<abstract xmlns="http://www.w3.org/1999/xhtml">

<p>Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.</p></abstract>

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Journal of Nematology

This work is licensed under the Creative Commons Attribution 4.0 International License.

{"article-title":"18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences"}

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying...

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Article Category: Research paper

Published Online: Apr 21, 2023

Page range: -

Received: Aug 01, 2022

DOI: https://doi.org/10.2478/jofnem-2023-0006

Keywords
biodiversity, database, ecology, metabarcoding, nematodes

© 2023 Gattoni et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

Article Category: Research paper

Published Online: Apr 21, 2023

Page range: -

Received: Aug 01, 2022

DOI: https://doi.org/10.2478/jofnem-2023-0006

Keywordsbiodiversity, database, ecology, metabarcoding, nematodes

© 2023 Gattoni et al., published by Sciendo

This work is licensed under the Creative Commons Attribution 4.0 International License.

Keywords
biodiversity, database, ecology, metabarcoding, nematodes