16:03 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/54077 |
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