A Multi-Gene Region Targeted Capture Approach to Detect Plant DNA in Environmental Samples: A Case Study From Coastal Environments

• DOI: 10.3389/fevo.2021.735744
• Publication Date: 2021-10-25T02:40:12Z
• Authors: Nicole R. Foster; Kor-jent van Dijk; Ed Biffin; Jennifer M. Young; Vicki A. Thomson; Bronwyn M. Gillan...; Alice R. Jones; Michelle Waycott
• Keywords: Environmental DNA

Metabarcoding of plant DNA recovered from environmental samples, termed (eDNA), has been used to detect invasive species, track biodiversity changes, and reconstruct past ecosystems. The P6 loop the trnL intron is most widely utilised gene region for metabarcoding plants due short fragment length subsequent ease recovery degraded DNA, which characteristic samples. However, taxonomic resolution this limited, often precluding species level identification. Additionally, targeting regions using universal primers can bias results as some taxa will amplify more effectively than others. To increase ability better resolve flowering (angiosperms) within reduce in amplification, we developed a multi-gene targeted capture method that simultaneously targets 20 chloroplast single assay across all species. Using approach, multiple three artificial mixtures down 0.001 ng/μL DNA. We tested detection successfully recovering target genes 10 Finally, applied approach sediment samples containing unknown compositions eDNA confidently detected were later verified with observation data. Targeting enabled species-level information be complex mixtures. Thus, here, confers an improved data on community composition, understand assemblages