Reconstructing phylogenetic relationships based on repeat sequence similarities
MetadataShow full item record
AbstractA recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, this novel approach makes use of the repeat sequence similarity matrices obtained from the comparative clustering analyses of RepeatExplorer 2, which are subsequently transformed to between-taxa distance matrices. These pairwise matrices are used to construct neighbour-joining trees for each of the top most-abundant clusters and they are finally summarized in a consensus network. This methodology was tested on three groups of angiosperms and one group of insects, resulting in congruent evolutionary hypotheses compared to more standard systematic analyses based on commonly used DNA markers. We propose that the combined application of these phylogenetic approaches based on repeat abundances and repeat sequence similarities could be helpful to understand mechanisms governing genome and repeatome evolution.
CitationVitales D, Garcia S, Dodsworth S (2020) 'Reconstructing phylogenetic relationships based on repeat sequence similarities', Molecular Phylogenetics and Evolution, 147, pp.106766.
- Genomic repeat abundances contain phylogenetic signal.
- Authors: Dodsworth S, Chase MW, Kelly LJ, Leitch IJ, Macas J, Novák P, Piednoël M, Weiss-Schneeweiss H, Leitch AR
- Issue date: 2015 Jan
- The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var 'Ridge Pineapple': organization and phylogenetic relationships to other angiosperms.
- Authors: Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H
- Issue date: 2006 Sep 30
- [Foundations of the new phylogenetics].
- Authors: Pavlinov IIa
- Issue date: 2004 Jul-Aug
- Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes.
- Authors: Gonçalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK
- Issue date: 2019 Sep
- Phylogeny of Campanuloideae (Campanulaceae) with emphasis on the utility of nuclear pentatricopeptide repeat (PPR) genes.
- Authors: Crowl AA, Mavrodiev E, Mansion G, Haberle R, Pistarino A, Kamari G, Phitos D, Borsch T, Cellinese N
- Issue date: 2014