References
- Baum, T. J., Wubben, M. J. E., Hardy, K. A., Su, H., and Rodermel, S. R.. 2000. A screen for Arabidopsis thaliana mutants with altered susceptibility to Heterodera schachtii. Journal of Nematology 32: 166-173.
- Blin, N., and Stafford, D. W.. 1976. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Research 3: 2303-2308.
- Bolger, A. M., Lohse, M., and Usadel, B.. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.
- Buchfink, B., Xie, C., and Huson, D. H.. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12 (1): 59-60.
- Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T. R.. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29 (1): 15-21.
- Eddy, S. R.. 2011. Accelerated Profile HMM Searches. PLoS Computational Biology 7 (10): e1002195.
- Eves-van den Akker, S., et al. 2016. The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence. Genome Biology 17: 124.
- Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G. A., Tate, J., and Bateman, A.. 2016. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Research 44 D1: D279-D285.
- Ganji, S., Wubben, M. J., and Jenkins, J. N.. 2013. Two simple methods for the collection of individual life stages of reniform nematode, Rotylenchulus reniformis. Journal of Nematology 45: 87-91.
- Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B. W., Nusbaum, C., Lindblad-Toh, K., Friedman, N., and Regev, A.. 2011. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nature Biotechnology 29: 644-652.
- Li, W., and Godzik, A.. 2006. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22 (13): 1658-1659.
- Parra, G., Bradnam, K., and Korf, I.. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067.
- Robinson, A. F., Inserra, R. N., Caswell-Chen, E. P., Vovlas, N., and Troccoli, A.. 1997. Rotylenchulus species: identification, distribution, host ranges, and crop plant resistance. Nematropica 27: 127-180.
- 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 (19): 3210-3212.