NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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The American Phytopathological Society
2023-11-01
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| Series: | Phytobiomes Journal |
| Subjects: | |
| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-07-22-0042-R |
| _version_ | 1797606246162890752 |
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| author | Hannah V. Baker Jorge R. Ibarra Caballero Cynthia Gleason Courtney E. Jahn Cedar N. Hesse Jane E. Stewart Inga A. Zasada |
| author_facet | Hannah V. Baker Jorge R. Ibarra Caballero Cynthia Gleason Courtney E. Jahn Cedar N. Hesse Jane E. Stewart Inga A. Zasada |
| author_sort | Hannah V. Baker |
| collection | DOAJ |
| description | 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 were 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; incomplete Linnaean lineages were corrected. NemaTaxa was compared with other available databases (specifically, PR2 and Silva v132) available for mothur, by comparing nematode taxonomic assignment of nematode communities collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda. 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. For example, only a small proportion of contigs (0 to 0.4%) for Chromadorea and Enoplea were unclassified using NemaTaxa compared with 5 to 80% for PR2. 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. |
| first_indexed | 2024-03-11T05:12:28Z |
| format | Article |
| id | doaj.art-dc32ad74c27146ce8ffcff78e3fcf5de |
| institution | Directory Open Access Journal |
| issn | 2471-2906 |
| language | English |
| last_indexed | 2024-03-11T05:12:28Z |
| publishDate | 2023-11-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Phytobiomes Journal |
| spelling | doaj.art-dc32ad74c27146ce8ffcff78e3fcf5de2023-11-17T18:31:54ZengThe American Phytopathological SocietyPhytobiomes Journal2471-29062023-11-017338539110.1094/PBIOMES-07-22-0042-RNemaTaxa: A New Taxonomic Database for Analysis of Nematode Community DataHannah V. Baker0Jorge R. Ibarra Caballero1Cynthia Gleason2Courtney E. Jahn3Cedar N. Hesse4Jane E. Stewart5Inga A. Zasada6Department of Plant Pathology, Washington State University, Pullman, WA 99163Department of Agricultural Biology, Colorado State University, Ft. Collins, CO 80523Department of Plant Pathology, Washington State University, Pullman, WA 99163Department of Agricultural Biology, Colorado State University, Ft. Collins, CO 80523Horticultural Crops Research Unit, USDA-Agriculture Research Service, Corvallis, OR 97330Department of Agricultural Biology, Colorado State University, Ft. Collins, CO 80523Horticultural Crops Research Unit, USDA-Agriculture Research Service, Corvallis, OR 97330High-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 were 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; incomplete Linnaean lineages were corrected. NemaTaxa was compared with other available databases (specifically, PR2 and Silva v132) available for mothur, by comparing nematode taxonomic assignment of nematode communities collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda. 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. For example, only a small proportion of contigs (0 to 0.4%) for Chromadorea and Enoplea were unclassified using NemaTaxa compared with 5 to 80% for PR2. 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.https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-07-22-0042-R18Sdatabasemothurnematode community analysisQIIME |
| spellingShingle | Hannah V. Baker Jorge R. Ibarra Caballero Cynthia Gleason Courtney E. Jahn Cedar N. Hesse Jane E. Stewart Inga A. Zasada NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data Phytobiomes Journal 18S database mothur nematode community analysis QIIME |
| title | NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data |
| title_full | NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data |
| title_fullStr | NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data |
| title_full_unstemmed | NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data |
| title_short | NemaTaxa: A New Taxonomic Database for Analysis of Nematode Community Data |
| title_sort | nemataxa a new taxonomic database for analysis of nematode community data |
| topic | 18S database mothur nematode community analysis QIIME |
| url | https://apsjournals.apsnet.org/doi/10.1094/PBIOMES-07-22-0042-R |
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