Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

0464568 - BÚ 2017 RIV GB eng J - Journal Article
Schmickl, Roswitha - Liston, A. - Zeisek, Vojtěch - Oberlander, Kenneth - Weitemier, K. - Straub, S. C. K. - Cronn, R. C. - Dreyer, L. L. - Suda, Jan
Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).
Molecular Ecology Resources. Roč. 16, č. 5 (2016), s. 1124-1135. ISSN 1755-098X. E-ISSN 1755-0998
R&D Projects: GA MŠMT(CZ) EE2.3.30.0048
Institutional support: RVO:67985939
Keywords : cytonuclear discordance * genome skimming * low-copy nuclear genes
Subject RIV: EF - Botanics
Impact factor: 7.332, year: 2016

To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb-Seq in phylogenetics.
Permanent Link: http://hdl.handle.net/11104/0265675