0440552 - BC 2016 RIV GB eng J - Článek v odborném periodiku
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
Grant CEP: GA ČR GBP501/12/G090
Institucionální podpora: RVO:60077344
Klíčová slova: Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics
Kód oboru RIV: EB - Genetika a molekulární biologie
Impakt faktor: 8.225, rok: 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.
Trvalý link: http://hdl.handle.net/11104/0245802