A targeted capture approach to generating reference sequence databases for chloroplast gene regions.

Autor: Foster NR; School of Biological Sciences University of Adelaide Adelaide South Australia Australia., van Dijk KJ; School of Biological Sciences University of Adelaide Adelaide South Australia Australia., Biffin E; State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia., Young JM; College of Science and Engineering Flinders University South Australia Australia., Thomson VA; School of Biological Sciences University of Adelaide Adelaide South Australia Australia., Gillanders BM; School of Biological Sciences University of Adelaide Adelaide South Australia Australia., Jones AR; School of Biological Sciences University of Adelaide Adelaide South Australia Australia., Waycott M; School of Biological Sciences University of Adelaide Adelaide South Australia Australia.; State Herbarium of South Australia Botanic Gardens and State Herbarium Adelaide South Australia Australia.
Jazyk: angličtina
Zdroj: Ecology and evolution [Ecol Evol] 2022 Apr 11; Vol. 12 (4), pp. e8816. Date of Electronic Publication: 2022 Apr 11 (Print Publication: 2022).
DOI: 10.1002/ece3.8816
Abstrakt: Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false-positive and false-negative detections. To improve our ability to generate reference sequence databases, we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant diversity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92%, which was achieved in a single assay (i.e., samples were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all samples could be discriminated to family level across all gene regions with some genes achieving greater resolution than others-which was also dependent on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci are sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.
Competing Interests: The authors declare no conflicts of interest.
(© 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
Externí odkaz: