Five life stage-specific transcriptome assemblies for the reniform nematode, Rotylenchulus reniformis Linford & Oliveira

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. Baum T. J. Wubben M. J. E. Hardy K. A. Su H. Rodermel S. R. 2000 A screen for Arabidopsis thaliana mutants with altered susceptibility to Heterodera schachtii Journal of Nematology 32 166 173 Search in Google Scholar

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. Blin N. Stafford D. W. 1976 A general method for isolation of high molecular weight DNA from eukaryotes Nucleic Acids Research 3 2303 2308 10.1093/nar/3.9.2303343085987581 Search in Google Scholar

Bolger, A. M., Lohse, M., and Usadel, B.. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. Bolger A. M. Lohse M. Usadel B. 2014 Trimmomatic: a flexible trimmer for Illumina sequence data Bioinformatics 30 2114 2120 10.1093/bioinformatics/btu170410359024695404 Search in Google Scholar

Buchfink, B., Xie, C., and Huson, D. H.. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods 12 (1): 59-60. Buchfink B. Xie C. Huson D. H. 2015 Fast and sensitive protein alignment using DIAMOND Nature Methods 12 (1) 59 60 10.1038/nmeth.317625402007 Search in Google Scholar

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. Dobin A. Davis C. A. Schlesinger F. Drenkow J. Zaleski C. Jha S. Batut P. Chaisson M. Gingeras T. R. 2013 STAR: ultrafast universal RNA-seq aligner Bioinformatics 29 (1) 15 21 10.1093/bioinformatics/bts635353090523104886 Search in Google Scholar

Eddy, S. R.. 2011. Accelerated Profile HMM Searches. PLoS Computational Biology 7 (10): e1002195. Eddy S. R. 2011 Accelerated Profile HMM Searches PLoS Computational Biology 7 (10) e1002195 10.1371/journal.pcbi.1002195319763422039361 Search in Google Scholar

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. 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 10.1186/s13059-016-0985-1490142227286965 Search in Google Scholar

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. 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. Bateman A. 2016 The Pfam protein families database: towards a more sustainable future Nucleic Acids Research 44 D1 D279 D285 10.1093/nar/gkv1344470293026673716 Search in Google Scholar

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. Ganji S. Wubben M. J. 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 Search in Google Scholar

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. 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. Regev A. 2011 Full-length transcriptome assembly from RNA-seq data without a reference genome Nature Biotechnology 29 644 652 10.1038/nbt.1883357171221572440 Search in Google Scholar

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. Li W. Godzik A. 2006 Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Bioinformatics 22 (13) 1658 1659 10.1093/bioinformatics/btl15816731699 Search in Google Scholar

Parra, G., Bradnam, K., and Korf, I.. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23: 1061-1067. Parra G. Bradnam K. Korf I. 2007 CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes Bioinformatics 23 1061 1067 10.1093/bioinformatics/btm07117332020 Search in Google Scholar

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. Robinson A. F. Inserra R. N. Caswell-Chen E. P. Vovlas N. Troccoli A. 1997 Rotylenchulus species: identification, distribution, host ranges, and crop plant resistance Nematropica 27 127 180 Search in Google Scholar

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. Simão F. A. Waterhouse R. M. Ioannidis P. Kriventseva E. V. Zdobnov E. M. 2015 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 31 (19) 3210 3212 10.1093/bioinformatics/btv35126059717 Search in Google Scholar