Gutenberg Open Science: Targeted NGS for species level phylogenomics : “made to measure” or “one size fits all”?

Please use this identifier to cite or link to this item: http://doi.org/10.25358/openscience-7980

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DC Field	Value	Language
dc.contributor.author	Kadlec, Malvina	-
dc.contributor.author	Bellstedt, Dirk U.	-
dc.contributor.author	Le Maitre, Nicholas C.	-
dc.contributor.author	Pirie, Michael	-
dc.date.accessioned	2022-10-13T09:30:17Z	-
dc.date.available	2022-10-13T09:30:17Z	-
dc.date.issued	2017
dc.identifier.uri	https://openscience.ub.uni-mainz.de/handle/20.500.12030/7995	-
dc.description.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.	en_GB
dc.description.sponsorship	DFG, Open Access-Publizieren Universität Mainz / Universitätsmedizin	de
dc.language.iso	eng	de
dc.rights	CC BY	*
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	*
dc.subject.ddc	580 Pflanzen (Botanik)	de_DE
dc.subject.ddc	580 Botanical sciences	en_GB
dc.title	Targeted NGS for species level phylogenomics : “made to measure” or “one size fits all”?	en_GB
dc.type	Zeitschriftenaufsatz	de
dc.identifier.doi	http://doi.org/10.25358/openscience-7980	-
jgu.type.dinitype	article	en_GB
jgu.type.version	Published version	de
jgu.type.resource	Text	de
jgu.organisation.department	FB 10 Biologie	de
jgu.organisation.number	7970	-
jgu.organisation.name	Johannes Gutenberg-Universität Mainz	-
jgu.rights.accessrights	openAccess	-
jgu.journal.title	PeerJ	de
jgu.journal.volume	5	de
jgu.pages.alternative	e3569	de
jgu.publisher.year	2017	-
jgu.publisher.name	PeerJ, Inc.	de
jgu.publisher.place	London	de
jgu.publisher.uri	http://dx.doi.org/10.7717/peerj.3569	de
jgu.publisher.issn	2167-8359	de
jgu.organisation.place	Mainz	-
jgu.subject.ddccode	580	de
opus.date.modified	2017-11-20T09:43:40Z
opus.subject.dfgcode	03-202
opus.organisation.string	FB 10: Biologie: Institut für Organismische und Molekulare Evolutionsbiologie	de_DE
opus.identifier.opusid	57144
opus.institute.number	1011
opus.metadataonly	false
opus.type.contenttype	Forschungsbericht	de_DE
opus.type.contenttype	Research Report	en_EN
opus.affiliated	Kadlec, Malvina
opus.affiliated	Pirie, Michael
jgu.publisher.doi	10.7717/peerj.3569	de
jgu.organisation.ror	https://ror.org/023b0x485	-
Appears in collections:	DFG-OA-Publizieren (2012 - 2017)

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