title: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).
abstract: Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. 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. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb-Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA cistron from 23 southern African Oxalis species. 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. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb-Seq in phylogenetics.
authors.affiliation: Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.
authors.forename: Roswitha
authors.initials: R
authors.lastname: Schmickl
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
authors.forename: Aaron
authors.initials: A
authors.lastname: Liston
authors.affiliation: Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.|Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01, Prague, Czech Republic.
authors.forename: Vojtěch
authors.initials: V
authors.lastname: Zeisek
authors.affiliation: Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.|Department of Conservation Ecology and Entomology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Oberlander
authors.affiliation: Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR, 97331, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Weitemier
authors.affiliation: Department of Biology, Hobart and William Smith Colleges, 213 Eaton Hall, Geneva, NY, 14456, USA.
authors.forename: Shannon C K
authors.initials: SC
authors.lastname: Straub
authors.affiliation: USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA.
authors.forename: Richard C
authors.initials: RC
authors.lastname: Cronn
authors.affiliation: Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
authors.forename: Léanne L
authors.initials: LL
authors.lastname: Dreyer
authors.affiliation: Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.|Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01, Prague, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Suda
mesh_terms: D000353:Africa, Southern; D005819:Genetic Markers; D014644:Genetic Variation; D016678:Genome; D060005:Genotyping Techniques / Q000379:methods*; D065825:Oxalidaceae / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D005819:Genetic Markers
keywords: Oxalis; cytonuclear discordance; genome skimming; low-copy nuclear genes; species tree; target enrichment