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

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...

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Bibliographic Details
Main Authors: Biffin, E. (Author), Foster, N.R (Author), Gillanders, B.M (Author), Jones, A.R (Author), Thomson, V.A (Author), van Dijk, K.-J (Author), Waycott, M. (Author), Young, J.M (Author)
Format: Article
Language:English
Published: John Wiley and Sons Ltd 2022
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Online Access:View Fulltext in Publisher
LEADER 02498nam a2200265Ia 4500
001 10.1002-ece3.8816
008 220510s2022 CNT 000 0 und d
020 |a 20457758 (ISSN) 
245 1 0 |a A targeted capture approach to generating reference sequence databases for chloroplast gene regions 
260 0 |b John Wiley and Sons Ltd  |c 2022 
856 |z View Fulltext in Publisher  |u https://doi.org/10.1002/ece3.8816 
520 3 |a 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. © 2022 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. 
650 0 4 |a angiosperms 
650 0 4 |a barcoding 
650 0 4 |a hybridization capture 
650 0 4 |a plastid 
700 1 |a Biffin, E.  |e author 
700 1 |a Foster, N.R.  |e author 
700 1 |a Gillanders, B.M.  |e author 
700 1 |a Jones, A.R.  |e author 
700 1 |a Thomson, V.A.  |e author 
700 1 |a van Dijk, K.-J.  |e author 
700 1 |a Waycott, M.  |e author 
700 1 |a Young, J.M.  |e author 
773 |t Ecology and Evolution