References
- Abad, P., Gouzy, J., Aury, J.-M., Castagnone-Sereno, P., Danchin, E. G. J., Deleury, E., Perfus-Barbeoch, L., Anthouard, V., Artiguenave, F., Blok, V. C., Caillaud, M.-C., Coutinho, P. M., Dasilva, C., De Luca, F., Deau, F., Esquibet, M., Flutre, T., Goldstone, J. V., Hamamouch, N., Hewezi, T., Jaillon, O., Jubin, C., Leonetti, P., Magliano, M., Maier, T. R., Markov, G. V., McVeigh, P., Pesole, G., Poulain, J., Robinson-Rechavi, M., Sallet, E., Ségurens, B., Steinbach, D., Tytgat, T., Ugarte, E., van Ghelder, C., Veronico, P., Baum, T. J., Blaxter, M., Bleve-Zacheo, T., Davis, E. L., Ewbank, J. J., Favery, B., Grenier, E., Henrissat, B., Jones, J. T., Laudet, V., Maule, A. G., Quesneville, H., Rosso, M.-N., Schiex, T., Smant, G., Weissenbach, J. and Wincker, P. 2008. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature Biotechnology 26:909–915.
- Andrews, S. 2018. FastQC – a quality control tool for high throughput sequence data. Babraham Bioinformatics, The Babraham Institute, Cambridge, available at: www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed January 15, 2019).
- Bebber, D. P., Holmes, T. and Gurr, S. J. 2014. The global spread of crop pests and pathogens. Global Ecology and Biogeography 23:1398–1407.
- Blanc-Mathieu, R., Perfus-Barbeoch, L., Aury, J.-M., Da Rocha, M., Gouzy, J., Sallet, E., Martin-Jimenez, C., Bailly-Bechet, M., Castagnone-Sereno, P., Flot, J.-F., Kozlowski, D. K., Cazareth, J., Couloux, A., Da Silva, C., Guy, J., Kim-Jo, Y.-J., Rancurel, C., Schiex, T., Abad, P., Wincker, P. and Danchin, E. G. J. 2017. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genetics 13:1–36, available at: https://doi.org/10.1371/journal.pgen.1006777.
- Bolger, A. M., Lohse, M. and Usadel, B. 2014. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120.
- Castagnone-Sereno, P. and Danchin, E. G. J. 2014. Parasitic success without sex – the nematode experience. Journal of Evolutionary Biology 27:1323–1333.
- Danchin, E. G. J., Arguel, M.-J., Campan-Fournier, A., Perfus-Barbeoch, L., Magliano, M., Rosso, M.-N., Da Rocha, M., Da Silva, C., Nottet, N., Labadie, K., Guy, J., Artiguenave, F. and Abad, P. 2013. Identification of novel target genes for safer and more specific control of root-knot nematodes from a pan-genome mining. PLoS Pathogens 9:1–15, available at: https://doi.org/10.1371/journal.ppat.1003745
- Gerič Stare, B., Strajnar, P., Širca, S., Susič, N. and Urek, G. 2018. Record of a new location for tropical root knot nematode Meloidogyne luci in Slovenia. EPPO Buletin 48:135–137.
- Gerič Stare, B., Strajnar, P., Susič, N., Urek, G. and Širca, S. 2017. Reported populations of Meloidogyne ethiopica in Europe identified as Meloidogyne luci. Plant Disease 101:1627–1632.
- Gerič Stare, B., Aydınlı, G., Devran, Z., Mennan, S., Strajnar, P, Urek, G. and Širca, S. 2019. Recognition of species belonging to Meloidogyne ethiopica group and development of a diagnostic method for its detection. European Journal of Plant Pathology 154:621–633, available at: https://doi.org/10.1007/s10658-019-01686-2
- Hussey, R. S. and Barker, K. R. 1973. Comparison of methods of collecting inocula for Meloidogyne spp., including a new technique. Plant Disease Reporter 57:1025–1028.
- Jones, J.T., Haegeman, A., Danchin, E. G. J., Gaur, H. S., Helder, J., Jones, M. G. K., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M. L. and Perry, R. N. 2013. Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology 14:946–961.
- Laetsch, D. R. and Blaxter, M. L. 2017. BlobTools: interrogation of genome assemblies. F1000Research 6:1287.
- Lunt, D. H., Kumar, S., Koutsovoulos, G. and Blaxter, M. L. 2014. The complex hybrid origins of the root knot nematodes revealed through comparative genomics. PeerJ 2:1, available at: https://doi.org/10.7717/peerj.356
- McClure, M. A., Kruk, T. H. and Misaghi, I. 1973. A method for obtaining quantities of clean Meloidogyne eggs. Journal of Nematology 5:230.
- Marçais, G. and Kingsford, C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770.
- Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., Cromer, J., Diener, S., Gajan, J., Graham, S., Houfek, T. D., Liu, Q., Mitros, T., Schaff, J., Schaffer, R., Scholl, E., Sosinski, B. R., Thomas, V. P. and Windham, E. 2008. Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences of the United States of America 105:14802–14807.
- Parra, G., Bradnam, K. and Korf, I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067.
- Ranallo-Benavidez, T. R., Jaron, K. S. and Schatz, M. C. (in press). GenomeScope 2.0 and Smudgeplots: reference-free profiling of polyploid genomes. Nature Communications.
- Sato, K., Kadota, Y., Gan, P., Bino, T., Uehara, T., Yamaguchi, K., Ichihashi, Y., Maki, N., Iwahori, H., Suzuki, T., Shigenobu, S. and Shirasu, K. 2018. High-quality genome sequence of the root-knot nematode Meloidogyne arenaria genotype A2-O. Genome Announcements 6:e00519–18.
- Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. and Zdobnov, E. M. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212.
- Somvanshi, V. S., Tathode, M., Shukla, R. N. and Rao, U. 2018. Nematode genome announcement: a draft genome for rice root-knot nematode, Meloidogyne graminicola. Journal of Nematology 50:111–116.
- Szitenberg, A., Salazar-Jaramillo, L., Blok, V. C., Laetsch, D. R., Joseph, S., Williamson, V. M., Blaxter, M. L. and Lunt, D. H. 2017. Comparative genomics of apomictic root-knot nematodes: hybridization, ploidy, and dynamic genome change. Genome Biology and Evolution 9:2844–2861.
- Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. K. and Earl, A. M. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PloS One 9:1–14, available at: https://doi.org/10.1371/journal.pone.0112963