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Genomic repeat abundances contain phylogenetic signal
- 1.0440552 - BC 2016 RIV GB eng J - Journal Article
Dodsworth, S. - Chase, M.W. - Kelly, L.J. - Leitch, I.J. - Macas, Jiří - Novák, Petr - Piednoël, M. - Weiß-Schneeweiss, H. - Leitch, A.R.
Genomic repeat abundances contain phylogenetic signal.
Systematic Biology. Roč. 64, č. 1 (2015), s. 112-126. ISSN 1063-5157. E-ISSN 1076-836X
R&D Projects: GA ČR GBP501/12/G090
Institutional support: RVO:60077344
Keywords : Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics
Subject RIV: EB - Genetics ; Molecular Biology
Impact factor: 8.225, year: 2015
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.
Permanent Link: http://hdl.handle.net/11104/0245802
Number of the records: 1