Amplicon sequence variant-based meiofaunal community composition revealed by DADA2 tool is compatible with species composition

Zoya Harbuzov, Valeria Farberova, Moshe Tom, Alberto Pallavicini, David Stanković, Tamar Lotan, Hadas Lubinevsky

Research output: Contribution to journalArticlepeer-review

Abstract

The present study is aimed at implementing the morphological identification-free amplicon sequence variant (ASV) concept for describing meiofaunal species composition, while strongly indicating reasonable compatibility with the underlying species. A primer pair was constructed and demonstrated to PCR amplify a 470–490 bp 18S barcode from a variety of meiofaunal taxa, high throughput sequenced using the Illumina 300 × 2 bps platform. Sixteen 18S multi-species HTS assemblies were created from meiofaunal samples and merged to one assembly of ~2,150,000 reads. Five quality scores (q = 35, 30, 25, 20, 15) were implemented to filter five 18S barcode assemblies, which served as inputs for the DADA2 software, ending with five reference ASV libraries. Each of these libraries was clustered, applying 3% dissimilarity threshold, revealed an average number of 1.38 ± 0.078 ASVs / cluster. Hence, demonstrating high level of ASV uniqueness. The libraries which were based on q ≤ 25 reached a near-asymptote number of ASVs which together with the low average number of ASVs / cluster, strongly indicated fair representation of the actual number of the underlying species. Hence, the q = 25 library was selected to be used as metabarcoding reference library. It contained 461 ASVs and 342–3% clusters with average number of 1.34 ± 1.036 ASV / cluster and their BLASTN annotation elucidated a variety of expected meiofaunal taxa. The sixteen assemblies of sample-specific paired reads were mapped to this reference library and sample ASV profiles, namely the list of ASVs and their proportional copy numbers were created and clustered.

Original languageEnglish
Article number100980
JournalMarine Genomics
Volume65
DOIs
StatePublished - Oct 2022

Bibliographical note

Publisher Copyright:
© 2022 Elsevier B.V.

Keywords

  • 18S-SSU-rRNA
  • Amplicon sequence variant (ASV)
  • Eastern Mediterranean
  • Illumina
  • Meiofauna
  • Metabarcoding
  • Molecular taxonomy

ASJC Scopus subject areas

  • Genetics
  • Aquatic Science

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