Autoren:	Kadlec, Malvina Bellstedt, Dirk U. Le Maitre, Nicholas C. Pirie, Michael
Titel:	Targeted NGS for species level phylogenomics : “made to measure” or “one size fits all”?
Online-Publikationsdatum:	13-Okt-2022
Erscheinungsdatum:	2017
Sprache des Dokuments:	Englisch
Zusammenfassung/Abstract:	Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica. The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for “one size fits all” universal markers, we should improve and make more accessible the tools necessary for developing “made to measure” ones.
DDC-Sachgruppe:	580 Pflanzen (Botanik) 580 Botanical sciences
Veröffentlichende Institution:	Johannes Gutenberg-Universität Mainz
Organisationseinheit:	FB 10 Biologie
Veröffentlichungsort:	Mainz
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-7980
Version:	Published version
Publikationstyp:	Zeitschriftenaufsatz
Nutzungsrechte:	CC BY
Informationen zu den Nutzungsrechten:	https://creativecommons.org/licenses/by/4.0/
Zeitschrift:	PeerJ 5
Seitenzahl oder Artikelnummer:	e3569
Verlag:	PeerJ, Inc.
Verlagsort:	London
Erscheinungsdatum:	2017
ISSN:	2167-8359
URL der Originalveröffentlichung:	http://dx.doi.org/10.7717/peerj.3569
DOI der Originalveröffentlichung:	10.7717/peerj.3569
Enthalten in den Sammlungen:	DFG-OA-Publizieren (2012 - 2017)