Open Access

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

Kaitlin Gattoni
Kaitlin Gattoni
, 
Eli M. S. Gendron
Eli M. S. Gendron
, 
Rebeca Sandoval-Ruiz
Rebeca Sandoval-Ruiz
, 
Abigail Borgemeier
Abigail Borgemeier
, 
J. Parr McQueen
J. Parr McQueen
, 
Rachel M. Shepherd
Rachel M. Shepherd
, 
Dieter Slos
Dieter Slos
, 
Thomas O. Powers
Thomas O. Powers
 and 
Dorota L. Porazinska
Dorota L. Porazinska
   | Apr 21, 2023
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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
© 2023 Gattoni et al., published by Sciendo
This work is licensed under the Creative Commons Attribution 4.0 International License.

Figure 1

Genetic location of primers commonly used in nematode metabarcoding. Depicted is the entire rRNA gene with close ups of 18S rRNA gene with possible primers aligned below it. The 18S rRNA primers were aligned with Caenorhabditis elegans SSU (GenBank accession number: AY268117, X03680 and MN519140) to define the base pair locations (indicated in grey). References for primer sets available in Supplemental Table 1.
Genetic location of primers commonly used in nematode metabarcoding. Depicted is the entire rRNA gene with close ups of 18S rRNA gene with possible primers aligned below it. The 18S rRNA primers were aligned with Caenorhabditis elegans SSU (GenBank accession number: AY268117, X03680 and MN519140) to define the base pair locations (indicated in grey). References for primer sets available in Supplemental Table 1.

Figure 2

An example of variation of taxonomic categories and ranks resulting in variable strings for Meloidogyne arenaria across the databases. The curated 18S-NemaBase includes standardized taxonomic ranks consisting of 13 Nematoda relevant categories (top row) and currently accepted classification as adopted by the WoRMS database. In contrast, the outdated in-house curated SILVA v111 and the current v138 consisted of variable strings and/or outdated classification (indicated in red) and missing relevant to nematodes taxonomic information (blank cells).
An example of variation of taxonomic categories and ranks resulting in variable strings for Meloidogyne arenaria across the databases. The curated 18S-NemaBase includes standardized taxonomic ranks consisting of 13 Nematoda relevant categories (top row) and currently accepted classification as adopted by the WoRMS database. In contrast, the outdated in-house curated SILVA v111 and the current v138 consisted of variable strings and/or outdated classification (indicated in red) and missing relevant to nematodes taxonomic information (blank cells).

Figure 3

Number of available 18S reference sequences for Nematoda at the order level within SILVA v111, v138, and 18S-NemaBase.
Number of available 18S reference sequences for Nematoda at the order level within SILVA v111, v138, and 18S-NemaBase.

List of primers depicted in Figure 1. Details include the primer name, author, and citation.

Primer Author Citation
F04 - R22 Fonseca et al., 2019 Fonseca, V. G., Carvalho, G. R., Sung, W., Johnson, H. F., Power, D. M., Neill, S. P., Packer, M., Blaxter, M. L., Lambshead, P. J. D., Thomas, W. K., and Creer, S. 2010. Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications 1(98). http://https://dol/10.1038/ncomms1095
SSU_F04 - SSU_R22 Blaxter et al., 1998 Blaxter, M. L., De Ley, P., Garey, J. R., Liu, L. X., Scheldeman, P., Vierstraete, A., Vanfleteren, J. R., Mackey, L. Y., Dorris, M., Frisse, L. M., Vida, J. T., and Thomas, W. K. 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392:71-75. http://https://dol/10.1038/32160
3NDf- 1132rmod Geisen et al., 2019 Geisen, S., Snoek, L. B., ten Hooven, F. C., Duyts, H., Kostenko, O., Bloem, J., Martens, H., Quist, C. W., Helder, J. A., and van den Putten, W. H. 2018. Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion. Methods In Ecology and Evolution 9:1366-1378. http://https://dol/10.1111/2041 -210x.12999
Ek-NSF573 - EK-NSR951 Mangot et al., 2013 Mangot, J.-F., Domaizon, I., Taib, N., Marouni, N., Duffaud, E., Bronner, G., and Debroas, D. 2013. Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environmental Microbiology 15: 1745-1758. http://https://dol.org/10.1111/1462-2920.12065
MMSF - MMSR Sidker et al., 2020 Sikder, M. M., Vestergård, M., Sapkota, R., Kyndt, T., and Nicolaisen, M. 2020. Evaluation of Metabarcoding Primers for Analysis of Soil Nematode Communities. Diversity 12(388). http://https://dol.org/10.3390/d12100388
EcoF - EcoR Waeyenberge et al., 2020 Waeyenberge, L., Sutter, N. D., Viaene, N., and Haegeman, A. 2019. New Insights Into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities. Diversity 11 (4):52. http://https://dol.org/10.3390/d11040052
18SILVOmidF - 18SILVOmidR Waeyenberge et al., 2020 Waeyenberge, L., Sutter, N. D., Viaene, N., and Haegeman, A. 2019. New Insights Into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities. Diversity 11 (4):52. http://https://dol.org/10.3390/d11040052
1813F- 2646R Holterman et al., 2006 Holterman M., van der Wurff A., van den Elsen S., van Megen H., Bongers T., Holovachov O., Bakker J., and Helder J., 2006. Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. Molecular Biology and Evolution 23:1792-1800. http://https://doi/10.1093/molbev/msl044
NemF - 18Sr2b Porazinska et al., 2009 and Sapkota et al., 2015 Porazinska, D. L, Giblin-Davis, R. M., Faller, L, Farmerie, W., Kanzaki, N., Morris, K., Powers, T. O., Tucker, A. E., Sung, W., and Thomas, W. K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resoures 9:1439-50. http://https://doi.Org/10.1111/j.1755-0998.2009.02611; Sapkota, R., and Nicolaisen, M. 2015. High-throughput sequencing of nematode communities from total soil DNA extractions. BMC Ecology 12(15) http://https://doi.org/10.1186/s12898-014-0034-4
NemFopt - 18Sr2bopt Waeyenberge et al., 2020 Waeyenberge, L., Sutter, N. D., Viaene, N., and Haegeman, A. 2019. New insights into nematode DNA-metabarcoding as revealed by the characterization of artificial and spiked nematode communities. Diversity 11 (4):52. http://https://dol.org/10.3390/d11040052
F-1183 - R-1631 Müller et al., 2019 and Starke et al., 2016 Müller, C. A., Pereira, L. D., Lopes, C., Cares, J., Borges, L. G. D., Giongo, A., Graeff-Teixeira, C., and Morassutti. 2019. Meiofaunal diversity In the Atlantic Forest soil: A quest for nematodes in a native reserve using eukaryotic metabarcoding analysis. Forest Ecology and Management 453. http://https://doi.Org/10.1016/j.foreco.2019.117591; Starke, R., Kermer, R., Ullmann-Zeunert, L., Baldwin, I. T., Seifert, J., Bastida, F., von Bergen, M., and Jehmlich, N. 2016. Bacteria dominate the short-term assimilation of plant-derived N in soil. Soil Biology and Biochemistry 96:30-38. http://https://doi.Org/10.1016/j.soilbio.2016.01.009
NF1 - 18Sr2b Porazinska et al., 2009 Porazinska, D. L, Giblin-Davis, R. M., Faller, L, Farmerie, W., Kanzaki, N., Morris, K., Powers, T. O., Tucker, A. E., Sung, W., and Thomas, W. K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resources 9:1439-50. http://https://doi.Org/10.1111/j.1755-0998.2009.02611
1391f- EukBr Amaral-Zettler et al., 2009 and Caporaso et al., 2012 Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., and Huse, S. M. 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One 4(7): 1 —9. http://https://doi.org/10.1371/journal.pone.0006372; Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L, Bauer, M., Gormley, N., Gilbert, J. A., Smith, G., and Knight, R. 2012. Ultra-high-throughput microbial community analysis on the lllumina HiSeq and MiSeq platforms. ISME Journal 6(8):1621-1624. http://https://doi.Org/10.1038/ismej.2012.8

The identities and number of 3 most populated genera across nematode orders in SILVA v111, SILVA V138, and 18S-NemaBase. The list is sorted from the largest to smallest number of total representative sequences.

Number of Taxa
Order Genus V111 V138 18S-NemaBase
Rhabditida Meloidogyne 109 218 238
Caenorhabditis 59 228 213
Bursaphelenchus 77 116 117
Trichinellida Trichinella 12 564 563
Capillaria 1 16 16
Aonchotheca 0 30 30
Dorylaimida Xiphinema 148 137 137
Longidorus 47 92 92
Enchodelus 9 12 12
Enoplida Halalaimus 43 43 43
Oxystomina 26 26 26
Oncholaimus 22 25 25
Triplonchida Paratrichodorus 34 57 57
Trichodorus 26 46 46
Tripyla 21 30 30
Desmodorida Leptonemella 1 19 19
Robbea 10 9 9
Laxus 4 9 9
Plectida Plectus 15 24 24
Chronogaster 5 7 7
Camacolaimus 2 5 5
Monhysterida Eumonhystera 3 11 11
Monhystera 3 8 8
Daptonema 8 10 10
Mononchida Mylonchulus 27 27 27
Mononchus 7 11 11
Clarkus 6 6 6
Araeolaimida Sabatieria 8 9 9
Axonolaimus 4 4 4
Ascolaimus 4 4 4
Mermithida Isomermis 9 9 9
Mermis 2 4 4
Pheromermis 0 2 2
Desmodorida Desmoscolex 1 2 2
Cyartonema 1 1 1

Tobrilidae species from the Western Nebraska Sandhills dataset assigned by v111, v138, and 18S-NemaBase, and 18S-NemaBase-supplemented databases. The numbers represent how many distinct ASVs assigned to that species.

Family Genus Species v111 v138-unmodified v138-modified 18S-NemaBase 18S-NemaBase-supplemented
Tobrilidae Brevitobrilus Brevitobrilus sp. Female SALCI Border 0 0 0 0 3
Tobrilidae Epitobrilus Epitobrilus sp. Male SALCI Border 0 0 0 0 4
Tobrilidae Epitobrilus Epitobrilus stefanskii 0 0 5 5 0
Tobrilidae Neotobrilus Neotobrilus sp. Female SALCI Island 0 0 0 0 1
Tobrilidae Semitobrilus Semitobrilus cf. pellucidus 1 JH-2014 0 0 3 3 0
Tobrilidae Tobrilus Tobrilus cf. gracilis 2 JH-2014 0 0 1 1 0
Tobrilidae Tobrilus Tobrilus gracilis 6 0 0 0 0
Tobrilidae Tobrilus Tobrilus pellucidus 0 0 1 1 1
Tobrilidae Tobrilus Tobrilus sp. Female SALCI Island 0 0 0 0 1
Tobrilidae Tobrilus Tobrilus sp. ZQZ-2010a 7 0 0 3 3
Total ASV/species 13/2 0 10/4 13/5 13/6
Nematode_environmental sample 0 0 14 0 0
Nematode_uncultured eukaryote 1 0 3 0 0
Uncultured nematode 29 0 0 0 0
BCP Clade 0 178 0 0 0
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Language:
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