REVAMP: Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline

McAllister, Sean; Paight, Christopher; Norton, Emily; Galaska, Matthew

doi:10.5670/oceanog.2023.231

i

REVAMP: Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline

2023
By McAllister, Sean ; Paight, Christopher ; Norton, Emily ; ...
Series: PMEL contribution no. 5528

Details

Journal Title:

Oceanography
Personal Author:

McAllister, Sean ; Paight, Christopher ; Norton, Emily ; Galaska, Matthew
NOAA Program & Office:

OAR (Oceanic and Atmospheric Research) ; PMEL (Pacific Marine Environmental Laboratory) ; CICOES (Cooperative Institute for Climate, Ocean and Ecosystem Studies)
Description:

The revolution and acceleration in DNA sequencing over the past three decades has driven the development of new biomolecular tools like environmental DNA (eDNA) metabarcoding for characterizing marine biodiversity. In order to operationalize eDNA approaches for routine NOAA observatories, new bioinformatic programs and improved organismal reference barcodes are needed to serve accurate and reliable biological data in a timely manner. To address these needs, we present Rapid Exploration and Visualization through an Automated Metabarcoding Pipeline (REVAMP), which provides streamlined end-to-end data processing from raw reads to data exploration, visualization, and hypothesis generation. One benefit of REVAMP is the ability to iteratively assess marker gene and reference database performance. Here, we used a filtered reference database that only included sequences uploaded prior to specified date cutoffs from 1995 to 2022 to analyze changes in eDNA metabarcoding taxonomic assignments, revealing patterns of uneven improvement in taxonomic assignment depth and accuracy across time, region, and marker sets. This work highlights the need for targeted reference sequencing efforts for key regional taxa and the importance of such efforts for improving eDNA biomonitoring approaches in the future.
Keywords:

Oceanography
Source:

Oceanography (2023)
Series:

PMEL contribution no. 5528
DOI:

https://doi.org/10.5670/oceanog.2023.231
ISSN:

1042-8275
Format:

PDF
Publisher:

The Oceanography Society
Document Type:

Journal Article
Funding:

Grant no. NA20OAR4320271
License:

https://creativecommons.org/licenses/by/4.0/
Rights Information:

CC BY
Compliance:

Submitted
Main Document Checksum:

urn:sha256:9b38e92c040a07b02b4be10134150a83bc93d1280043ad818b4369c053ef9569
Download URL:

https://repository.library.noaa.gov/view/noaa/56319/noaa_56319_DS1.pdf
File Type:

[PDF - 2.94 MB ]

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