Genome Assembly and Annotation of the Alfalfa Cyst Nematode (Heterodera medicaginis)

Postnikova, Olga A.; Wram, Catherine; Grinstead, Sam; Vieira, Paulo; Nemchinov, Lev G.

doi:10.2478/jofnem-2025-0047

Abstract

The alfalfa cyst nematode (Heterodera medicaginis) is an invasive and pathogenic species parasitizing the agriculturally important forage crop alfalfa (Medicago sativa L.). To date, no genome assembly of H. medicaginis has been reported in the literature. In this study, for the first time, we assembled a draft genome of this species. This research is important as it provides genomic insights into a damaging pest recently discovered in the United States that affects the third most valuable crop in the country.

References

Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., Bidwell, S. L., Brown, L. C., Clark, K., Davis, E. W., Smith-White, B., Hlavina, W., Pruitt, K. D., Schneider, V. A., and Murphy, T. D. 2024. Rapid and sensitive detection of genome contamination at scale with FCS-GX. Genome Biology 25(1):60. doi: 10.1186/s13059-024-03198-7
Open DOI Search in Google Scholar Back to article
Bali, S., and Gleason, C. 2024. Unveiling the diversity: Plant parasitic nematode effectors and their plant interaction partners. Molecular Plant-Microbe Interactions: MPMI 37(3):179–189. doi: 10.1094/MPMI-09-23-0124-FI
Open DOI Search in Google Scholar Back to article
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., and Borodovsky, M. 2021. BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics 3(1):lqaa108. doi: 10.1093/nargab/lqaa108
Open DOI Search in Google Scholar Back to article
Brůna, T., Lomsadze, A., and Borodovsky, M. 2020. GeneMark-EP+: Eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genomics and Bioinformatics 2:lqaa026. doi: 10.1093/nargab/lqaa026
Open DOI Search in Google Scholar Back to article
Buchfink, B., Xie, C., and Huson, D. H. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12:59–60. doi: 10.1038/nmeth.3176
Open DOI Search in Google Scholar Back to article
Chakraborty, M., Baldwin-Brown, J. G., Long, A. D., and Emerson, J. J. 2016. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Research 44:e147. doi: 10.1093/nar/gkw654
Open DOI Search in Google Scholar Back to article
Chen, Y., Zhang, Y., Wang, A. Y., Gao, M., and Chong, Z. 2021. Accurate long-read de novo assembly evaluation with inspector. Genome Biology 22:312. doi: 10.1186/s13059-021-02527-4
Open DOI Search in Google Scholar Back to article
Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., and Li, H. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10(2):giab008. doi: 10.1093/gigascience/giab008
Open DOI Search in Google Scholar Back to article
Gerber, K., and Maas, P. W. T. H. 1982. A redescription of Heterodera medicaginis Kirjanova. Nematologica 28:94–100. doi: 10.1163/187529282X00547
Open DOI Search in Google Scholar Back to article
Gotoh, O. 2008. A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence. Nucleic Acids Research 36:2630–2638. doi: 10.1093/nar/gkn105
Open DOI Search in Google Scholar Back to article
Hallgren, J., Tsirigos, K. D., Pedersen, M. D., Almagro Armenteros, J. J., Marcatili, P., Nielsen, H., Krogh, A., and Winther, O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. bioRxiv. 2022.04.08.487609; doi: 10.1101/2022.04.08.487609
Open DOI Search in Google Scholar Back to article
Handoo, Z.A., Skantar, A.M., Hafez, S.A., Kantor, M.R., Hult, M.N., Rogers, S.T. 2020. Molecular and morphological characterization of the alfalfa cyst nematode, Heterodera medicaginis, from Utah. Journal of Nematology. 19:1065–1081. doi: 10.21307/jofnem-2020-015
Open DOI Search in Google Scholar Back to article
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., and Stanke, M. 2016. BRAKER1: Unsupervised RNASeq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics (Oxford, England) 32: 767–769. doi: 10.1093/bioinformatics/btv661
Open DOI Search in Google Scholar Back to article
Hoff, K. J., Lomsadze, A., Borodovsky, M., and Stanke, M. 2019. Whole-genome annotation with BRAKER. Pp. 65–95 in Martin Kollmar, ed. Gene prediction. New York, NY: Humana.
Search in Google Scholar Back to article
Howe, K. L., Bolt, B. J., Shafie, M., Kersey, P., and Berriman, M. 2017. WormBase ParaSite − a comprehensive resource for helminth genomics. Molecular and Biochemical Parasitology 215:2–10. doi: 10.1016/j.molbiopara.2016.11.005
Open DOI Search in Google Scholar Back to article
Iwata, H., and Gotoh, O. 2012. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features. Nucleic Acids Research 40:e161. doi: 10.1093/nar/gks708
Open DOI Search in Google Scholar Back to article
Jones, J. T., Haegeman, A., Danchin, E. G., Gaur, H. S., Helder, J., Jones, M. G., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M., and Perry, R. N. 2013. Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology 14:946–961. doi: 10.1111/mpp.12057
Open DOI Search in Google Scholar Back to article
Kirjanova, E. S., and Krall, E. L. 1971. Parasitic nematodes of plants and their control, vol. II. Leningrad: Nauka. P. 522.
Search in Google Scholar Back to article
Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H., and Phillippy, A. M. 2017. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722–736. doi: 10.1101/gr.215087.116
Open DOI Search in Google Scholar Back to article
Laetsch, D.R., and Blaxter, M.L. 2017. BlobTools: Interrogation of genome assemblies. F1000Research 6:1287.
Search in Google Scholar Back to article
Lilley, C. J., Maqbool, A., Wu, D., Yusup, H. B., Jones, L. M., Birch, P. R. J., Banfield, M. J., Urwin, P. E., and Eves-van den Akker, S. 2018. Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene. Plos Genetics 14:e1007310. doi: 10.1371/journal.pgen.1007310
Open DOI Search in Google Scholar Back to article
Lomsadze, A., Ter-Hovhannisyan, V., Chernoff, Y. O., and Borodovsky, M. 2005. Gene identification in novel eukaryotic genomes by self-training algorithm. Nucleic Acids Research 33:6494–6506. doi: 10.1093/nar/gki937
Open DOI Search in Google Scholar Back to article
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., and Zdobnov, E. M. 2021. BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution 38:4647–4654. doi: 10.1093/molbev/msab199
Open DOI Search in Google Scholar Back to article
Masonbrink, R., Maier, T. R., Muppirala, U., Seetharam, A. S., Lord, E., Juvale, P. S., Schmutz, J., Johnson, N. T., Korkin, D., Mitchum, M. G., Mimee, B., Eves-van den Akker, S., Hudson, M., Severin, A. J., and Baum, T. J. 2019. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 20:119. doi: 10.1186/s12864-019-5485-8
Open DOI Search in Google Scholar Back to article
Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D., and Gurevich, A. 2018. Versatile genome assembly evaluation with QUAST-LG. Bioinformatics (Oxford, England) 34: i142–i150. doi: 10.1093/bioinformatics/bty266
Open DOI Search in Google Scholar Back to article
Molloy, B., Shin, D. S., Long, J., Pellegrin, C., Senatori, B., Vieira, P., Thorpe, P. J., Damm, A., Ahmad, M., Vermeulen, K., Derevnina, L., Wei, S., Sperling, A., Reyes Estévez, E., Bruty, S., de Souza, V. H. M., Kranse, O. P., Maier, T., Baum, T., and Eves-van den Akker, S. 2024. The origin, deployment, and evolution of a plant-parasitic nematode effectorome. Plos Pathogens 20:e1012395. doi: 10.1371/journal.ppat.1012395
Open DOI Search in Google Scholar Back to article
Núñez-Rodríguez, L. A., Wram, C. L., Hesse, C., and Zasada, I. A. 2024. Genome Announcement: Draft Genome Assembly of Heterodera humuli Generated Using Long-Read Sequencing. J. Nematol. 56:1. doi: 10.2478/jofnem-2024-0029
Open DOI Search in Google Scholar Back to article
Powers, T., Skantar, A., Harris, T., Higgins, R., Mullin, P., Hafez, S., Handoo, Z., Todd, T., and Powers, K. 2019. DNA barcoding evidence for the North American presence of alfalfa cyst nematode, Heteroderamedicaginis. Journal of Nematology 51:1–17. doi: 10.21307/jofnem-2019-016
Open DOI Search in Google Scholar Back to article
Pokhare, S. S., Thorpe, P., Hedley, P., Morris, J., Habash, S. S., Elashry, A., Eves-van den Akker, S., Grundler, F. M. W., Jones, J. 2020. Signatures of adaptation to a monocot host in the plant-parasitic cyst nematode Heterodera sacchari, The Plant Journal 103: 1263–1274. doi: 10.1111/tpj.14910
Open DOI Search in Google Scholar Back to article
Quinlan, A. R., and Hall, I. M. 2010. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) 26(6):841–842. doi: 10.1093/bioinformatics/btq033
Open DOI Search in Google Scholar Back to article
Ruan, J., and Li, H. 2019. Fast and accurate long-read assembly with wtdbg2. Nature Methods 17:155–158. doi: 10.1038/s41592-019-0669-3
Open DOI Search in Google Scholar Back to article
Siddique, S., Radakovic, Z. S., Hiltl, C., Pellegrin, C., Baum, T. J., Beasley, H., Bent, A. F., Chitambo, O., Chopra, D., Danchin, E. G. J., Grenier, E., Habash, S. S., Hasan, M. S., Helder, J., Hewezi, T., Holbein, J., Holterman, M., Janakowski, S., Koutsovoulos, G. D., Kranse, O. P., Lozano-Torres, J. L., Maier, T. R., Masonbrink, R. E., Mendy, B., Riemer, E., Sobczak, M., Sonawala, U., Sterken, M. G., Thorpe, P., van Steenbrugge, J. J. M., Zahid, N., Grundler, F., and Evesvan den Akker, S. 2022. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5. Nature Communications 13:6190. doi: 10.1038/s41467-022-33769-w
Open DOI Search in Google Scholar Back to article
Skantar, A. M., and Carta, L. K. 2004. Molecular characterization and phylogenetic evaluation of the Hsp90 gene from selected nematodes. J Nematol. 36: 466–480.
Search in Google Scholar Back to article
Smit, A. F. A., and Hubley, R. 2015a. RepeatModeler Open-1.0 (2008–2015). http://www.repeatmasker.org
Search in Google Scholar Back to article
Smit, A. F. A., and Hubley, R. 2015b. RepeatMasker Open-4.0 (2013–2015). http://www.repeatmasker.org
Search in Google Scholar Back to article
Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics (Oxford, England) 24:637–644. doi: 10.1093/bioinformatics/btn013
Open DOI Search in Google Scholar Back to article
Stanke, M., Schöffmann, O., Morgenstern, B., and Waack, S. 2006. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics 7:62. doi: 10.1186/1471-2105-7-62
Open DOI Search in Google Scholar Back to article
Steinberg, D. 1932. The Lucerne nematode. Zashchita Rast. Vredit 3:71–80. (In Russian).
Search in Google Scholar Back to article
Subbotin, S. A., Ocampo, M., and Baldwin, J. G. 2010. Systematics of cyst nematodes (nematode: heteroderinae), nematology monographs and perspectives. P. 351 in D. J. Hunt, and R. N. Perry, eds. Biology and evolution. Boston: Brill Leiden.
Search in Google Scholar Back to article
Subbotin, S. A., Palomares-Rius, J. E., Córdoba-Sánchez, M., Roubtsova, T. V., Bostock, R. M., Fournet, S., Grenier, E., Veronico, P., Maafi, Z. T., and Castillo, P. 2025. DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the goettingiana group from the genus Heterodera (tylenchida: heteroderidae). Nematology: International Journal of Fundamental and Applied Nematological Research 1–21. doi: 10.1163/15685411-bja10420
Open DOI Search in Google Scholar Back to article
Teufel, F., Almagro Armenteros, J. J., Johansen, A. R., Gíslason, M. H., Pihl, S. I., Tsirigos, K. D., Winther, O., Brunak, S., von Heijne, G., and Nielsen, H. 2022. SignalP 6.0 predicts all five types of signal peptides using protein language models. Nature Biotechnology 40(7):1023–1025. doi: 10.1038/s41587-021-01156-3
Open DOI Search in Google Scholar Back to article
Wick, R. R., Judd, L. M., Gorrie, C. L., and Holt, K. E. 2017. Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomics 3(10):e000132. doi: 10.1099/mgen.0.000132
Open DOI Search in Google Scholar Back to article
Wram, C. L., Hesse, C. N., Handoo, Z. A., Pahceco, F. H., and Zasada, I. A. 2022. Genome announcement: The draft genome of the carrot cyst nematode Heterodera carotae. Journal of Nematology 54:20220014. doi: 10.2478/jofnem-2022-0014
Open DOI Search in Google Scholar Back to article

Genome Assembly and Annotation of the Alfalfa Cyst Nematode (Heterodera medicaginis)

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