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High-throughput sequencing of 5S-IGS in oaks – exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples
Swedish Museum of Natural History, Department of Paleobiology.ORCID iD: 0000-0001-9535-1206
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2021 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 21, p. 495-510Article in journal (Refereed) Published
Abstract [en]

Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2021. Vol. 21, p. 495-510
National Category
Natural Sciences Other Earth and Related Environmental Sciences
Research subject
Diversity of life; The changing Earth
Identifiers
URN: urn:nbn:se:nrm:diva-4503DOI: 10.1111/1755-0998.13264OAI: oai:DiVA.org:nrm-4503DiVA, id: diva2:1618557
Note

G.W.G. has been funded by the Austrian Science Fund FWF (Project no. M-1751-B16). E.D.S. and G.W.G. gratefully acknowledge the support of the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig funded by the German Research Foundation (FZT 118), which financed the sequencing

Available from: 2021-12-09 Created: 2021-12-09 Last updated: 2021-12-10Bibliographically approved

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Publisher's full texthttps://doi.org/10.1111/1755-0998.13264

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