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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., and Pevzner, P. A. 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455–477. BankevichA. NurkS. AntipovD. GurevichA. A. DvorkinM. KulikovA. S. LesinV. M. NikolenkoS. I. PhamS. PrjibelskiA. D. PyshkinA. V. SirotkinA. V. VyahhiN. TeslerG. AlekseyevM. A. PevznerP. A. 2012 SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing Journal of Computational Biology 19 455 477 10.1089/cmb.2012.0021334251922506599 Search in Google Scholar

Berney, M. F., and Bird, G. W. 1992. Distribution of Heterodera carotae and Meloidogyne hapla in Michigan carrot production. Journal of Nematology 24:776–778. BerneyM. F. BirdG. W. 1992 Distribution of Heterodera carotae and Meloidogyne hapla in Michigan carrot production Journal of Nematology 24 776 778 Search in Google Scholar

CABI. 2021. Heterodera carotae (carrot cyst nematode). in Invasive species compendium. Wallingford, UK: CAB International. www.cabi.org/isc CABI 2021 Heterodera carotae (carrot cyst nematode) in Invasive species compendium Wallingford, UK CAB International www.cabi.org/isc Search in Google Scholar

Edgar, R. C. 2004. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:113. EdgarR. C. 2004 MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 5 113 10.1186/1471-2105-5-11351770615318951 Search in Google Scholar

Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461. EdgarR. C. 2010 Search and clustering orders of magnitude faster than BLAST Bioinformatics 26 2460 2461 10.1093/bioinformatics/btq46120709691 Search in Google Scholar

Escobar-Avila, I. M., López-Villegas, E. Ó., Subbotin, S. A., and Tovar-Soto, A. 2018. First report of carrot cyst nematode Heterodera carotae in Mexico: Morphological, molecular characterization, and host range study. Journal of Nematology 50: 229–242. Escobar-AvilaI. M. López-VillegasE. Ó. SubbotinS. A. Tovar-SotoA. 2018 First report of carrot cyst nematode Heterodera carotae in Mexico: Morphological, molecular characterization, and host range study Journal of Nematology 50 229 242 10.21307/jofnem-2018-021690936130451440 Search in Google Scholar

Esquibet, M., Gautier, C., Piriou, C., Grenier, E., Fournet, S., and Montarry, J. 2020. Evidence of strong gene flow among French populations of the carrot cyst nematode Heterodera carotae. Plant Pathology 69:168–176. EsquibetM. GautierC. PiriouC. GrenierE. FournetS. MontarryJ. 2020 Evidence of strong gene flow among French populations of the carrot cyst nematode Heterodera carotae Plant Pathology 69 168 176 10.1111/ppa.13102 Search in Google Scholar

Fenwick, D. 1940. Methods for the recovery and counting of cysts of Heterodera schachtii from soil. Journal of Helminthology 18:155–172. FenwickD. 1940 Methods for the recovery and counting of cysts of Heterodera schachtii from soil Journal of Helminthology 18 155 172 10.1017/S0022149X00031485 Search in Google Scholar

Greco, N., D’Addabbo, T., Brandonisio, A., and Elia, F. 1993. Damage to Italian crops caused by cyst-forming nematodes. Journal of Nematology 25:836–842. GrecoN. D’AddabboT. BrandonisioA. EliaF. 1993 Damage to Italian crops caused by cyst-forming nematodes Journal of Nematology 25 836 842 Search in Google Scholar

Gurevich, A., Saveliev, V., Vyahhi, N., and Tesler, G. 2013. QUAST: Quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. GurevichA. SavelievV. VyahhiN. TeslerG. 2013 QUAST: Quality assessment tool for genome assemblies Bioinformatics 29 1072 1075 10.1093/bioinformatics/btt086362480623422339 Search in Google Scholar

Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M., and Stanke, M. 2016. BRAKER1: Unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32:767–769. HoffK. J. LangeS. LomsadzeA. BorodovskyM. StankeM. 2016 BRAKER1: Unsupervised RNA-seq-based genome annotation with GeneMark-ET and AUGUSTUS Bioinformatics 32 767 769 10.1093/bioinformatics/btv661607816726559507 Search in Google Scholar

Howe, K. L., Bolt, B. J., Cain, S., Chan, J., Chen, W. J., Davis, P., Done, J., Down, T., Gao, S., Grove, C., Harris, T. W., Kishore, R., Lee, R., Lomax, J., Li, Y., Muller, H.-M., Nakamura, C., Nuin, P., Paulini, M., Raciti, D., Schindelman, G., Stanley, E., Tuli, M. A., Van Auken, K., Wang, D., Wang, X., Williams, G., Wright, A., Yook, K., Berriman, M., Kersey, P., Schedl, T., Stein, L., and Sternberg, P. W. 2016. WormBase 2016: Expanding to enable helminth genomic research. Nucleic Acids Research 44:D774–D780. HoweK. L. BoltB. J. CainS. ChanJ. ChenW. J. DavisP. DoneJ. DownT. GaoS. GroveC. HarrisT. W. KishoreR. LeeR. LomaxJ. LiY. MullerH.-M. NakamuraC. NuinP. PauliniM. RacitiD. SchindelmanG. StanleyE. TuliM. A. Van AukenK. WangD. WangX. WilliamsG. WrightA. YookK. BerrimanM. KerseyP. SchedlT. SteinL. SternbergP. W. 2016 WormBase 2016: Expanding to enable helminth genomic research Nucleic Acids Research 44 D774 D780 10.1093/nar/gkv1217470286326578572 Search in Google Scholar

Howe, K. L., Bolt, B. J., Shafie, M., Kersey, P., and Berriman, M. 2017. WormBase ParaSite − a comprehensive resource for helminth genomics. Molecular and Biochemical Parasitology 215:2–10. HoweK. L. BoltB. J. ShafieM. KerseyP. BerrimanM. 2017 WormBase ParaSite − a comprehensive resource for helminth genomics Molecular and Biochemical Parasitology 215 2 10 10.1016/j.molbiopara.2016.11.005548635727899279 Search in Google Scholar

Krueger, F. 2020. Babraham Bioinformatics – Trim Galore! http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/. KruegerF. 2020 Babraham Bioinformatics – Trim Galore! http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/. Search in Google Scholar

Kumar, S., Jones, M., Koutsovoulos, G., Clarke, M., and Blaxter, M. 2013. Blobology: Exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Frontiers in Genetics 4:237. KumarS. JonesM. KoutsovoulosG. ClarkeM. BlaxterM. 2013 Blobology: Exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots Frontiers in Genetics 4 237 10.3389/fgene.2013.00237384337224348509 Search in Google Scholar

Madani, M., Palomares-Rius, J. E., Vovlas, N., Castillo, P., and Tenuta, M. 2018. Integrative diagnosis of carrot cyst nematode (Heterodera carotae) using morphology and several molecular markers for an accurate identification. European Journal of Plant Pathology 150:1023–1039. MadaniM. Palomares-RiusJ. E. VovlasN. CastilloP. TenutaM. 2018 Integrative diagnosis of carrot cyst nematode (Heterodera carotae) using morphology and several molecular markers for an accurate identification European Journal of Plant Pathology 150 1023 1039 10.1007/s10658-017-1342-2 Search in Google Scholar

Masonbrink, R., Maier, T. R., Muppirala, U., Seetharam, A. S., Lord, E., Juvale, P. S., Schmutz, J., Johnson, N. T., Korkin, D., Mitchum, M. G., Mimee, B., Eves-van den Akker, S., Hudson, M., Severin, A. J., and Baum, T. J. 2019. The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes. BMC Genomics 20:119. MasonbrinkR. MaierT. R. MuppiralaU. SeetharamA. S. LordE. JuvaleP. S. SchmutzJ. JohnsonN. T. KorkinD. MitchumM. G. MimeeB. Eves-van den AkkerS. HudsonM. SeverinA. J. BaumT. J. 2019 The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes BMC Genomics 20 119 10.1186/s12864-019-5485-8636777530732586 Search in Google Scholar

Nurk, S., Meleshko, D., Korobeynikov, A., and Pevzner, P. A. 2017. metaSPAdes: A new versatile metagenomic assembler. Genome Research 27: 824–834. NurkS. MeleshkoD. KorobeynikovA. PevznerP. A. 2017 metaSPAdes: A new versatile metagenomic assembler Genome Research 27 824 834 10.1101/gr.213959.116541177728298430 Search in Google Scholar

Price, M. N., Dehal, P. S., and Arkin, A. P. 2010. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE 5:e9490. PriceM. N. DehalP. S. ArkinA. P. 2010 FastTree 2 – approximately maximum-likelihood trees for large alignments PLoS ONE 5 e9490 10.1371/journal.pone.0009490283573620224823 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 31:3210–3212. SimãoF. A. WaterhouseR. M. IoannidisP. KriventsevaE. V. ZdobnovE. M. 2015 BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics 31 3210 3212 10.1093/bioinformatics/btv35126059717 Search in Google Scholar

Stöver, B. C., and Müller, K. F. 2010. TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7. StöverB. C. MüllerK. F. 2010 TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses BMC Bioinformatics 11 7 10.1186/1471-2105-11-7280635920051126 Search in Google Scholar

Subbotin, S. A., Mundo-Ocampo, M., and Baldwin, J. G. 2010. Systematics of cyst nematodes (Nematoda: Heteroderinae). in D. J. Hunt and R. N. Perry, eds. Nematology monographs and perspectives 8B. Netherlands: Brill, p. 124–126. SubbotinS. A. Mundo-OcampoM. BaldwinJ. G. 2010 Systematics of cyst nematodes (Nematoda: Heteroderinae) in HuntD. J. PerryR. N. eds. Nematology monographs and perspectives 8B Netherlands Brill 124 126 10.1163/ej.9789004164345.i-512 Search in Google Scholar

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J., and Schatz, M. C. 2017. GenomeScope: Fast reference-free genome profiling from short reads. Bioinformatics 33:2202–2204. VurtureG. W. SedlazeckF. J. NattestadM. UnderwoodC. J. FangH. GurtowskiJ. SchatzM. C. 2017 GenomeScope: Fast reference-free genome profiling from short reads Bioinformatics 33 2202 2204 10.1093/bioinformatics/btx153587070428369201 Search in Google Scholar

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S. A., and Earl, A. M. 2014. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963. WalkerB. J. AbeelT. SheaT. PriestM. AbouellielA. SakthikumarS. CuomoC. A. ZengQ. WortmanJ. YoungS. A. EarlA. M. 2014 Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement PLoS ONE 9 e112963 10.1371/journal.pone.0112963423734825409509 Search in Google Scholar

Yoder, M., De Ley, I. T., Wm King, I., Mundo-Ocampo, M., Mann, J., Blaxter, M., Poiras, L., and De Ley, P. 2006. DESS: A versatile solution for preserving morphology and extractable DNA of nematodes. Nematology 8:367–376. YoderM. De LeyI. T. Wm KingI. Mundo-OcampoM. MannJ. BlaxterM. PoirasL. De LeyP. 2006 DESS: A versatile solution for preserving morphology and extractable DNA of nematodes Nematology 8 367 376 10.1163/156854106778493448 Search in Google Scholar

Yu, Q., Ponomareva, E., Van Dyk, D., McDonald, M. R., Sun, F., Madani, M., and Tenuta, M. 2017. First report of the carrot cyst nematode (Heterodera carotae) from carrot fields in Ontario, Canada. Plant Disease 101:1056–1056. YuQ. PonomarevaE. Van DykD. McDonaldM. R. SunF. MadaniM. TenutaM. 2017 First report of the carrot cyst nematode (Heterodera carotae) from carrot fields in Ontario, Canada Plant Disease 101 1056 1056 10.1094/PDIS-01-17-0070-PDN Search in Google Scholar

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