NemaTaxa: A new taxonomic database for analysis of nematode community data

Abstract

High throughput amplicon sequencing of nematode communities has the potential to 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 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.