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

Gattoni, Kaitlin; Gendron, Eli M. S.; Sandoval-Ruiz, Rebeca; Borgemeier, Abigail; McQueen, J. Parr; M. Shepherd, Rachel; Slos, Dieter; O. Powers, Thomas; L. Porazinska, Dorota

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

Volume 55 (2023): Issue 1 (February 2023)

By:

Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval-Ruiz, Abigail Borgemeier, J. Parr McQueen, Rachel M. Shepherd, Dieter Slos, Thomas O. Powers and Dorota L. Porazinska

Open Access

|Apr 2023

Figures & Tables

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.

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 In contrast, the outdated in-house curated SILVA v111 and the current v138 consisted of variable strings and/or outdated classification (indicated in red) and missing relevant to nematodes taxonomic information (blank cells).

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

DOI: https://doi.org/10.2478/jofnem-2023-0006 | Journal eISSN: 2640-396X | Journal ISSN: 0022-300X

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Language: English

Submitted on: Aug 1, 2022

Published on: Apr 21, 2023

Published by: Society of Nematologists, Inc.

In partnership with: Paradigm Publishing Services

Publication frequency: 1 issue per year

Keywords:

ecology,

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© 2023 Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval-Ruiz, Abigail Borgemeier, J. Parr McQueen, Rachel M. Shepherd, Dieter Slos, Thomas O. Powers, Dorota L. Porazinska, published by Society of Nematologists, Inc.
This work is licensed under the Creative Commons Attribution 4.0 License.

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

Figures & Tables

Figure 1

Figure 2

Figure 3

List of primers depicted in Figure 1_ Details include the primer name, author, and citation_

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_

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_

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