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001-es BibID:	BIBFORM108218
035-os BibID:	(WOS)000823437500001 (Scopus)85134074155
Első szerző:	Laczkó Levente (biológus)
Cím:	The RadOrgMiner pipeline : Automated genotyping of organellar loci from RADseq data / Levente Laczkó, Sándor Jordán, Gábor Sramkó
Dátum:	2022
ISSN:	2041-210X
Megjegyzések:	Different versions of Restriction-site-Associated DNA sequencing (RADseq) have become powerful and popular tools in molecular ecology. Although RADseq datasets are generally regarded as representative of the nuclear genome, reduced representation genomic libraries may also sample the organellar (i.e. the mitochondrial and, in the case of plants, the plastid) DNA. This cytoplasmic genetic variance provides a better understanding of evolutionary history by uncovering past hybridisation and identifying maternal or, rarely, paternal lineage due to rapid lineage sorting. We developed a pipeline that is based on existing bioinformatic tools to automatically mine and genotype organellar loci from RADseq libraries. The efficacy of our pipeline is tested on eight publicly available datasets spanning different phylogenetic levels (i.e. from family-level phylogenies to phylogeography) and RADseq methods (sdRAD, ddRAD, ezRAD, GBS) for genotyping mitochondrial and plastid loci, which were subject to phylogenetic tree reconstruction. In all cases, organellar phylogenies adequately supplemented the original studies by corroborating the large-scale picture based on RADseq or by bringing additional evidence on past or contemporary hybridisation. RADseq methods designed to achieve larger horizontal coverage (i.e. ddRAD, ezRAD) yielded longer organellar alignments, but sdRAD and GBS still provided valuable polymorphic organellar loci at no additional sequencing effort.
Tárgyszavak:	Természettudományok Biológiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban folyóiratcikk
Megjelenés:	Methods in Ecology and Evolution. - 13 : 9 (2022), p. 1962-1975. -
További szerzők:	Jordán Sándor (1992-) Sramkó Gábor (1981-) (biológus)
Pályázati támogatás:	OTKA FK137962 OTKA ÚNKP-20-4-I-DE-290 egyéb
Internet cím:	Szerző által megadott URL DOI Intézményi repozitóriumban (DEA) tárolt változat
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