Authors
Dodsworth, StevenChase, Mark W.
Kelly, Laura J.
Leitch, Ilia J.
Macas, Jiří
Novak, Petr
Piednoel, Mathieu
Weiss-Schneeweiss, Hanna
Leitch, Andrew R.
Issue Date
2014-09-25Subjects
genomicsnext-generation sequencing
molecular systematics
repetitive DNA
phylogenetics
continuous characters
C400 Genetics
Metadata
Show full item recordAbstract
A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic 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.Citation
Dodsworth S., Chase M., Kelly L., Leitch I., Macas J., Novak P., Piednoel M., Weiss-Schneeweiss H., Leitch A. (2015) 'Genomic repeat abundances contain phylogenetic signal', Systematic Biology, 64 (1), pp.112-126.Publisher
Oxford University PressJournal
Systematic BiologyAdditional Links
https://academic.oup.com/sysbio/article/64/1/112/2848261Type
ArticleLanguage
enISSN
1063-5157ae974a485f413a2113503eed53cd6c53
10.1093/sysbio/syu080
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- Creative Commons
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