References
- Adrian, S. R., & Hubley, R. (2023). RepeatMasker [Online].
https://www.repeatmasker.org/ - Alford, D. V. (2012). Chapter 4 - Miscellaneous Pests. In D. V. Alford (Ed.), Pests of Ornamental Trees, Shrubs and Flowers (2nd ed., pp. 87–112). Academic Press.
- Alonge, M., Lebeigle, L., Kirsche, M., Jenike, K., Ou, S., Aganezov, S., Wang, X., Lippman, Z. B., Schatz, M. C., & Soyk, S. (2022). Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology, 23(1), 258.
https://doi.org/10.1186/s13059-022-02758-2 - Álvarez-Ortega, S., Brito, J. A., & Subbotin, S. A. (2019). Multigene phylogeny of root-knot nematodes and molecular characterization of Meloidogyne nataliei Golden, Rose & Bird, 1981 (Nematoda: Tylenchida). Scientific Reports, 9(1), 11788.
https://doi.org/10.1038/s41598-019-48283-9 - Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455–477.
https://doi.org/10.1089/cmb.2012.0042 - Brinkman, H., Goossens, J. J. M., & Van Riel, H. R. (1996). Comparative host suitability of selected crop plants to Meloidogyne chitwoodi. Anzeiger für Schädlingskunde, Pflanzenschutz, Umweltschutz, 69(5), 127–129.
- Castagnone-Sereno, P., Danchin, E. G. J., Perfus-Barbeoch, L., & Abad, P. (2013). Diversity and evolution of root-knot nematodes, genus Meloidogyne: New insights from the genomic era. Annual Review of Phytopathology, 51, 203–220.
https://doi.org/10.1146/annurev-phyto-082712-102316 - Challis, R. B., Mark, R., Richards, E., Rajan, J., & Cochrane, G. (2023). Filtering a Dataset [Online].
https://blobtoolkit.genomehubs.org/blobtools2/blobtools2-tutorials/filtering-a-dataset/ - Dai, D., Xie, C., Zhou, Y., Bo, D., Zhang, S., Mao, S., Liao, Y., Cui, S., Zhu, Z., Wang, X., Li, F., Peng, D., Zheng, J., & Sun, M. (2023). Unzipped chromo-some-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization. Nature Communications, 14(1), 7156.
https://doi.org/10.1038/s41467-023-42861-5 - Elling, A. A. (2013). Major emerging problems with minor Meloidogyne species. Phytopathology, 103(10), 1092–1102.
https://doi.org/10.1094/PHYTO-03-13-0081-R - EPPO. (2023). Meloidogyne fallax Distribution [Online].
https://gd.eppo.int/taxon/MELGFA/distribution - Flynn, J. M., Hubley, R., Goubert, C., Rosen, J., Clark, A. G., Feschotte, C., & Smit, A. F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences, 117(17), 9451–9457.
https://doi.org/10.1073/pnas.1921008117 - Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: Quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075.
https://doi.org/10.1093/bioinformatics/btt089 - Illumina. (2023). Illumina NovaSeq 6000 [Online].
https://emea.illumina.com/systems/sequencing-platforms/novaseq.html - Krueger, F. (2012). Trim Galore [Online].
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ - Laetsch, D., & Blaxter, M. (2017). BlobTools: Interrogation of genome assemblies [version 1; peer review: 2 approved with reservations]. F1000Research, 6, 1504.
https://doi.org/10.12688/f1000research.12609.1 - Lee, S., Nguyen, L. T., Hayes, B. J., & Ross, E. (2021). Prowler: A novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics.
https://doi.org/10.1093/bioinformatics/btab744 - Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols, 1(11), e243.
https://doi.org/10.1002/cphc.243 - Nischwitz, C., Skantar, A., Handoo, Z. A., Hult, M. N., Schmitt, M. E., & McClure, M. A. (2013). Occurrence of Meloidogyne fallax in North America, and molecular characterization of M. fallax and M. minor from U.S. Golf Course Greens. Plant Disease, 97(11), 1438–1444.
https://doi.org/10.1094/PDIS-04-13-0361-RE - Oxford Nanopore Technologies. (2023). PromethION [Online].
https://nanoporetech.com/products/promethion - QIAGEN. (2015). QIAGEN Genomic DNA Handbook [Online].
https://www.qiagen.com/us/resources/download.aspx?id=d2b85b26-16dd-4259-a3a7-a08cbd2a08a3&lang=en - Santo, G., O’Bannon, J., Finley, A., & Golden, A. (1981). Occurrence and host range of a new root-knot nematode (Meloidogyne chitwoodi) in the Pacific Northwest. Plant Disease, 64(10), 951–952.
https://doi.org/10.1094/PD-64-951 - Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS ONE, 11(8), e0163962.
https://doi.org/10.1371/journal.pone.0163962 - Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta, e191.
https://doi.org/10.1002/imt2.191 - Van Der Beek, J. G., & Karssen, G. (1997). Interspecific hybridization of meiotic parthenogenetic Meloidogyne chitwoodi and M. fallax. Phytopathology, 87(10), 1061–1066.
https://doi.org/10.1094/PHYTO.1997.87.10.1061 - Waeyenberge, L., & Moens, M. (2001). Meloidogyne chitwoodi and M. fallax in Belgium. Nematologia Mediterranea, 29(1), 91–97.
- Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257.
https://doi.org/10.1186/s13059-019-1891-0 - Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Peters, B. A., Fan, G., Liu, X., Xu, X., Deng, L., & Zhang, Y. (2020). TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience, 9(12), giaa144.
https://doi.org/10.1093/gigascience/giaa144