A draft genome of a field-collected Steinernema feltiae strain NW

Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215:403–410. Altschul S. F. Gish W. Miller W. Myers E. W. and Lipman D. J. 1990 . Basic local alignment search tool . Journal of Molecular Biology 215 : 403 – 410 . 10.1016/S0022-2836(05)80360-2 Search in Google Scholar

Biemont, C. 2008. Genome size evolution: within-species variation in genome size. Heredity 101:297–298. Biemont C. 2008 . Genome size evolution: within-species variation in genome size . Heredity 101 : 297 – 298 . 10.1038/hdy.2008.8018665185 Search in Google Scholar

Barriere, A. and Felix, M.-A. 2005. High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Current Biology 15:1176–1184. Barriere A. and Felix M.-A. 2005 . High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations . Current Biology 15 : 1176 – 1184 . 10.1016/j.cub.2005.06.02216005289 Search in Google Scholar

Bolger, M. E., Weisshaar, B., Scholz, U., Stein, N., Usadel, B. and Mayer, K. F. X. 2014. Plant genome sequencing – applications for crop improvement. Current Opinion in Biotechnology 26:31–37. Bolger M. E. Weisshaar B. Scholz U. Stein N. Usadel B. and Mayer K. F. X. 2014 . Plant genome sequencing – applications for crop improvement . Current Opinion in Biotechnology 26 : 31 – 37 . 10.1016/j.copbio.2013.08.01924679255 Search in Google Scholar

Bosco, G., Campbell, P., Leiva-Neto, J. T. and Markow, T. A. 2007. Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177:1277–1290. Bosco G. Campbell P. Leiva-Neto J. T. and Markow T. A. 2007 . Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species . Genetics 177 : 1277 – 1290 . 10.1534/genetics.107.075069214799618039867 Search in Google Scholar

Cantarel, B. L., Korf, I., Robb, S. M., Parra, G., Ross, E., Moore, B., Holtm, C., Sánchez Alvarado, A and Yandell, M. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188–196. Cantarel B. L. Korf I. Robb S. M. Parra G. Ross E. Moore B. Holtm C. Sánchez Alvarado A and Yandell M. 2008 . MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes . Genome Research 18 : 188 – 196 . 10.1101/gr.6743907213477418025269 Search in Google Scholar

Castillo, J. C., Reynolds, S. E. and Eleftherianos, I. 2011. Insect immune responses to nematode parasites. Trends in Parasitology 27:537–547. Castillo J. C. Reynolds S. E. and Eleftherianos I. 2011 . Insect immune responses to nematode parasites . Trends in Parasitology 27 : 537 – 547 . 10.1016/j.pt.2011.09.00121982477 Search in Google Scholar

Chang, Z. D., Serra, L., Lu, D., Mortazavi, A. and Dillman, A. R. 2019. A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema. PLoS Pathogens 15:1–29. Chang Z. D. Serra L. Lu D. Mortazavi A. and Dillman A. R. 2019 . A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema . PLoS Pathogens 15 : 1 – 29 . 10.1371/journal.ppat.1007626651311131042778 Search in Google Scholar

Cires, E., Cuesta, C., Revilla, M. Á. and Prieto, J. A. F. 2010. Intraspecific genome size variation and morphological differentiation of Ranunculus parnassifolius (Ranunculaceae), an Alpine–Pyrenean–Cantabrian polyploid group. Biological Journal of the Linnean Society 101:251–271. Cires E. Cuesta C. Revilla M. Á. and Prieto J. A. F. 2010 . Intraspecific genome size variation and morphological differentiation of Ranunculus parnassifolius (Ranunculaceae), an Alpine–Pyrenean–Cantabrian polyploid group . Biological Journal of the Linnean Society 101 : 251 – 271 . 10.1111/j.1095-8312.2010.01517.x Search in Google Scholar

Clum, A. 2018. Genome assembly. In de Vries, R., Tsang, A. and Grigoriev, I. (Eds), Fungal genomics. Methods in molecular biology. Humana Press, New York, NY, pp. 141–153. Clum A. 2018 . Genome assembly . In de Vries R. Tsang A. and Grigoriev I. (Eds), Fungal genomics. Methods in molecular biology . Humana Press , New York, NY , pp. 141 – 153 . Search in Google Scholar

Dallery, J. F., Lapalu, N., Zampounis, A., Pigné, S., Luyten, I., Amselem, J., Wittenberg, A. H. J., Zhou, S., de Queiroz, M. V., Robin, G. P., Auger, A., Hainaut, M., Henrissat, B., Kim, K. T., Lee, Y. H., Lespinet, O., Schwartz, D. C., Thon, M. R. and O’Connell, R. J. 2017. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 18:1–22. Dallery J. F. Lapalu N. Zampounis A. Pigné S. Luyten I. Amselem J. Wittenberg A. H. J. Zhou S. de Queiroz M. V. Robin G. P. Auger A. Hainaut M. Henrissat B. Kim K. T. Lee Y. H. Lespinet O. Schwartz D. C. Thon M. R. and O’Connell R. J. 2017 . Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters . BMC Genomics 18 : 1 – 22 . 10.1186/s12864-017-4083-x557632228851275 Search in Google Scholar

Dillman, A. R., Macchietto, M., Porter, C. F., Rogers, A., Williams, B., Antoshechkin, I., Lee, M. M., Goodwin, Z., Lu, X., Lewis, E. E., Goodrich-Blair, H., Stock, S. P., Adam, B. J., Sternberg, P. W. and Mortazavi, A. 2015. Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biology 16:1–21. Dillman A. R. Macchietto M. Porter C. F. Rogers A. Williams B. Antoshechkin I. Lee M. M. Goodwin Z. Lu X. Lewis E. E. Goodrich-Blair H. Stock S. P. Adam B. J. Sternberg P. W. and Mortazavi A. 2015 . Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks . Genome Biology 16 : 1 – 21 . 10.1186/s13059-015-0746-6457876226392177 Search in Google Scholar

Donn, S., Griffiths, B. S., Neilson, R. and Daniell, T. J. 2008. DNA extraction from soil nematodes for multi-sample community studies. Applied Soil Ecology 38:20–26. Donn S. Griffiths B. S. Neilson R. and Daniell T. J. 2008 . DNA extraction from soil nematodes for multi-sample community studies . Applied Soil Ecology 38 : 20 – 26 . 10.1016/j.apsoil.2007.08.006 Search in Google Scholar

Farslow, J. C., Lipinski, K. J., Packard, L. B., Edgley, M. L., Taylor, J., Flibotte, S., Moerman, G. D., Katju, V. and Bergthorsson, U. 2015. Rapid increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans. BMC Genomics 16:1–18. Farslow J. C. Lipinski K. J. Packard L. B. Edgley M. L. Taylor J. Flibotte S. Moerman G. D. Katju V. and Bergthorsson U. 2015 . Rapid increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans . BMC Genomics 16 : 1 – 18 . 10.1186/s12864-015-2253-2467370926645535 Search in Google Scholar

Fuentes-Pardo, A. P. and Ruzzante, D. E. 2017. Whole-genome sequencing approaches for conservation biology: advantages, limitations and practical recommendations. Molecular Ecology 26:5369–5406. Fuentes-Pardo A. P. and Ruzzante D. E. 2017 . Whole-genome sequencing approaches for conservation biology: advantages, limitations and practical recommendations . Molecular Ecology 26 : 5369 – 5406 . 10.1111/mec.1426428746784 Search in Google Scholar

Goodrich-Blair, H. 2007. They’ve got a ticket to ride: Xenorhabdus nematophila-Steinernema carpocapsae symbiosis. Current Opinion in Microbiology 10:225–230. Goodrich-Blair H. 2007 . They’ve got a ticket to ride: Xenorhabdus nematophila-Steinernema carpocapsae symbiosis . Current Opinion in Microbiology 10 : 225 – 230 . 10.1016/j.mib.2007.05.00617553732 Search in Google Scholar

Gunn, B. F., Baudouin, L., Beulé, T., Ilbert, P., Duperray, C., Crisp, M., Issali, A., Konan, J. L. and Rival, A. 2015. Ploidy and domestication are associated with genome size variation in Palms. American Journal of Botany 102:1625–1633. Gunn B. F. Baudouin L. Beulé T. Ilbert P. Duperray C. Crisp M. Issali A. Konan J. L. and Rival A. 2015 . Ploidy and domestication are associated with genome size variation in Palms . American Journal of Botany 102 : 1625 – 1633 . 10.3732/ajb.150016426437888 Search in Google Scholar

Huang, H., Tong, Y., Zhang, Q.-J. and Gao, L.-Z. 2013. Genome size variation among and within Camellia species by using flow cytometric analysis. PLoS One 8:1–14. Huang H. Tong Y. Zhang Q.-J. and Gao L.-Z. 2013 . Genome size variation among and within Camellia species by using flow cytometric analysis . PLoS One 8 : 1 – 14 . 10.1371/journal.pone.0064981366457123724111 Search in Google Scholar

Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. and Stanke, M. 2015. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 5:767–769. Hoff K. J. Lange S. Lomsadze A. Borodovsky M. and Stanke M. 2015 . BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS . Bioinformatics 5 : 767 – 769 . Search in Google Scholar

Jess, S. and Bingham, J. F. 2004. Biological control of sciarid and phorid pests of mushroom with predatory mites from the genus Hypoaspis (Acari: Hypoaspidae) and the entomopathogenic nematode Steinernema feltiae. Bulletin of Entomological Research 94:159–167. Jess S. and Bingham J. F. 2004 . Biological control of sciarid and phorid pests of mushroom with predatory mites from the genus Hypoaspis (Acari: Hypoaspidae) and the entomopathogenic nematode Steinernema feltiae . Bulletin of Entomological Research 94 : 159 – 167 . 10.1079/BER200328615153298 Search in Google Scholar

Kaya, H. K. and Stock, S. P. 1997. Techniques in insect nematology. In Lacey, L. A. (Ed.). Manual of techniques in insect pathology, biological techniques series. Academic Press, San Diego, CA, pp. 281–324. Kaya H. K. and Stock S. P. 1997 . Techniques in insect nematology . In Lacey L. A. (Ed.). Manual of techniques in insect pathology, biological techniques series . Academic Press , San Diego, CA , pp. 281 – 324 . Search in Google Scholar

Kim, D., Langmead, B. and Salzberg, S. L. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357–360. Kim D. Langmead B. and Salzberg S. L. 2015 . HISAT: a fast spliced aligner with low memory requirements . Nature Methods 12 : 357 – 360 . 10.1038/nmeth.3317465581725751142 Search in Google Scholar

Kingan, S. B., Urban, J., Lambert, C. C., Baybayan, P., Childers, A. K., Coates, B., Scheffler, B., Hackett, K., Korlach, J. and Geib, S. M. 2019. A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II System. GigaScience 8:1–10. Kingan S. B. Urban J. Lambert C. C. Baybayan P. Childers A. K. Coates B. Scheffler B. Hackett K. Korlach J. and Geib S. M. 2019 . A high-quality genome assembly from a single, field-collected spotted lanternfly (Lycorma delicatula) using the PacBio Sequel II System . GigaScience 8 : 1 – 10 . 10.1093/gigascience/giz122679140131609423 Search in Google Scholar

Kolmogorov, M., Armstrong, J., Raney, B. J., Streeter, I., Dunn, M., Yang, F., Odom, D., Flicek, P., Keane, T. M., Thybert, D., Paten, B. and Pham, S. 2018. Chromosome assembly of large and complex genomes using multiple references. Genome Research 28:1720–1732. Kolmogorov M. Armstrong J. Raney B. J. Streeter I. Dunn M. Yang F. Odom D. Flicek P. Keane T. M. Thybert D. Paten B. and Pham S. 2018 . Chromosome assembly of large and complex genomes using multiple references . Genome Research 28 : 1720 – 1732 . 10.1101/gr.236273.118621164330341161 Search in Google Scholar

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. 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 . 10.1101/gr.215087.116541176728298431 Search in Google Scholar

Lacey, L. A. and Georgis, R. 2012. Entomopathogenic nematodes for control of insect pests above and below ground with comments on commercial production. Journal of Nematology 44:218–225. Lacey L. A. and Georgis R. 2012 . Entomopathogenic nematodes for control of insect pests above and below ground with comments on commercial production . Journal of Nematology 44 : 218 – 225 . Search in Google Scholar

Lacey, L. A., Arthurs, S. P., Unruh, T. R., Headrick, H. and Fritts, R. 2006. Entomopathogenic nematodes for control of codling moth (Lepidoptera: Tortricidae) in apple and pear orchards: effect of nematode species and seasonal temperatures, adjuvants, application equipment, and post-application irrigation. Biological Control 37:214–223. Lacey L. A. Arthurs S. P. Unruh T. R. Headrick H. and Fritts R. 2006 . Entomopathogenic nematodes for control of codling moth (Lepidoptera: Tortricidae) in apple and pear orchards: effect of nematode species and seasonal temperatures, adjuvants, application equipment, and post-application irrigation . Biological Control 37 : 214 – 223 . 10.1016/j.biocontrol.2005.09.015 Search in Google Scholar

Leinaas, H. P., Jalal, M., Gabrielsen, T. M. and Hessen, D. O. 2016. Inter- and intraspecific variation in body- and genome size in calanoid copepods from temperate and arctic waters. Ecology and Evolution 6:5585–5595. Leinaas H. P. Jalal M. Gabrielsen T. M. and Hessen D. O. 2016 . Inter- and intraspecific variation in body- and genome size in calanoid copepods from temperate and arctic waters . Ecology and Evolution 6 : 5585 – 5595 . 10.1002/ece3.2302498357627547339 Search in Google Scholar

Lu, D., Baiocchi, T. and Dillman, A. R. 2016. Genomics of entomopathogenic nematodes and implications for pest control. Trends in Parasitology 32:588–598. Lu D. Baiocchi T. and Dillman A. R. 2016 . Genomics of entomopathogenic nematodes and implications for pest control . Trends in Parasitology 32 : 588 – 598 . 10.1016/j.pt.2016.04.008496910127142565 Search in Google Scholar

Marçais, G., Delcher, A. L., Phillippy, A. M., Coston, R., Salzberg, S. L. and Zimin, A. 2018. MUMmer4: a fast and versatile genome alignment system. PLoS Computational Biology 14:1–14. Marçais G. Delcher A. L. Phillippy A. M. Coston R. Salzberg S. L. and Zimin A. 2018 . MUMmer4: a fast and versatile genome alignment system . PLoS Computational Biology 14 : 1–14 . 10.1371/journal.pcbi.1005944580292729373581 Search in Google Scholar

Myers, E. W., Sutton, G. G., Delcher, A. L., Dew, I. M., Fasulo, D. P., Flanigan, M. J., Kravitz, S. A., Mobarry, C. M., Reinert, K. H., Remington, K. A., Anson, E. L., Bolanos, R. A., Chou, H. H., Jordan, C. M., Halpern, A. L., Lonardi, S., Beasley, E. M., Brandon, R. C., Chen, L., Dunn, P. J., Lai, Z., Liang, Y., Nusskern, D. R., Zhan, M., Zhang, Q., Zheng, X., Rubin, G. M., Adams, M. D. and Venter, J. C. 2000. A whole-genome assembly of Drosophila. Science 287:2196–2204. Myers E. W. Sutton G. G. Delcher A. L. Dew I. M. Fasulo D. P. Flanigan M. J. Kravitz S. A. Mobarry C. M. Reinert K. H. Remington K. A. Anson E. L. Bolanos R. A. Chou H. H. Jordan C. M. Halpern A. L. Lonardi S. Beasley E. M. Brandon R. C. Chen L. Dunn P. J. Lai Z. Liang Y. Nusskern D. R. Zhan M. Zhang Q. Zheng X. Rubin G. M. Adams M. D. and Venter J. C. 2000 . A whole-genome assembly of Drosophila . Science 287 : 2196 – 2204 . 10.1126/science.287.5461.219610731133 Search in Google Scholar

Noosidum, A., Hodson, A. K., Lewis, E. E. and Chandrapatya, A. 2010. Characterization of new entomopathogenic nematodes from Thailand: foraging behavior and virulence to the greater wax moth, Galleria mellonella L. (Lepidoptera: Pyralidae). Journal of Nematology 42:281–291. Noosidum A. Hodson A. K. Lewis E. E. and Chandrapatya A. 2010 . Characterization of new entomopathogenic nematodes from Thailand: foraging behavior and virulence to the greater wax moth, Galleria mellonella L. (Lepidoptera: Pyralidae) . Journal of Nematology 42 : 281 – 291 . Search in Google Scholar

Palková, Z. 2004. Multicellular microorganisms: laboratory versus nature. EMBO Reports 5:470–476. Palková Z. 2004 . Multicellular microorganisms: laboratory versus nature . EMBO Reports 5 : 470 – 476 . 10.1038/sj.embor.7400145129905615184977 Search in Google Scholar

Rhoads, A. and Au, K. F. 2015. PacBio sequencing and its applications. Genomics, Proteomics & Bioinformatics 13:278–289. Rhoads A. and Au K. F. 2015 . PacBio sequencing and its applications . Genomics, Proteomics & Bioinformatics 13 : 278 – 289 . 10.1016/j.gpb.2015.08.002467877926542840 Search in Google Scholar

Rodríguez-Leal, D., Lemmon, Z. H., Man, J., Bartlett, M. E. and Lippman, Z. B. 2017. Engineering quantitative trait variation for crop improvement by genome editing. Cell 171:470–480.e8. Rodríguez-Leal D. Lemmon Z. H. Man J. Bartlett M. E. and Lippman Z. B. 2017 . Engineering quantitative trait variation for crop improvement by genome editing . Cell 171 : 470 – 480.e8 . 10.1016/j.cell.2017.08.03028919077 Search in Google Scholar

Smit, A. F. A., Hubley, R. and Green, P. 2013-2015. RepeatMasker Open-4.0, available at: http://www.repeatmasker.org/faq.html Search in Google Scholar

Sterken, M. G., Snoek, L. B., Kammenga, J. E. and Andersen, E. C. 2015. The laboratory domestication of Caenorhabditis elegans. Trends in Genetics 31:224–231. Sterken M. G. Snoek L. B. Kammenga J. E. and Andersen E. C. 2015 . The laboratory domestication of Caenorhabditis elegans . Trends in Genetics 31 : 224 – 231 . 10.1016/j.tig.2015.02.009441704025804345 Search in Google Scholar

Toba, H. H., Lindegren, J. E., Turner, J. E. and Vail, P. V. 1983. Susceptibility of the Colorado potato beetle and the sugarbeet wireworm to Steinernema feltiae and S. glaseri. Journal of Nematology 15:597–601. Toba H. H. Lindegren J. E. Turner J. E. and Vail P. V. 1983 . Susceptibility of the Colorado potato beetle and the sugarbeet wireworm to Steinernema feltiae and S. glaseri . Journal of Nematology 15 : 597 – 601 . Search in Google Scholar

Wang, L., He, F., Huang, Y., He, J., Yang, S., Zeng, J., Deng, C., Jiang, X., Fang, Y., Wen, S., Xu, R., Yu, H., Yang, X., Zhong, G., Chen, C., Yan, X., Zhou, C., Zhang, H., Xie, Z., Larkin, R. M., Deng, X. and Xu, Q. 2018. Genome of wild mandarin and domestication history of mandarin. Molecular Plant 11:1024–1037. Wang L. He F. Huang Y. He J. Yang S. Zeng J. Deng C. Jiang X. Fang Y. Wen S. Xu R. Yu H. Yang X. Zhong G. Chen C. Yan X. Zhou C. Zhang H. Xie Z. Larkin R. M. Deng X. and Xu Q. 2018 . Genome of wild mandarin and domestication history of mandarin . Molecular Plant 11 : 1024 – 1037 . 10.1016/j.molp.2018.06.00129885473 Search in Google Scholar

Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V. and Zdobnov, E. M. 2017. BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution 35:543–548. Waterhouse R. M. Seppey M. Simão F. A. Manni M. Ioannidis P. Klioutchnikov G. Kriventseva E. V. and Zdobnov E. M. 2017 . BUSCO applications from quality assessments to gene prediction and phylogenomics . Molecular Biology and Evolution 35 : 543 – 548 . 10.1093/molbev/msx319585027829220515 Search in Google Scholar

Wu, S., Lau, K. H., Cao, Q., Hamilton, J. P., Sun, H., Zhou, C., Eserman, L., Gemenet, D. C., Olukolu, B. A., Wang, H., Crisovan, E., Godden, G. T., Jiao, C., Wang, X., Kitavi, M., Manrique-Carpintero, N., Vaillancourt, B., Wiegert-Rininger, K., Yang, X., Bao, K., Schaff, J., Kreuze, J., Gruneberg, W., Khan, A., Ghislain, M., Ma, D., Jiang, J., Mwanga, R. O. M, Leebens-Mack, J., Coin, L. J. M., Yencho, G. C., Buell, C. R. and Fei, Z. 2018. Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement. Nature Communications 9:1–12. Wu S. Lau K. H. Cao Q. Hamilton J. P. Sun H. Zhou C. Eserman L. Gemenet D. C. Olukolu B. A. Wang H. Crisovan E. Godden G. T. Jiao C. Wang X. Kitavi M. Manrique-Carpintero N. Vaillancourt B. Wiegert-Rininger K. Yang X. Bao K. Schaff J. Kreuze J. Gruneberg W. Khan A. Ghislain M. Ma D. Jiang J. Mwanga R. O. M Leebens-Mack J. Coin L. J. M. Yencho G. C. Buell C. R. and Fei Z. 2018 . Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement . Nature Communications 9 : 1 – 12 . 10.1038/s41467-018-06983-8621495730389915 Search in Google Scholar

White, G. E. 1927. A method for obtaining infective nematode larvae from cultures. Science 66:302–303. White G. E. 1927 . A method for obtaining infective nematode larvae from cultures . Science 66 : 302 – 303 . 10.1126/science.66.1709.302.b Search in Google Scholar