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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Publications at this Location » Publication #395716
Research Project: Development of Knowledge-based Approaches for Disease Management in Small Fruit and Nursery Crops

Location: Horticultural Crops Disease and Pest Management Research Unit

Title: Nemataxa: a new taxonomic database for analysis of nematode community data

Author
item BAKER, H - Washington State University
item IBARRA CABALLERO, J - Colorado State University
item GLEASON, C - Washington State University
item JAHN, C - Colorado State University
item Hesse, Cedar
item STEWART, J - Colorado State University
item Zasada, Inga

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/11/2023
Publication Date: 11/13/2023
Citation: Baker, H., Ibarra Caballero, J., Gleason, C., Jahn, C., Hesse, C.N., Stewart, J., Zasada, I.A. 2023. Nemataxa: a new taxonomic database for analysis of nematode community data. Phytobiomes Journal. 7:385-391. https://doi.org/10.1094/PBIOMES-07-22-0042-R.
DOI: https://doi.org/10.1094/PBIOMES-07-22-0042-R

Interpretive Summary: Nematodes are one of the most abundant groups of nematodes in the soil and play important ecological roles. Currently, characterizing nematode communities in soil using DNA methods is challenging due to the lack of reliable databases. The purpose of this research was to develop a database of nematode DNA data to allow for the analysis of DNA datasets. The database performed better than currently available databases. This datebase is free for use to the general public.

Technical Abstract: High throughput amplicon sequencing of nematode communities has the potential to greatly increase our understanding of nematode community ecology. A current constraint to the widespread implementation of amplicon sequencing is the lack of sequence databases with consistent taxonomic naming schemes. Focusing on 18S sequence data, we developed NemaTaxa, a manually curated database that can be used with QIIME and mothur analysis platforms. Nematode 18S sequence data was downloaded from NCBI from which both Nematoda universal primers NF1 and 18Sr2b aligned. Taxonomic strings were trimmed to include only classical Linnaean lineages to genera within Nematoda; missing taxonomic data were completed manually. NemaTaxa was compared with other available databases, specifically PR2 and Silva v132, available for mothur using data collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda and estimates of diversity. NemaTaxa resolves classification at the genus, family and order levels while PR2 always has a portion of sequences assigned at the class level due to incomplete taxonomic strings. The Silva v132 database available in mothur is of limited use unusable because of the greatly reduced number of nematode sequences available in the database, making classification only possible to the level of order. NemaTaxa offers an “off the shelf” database that can be used by nonexperts in nematology wanting to explore nematode community ecology, and therefore, will allow for inclusion of nematodes in soil ecology studies that employ amplicon sequencing for other organisms such as fungi and bacteria.