Genomic repeat abundances contain phylogenetic signal

Steven Dodsworth
,
Mark W. Chase
,
Laura J. Kelly
,
Ilia J. Leitch
,
Jiří Macas
,
Petr Novak

University of Western Australia
,
Royal Botanic Gardens, Kew
,
Queen Mary University of London
,
Biology Centre of Academy of Sciences of the Czech Republic
,
Ludwig Maximilian University of Munich
,
University of Vienna

Research Output: Contribution to journal Article Peer-review

Open access

Abstract

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.