A draft genome for a species of Halicephalobus (Panagrolaimidae)

Anderson R. C. , Linder K. E. and Peregrine A. S. 1998. Halicephalobus gingivalis (Stefanski, 1954) from a fatal infection in a horse in Ontario, Canada with comments on the validity of H. deletrix and a review of the genus. Parasite 5: 255–61. Search in Google Scholar

Anderson R. V. and Bemrick W. J. 1965. Micronema deletrix, a saprophagous nematode inhabiting a nasal tumor of a horse. Proceedings of the Helminthological Society of Washington 32: 74–5. Search in Google Scholar

Andrássy I. 1952. Freilebende Nematoden aus dem Bükk-Gebirge. Annales historico-naturales Musei Nationalis Hungarici 2: 13–65. Search in Google Scholar

Andrássy I. 1984. Klasse Nematoda, Gustav Fischer Verlag, Stuttgart.10.1515/9783112484586 Search in Google Scholar

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: 455–77.10.1089/cmb.2012.0021334251922506599 Search in Google Scholar

Bernt M. , Donath A. , Jühling F. , Externbrink F. , Florentz C. , Fritzsch G. , Pütz J. , Middendorf M. and Stadler P. F. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69: 313–19.10.1016/j.ympev.2012.08.02322982435 Search in Google Scholar

Blaxter M. , De Ley P. , Garey J. R. , Liu L. X. , Scheldeman P. , Vierstraete A. , Vanfleteren J. R. , Mackey L. Y. , Dorris M. , Frisse L. M. , Vida J. T. and Thomas W. K. 1998. A molecular evolutionary framework for the phylum Nematoda. Nature 392: 71–5.10.1038/321609510248 Search in Google Scholar

Blunden A. S. , Khalil L. F. and Webbon P. M. 1987. Halicephalobus deletrix infection in a horse. Equine Veterinary Journal 19: 255–60.10.1111/j.2042-3306.1987.tb01399.x3608968 Search in Google Scholar

Borgonie G. , Garcia-Moyano A. , Litthauer D. , Bert W. , Bester A. , van Heerden E. , Moller C. , Erasmus M. and Onstott T. C. 2011. Nematoda from the terrestrial deep subsurface of South Africa. Nature 474: 79–82.10.1038/nature0997421637257 Search in Google Scholar

Długosz M. and Deorowicz S. 2017. RECKONER: read error corrector based on KMC. Bioinformatics 33: 1086–9.10.1093/bioinformatics/btw74628062451 Search in Google Scholar

Drezen E. , Rizk G. , Chikhi R. , Deltel C. , Lemaitre C. , Peterlongo P. and Lavenier D. 2014. GATB: genome assembly & analysis tool box. Bioinformatics 30: 2959–61.10.1093/bioinformatics/btu406418425724990603 Search in Google Scholar

Félix M. A. , Braendle C. and Cutter A. D. 2014. A streamlined system for species diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with name designations for 15 distinct biological species. PLoS One 9: e0118327.10.1371/journal.pone.0094723398424424727800 Search in Google Scholar

Foley J. R. , Chouvenc T. , Giblin-Davis R. M. , Su N. Y. and Kanzaki N. 2018. Phoresy and within-colony transmission of nematodes associated with alates of subterranean termites (Isoptera: Rhinotermitidae). Environmental Entomology 47: 1107–16.10.1093/ee/nvy09329945250 Search in Google Scholar

Hoogstraten J. and Young W. G. 1975. Meningo-encephalomyelitis due to the saprophagous nematode, Micronema deletrix . The Canadian Journal of Neurological Sciences, 2:121–6.10.1017/S0317167100020102 Search in Google Scholar

International Helminth Genomes Consortium 2018. Comparative genomics of the major parasitic worms. Nature Genetics . 51:163–74.10.1038/s41588-018-0262-1634904630397333 Search in Google Scholar

Kanzaki N. , Ragsdale E. J. , Herrmann M. , Susoy V. and Sommer R. J. 2013. Two androdioecious and one dioecious new species of Pristionchus (Nematoda: Diplogastridae): new reference points for the evolution of reproductive mode. Journal of Nematology 45: 172–94. Search in Google Scholar

Köhler A. 2011. Description of Halicephalobus similigaster (Andrássy, 1952) and a comparison with its junior synonyms H. minutus (Körner, 1954) syn. n. and H. parvus (Körner, 1954) syn. n. (Nematoda: Panagrolaimidae). Nematology 13: 287–93. 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. Search in Google Scholar

Lewis S. C. , Dyal L. A. , Hilburn C. F. , Weitz S. , Liau W. S. , Lamunyon C. W. and Denver D. R. 2009. Molecular evolution in Panagrolaimus nematodes: origins of parthenogenesis, hermaphroditism and the Antarctic species P. davidi . BMC Evolutionary Biology 9: 15. Search in Google Scholar

Lukashin A. V. and Borodovsky M. 1998. GeneMark.hmm: new solutions for gene finding. Nucleic Acids Research 26: 1107–15.10.1093/nar/26.4.11071473379461475 Search in Google Scholar

Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10–2.10.14806/ej.17.1.200 Search in Google Scholar

Nadler S. A. , Carreno R. A. , Adams B. J. , Kinde H. , Baldwin J. G. and Mundo-Ocampo M. 2003. Molecular phylogenetics and diagnosis of soil and clinical isolates of Halicephalobus gingivalis (Nematoda: Cephalobina: Panagrolaimoidea), an opportunistic pathogen of horses. International Journal for Parasitology 33: 1115–25. Search in Google Scholar

Peters B. G. 1928. On the bionomics of the vinegar eelworm. Journal of Helminthology 6: 1–38.10.1017/S0022149X00029771 Search in Google Scholar

Ricci C. and Pagani M. 1997. Desiccation of Panagrolaimus rigidus (Nematoda): survival, reproduction and the influence on the internal clock. Hydrobiologia 347: 1–13. Search in Google Scholar

Schiffer P. H. , Danchin E. G. J. , Burnell A. M. , Schiffer A.-M. , Creevey C. J. , Wong S. , Dix I. , O’Mahony G. , Culleton B. A. , Rencurel C. , Stier G. , Martínez-Salazar A. , Marconi A. , Trivedi U. , Kroiher M. , Thorne M. A. S. , Schierenberg E. , Wiehe T. and Blaxter M. Under review. Signatures of the evolution of parthenogenesis and cryptobiosis in panagrolaimid nematodes. bioRxiv 159152. 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): 3210–2.10.1093/bioinformatics/btv35126059717 Search in Google Scholar

Srinivasan J. , Dillman A. R. , Macchietto M. G. , Heikkinen L. , Lakso M. , Fracchia K. M. , Antoshechkin I. , Mortazavi A. , Wong G. and Sternberg P. W. 2013. The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle. Genetics 193: 1279–95.10.1534/genetics.112.148809360610323410827 Search in Google Scholar

Stanke M. and Waack S. 2003. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19: ii215–ii225.10.1093/bioinformatics/btg108014534192 Search in Google Scholar

Steel H. , Vandecasteele B. , Willekens K. , Sabbe K. , Moens T. and Bert W. 2012. Nematode communities and macronutrients in composts and compost-amended soils as affected by feedstock composition. Applied Soil Ecology 61: 100–12.10.1016/j.apsoil.2012.05.004 Search in Google Scholar

Treonis A. M. and Wall D. H. 2005. Soil nematodes and desiccation survival in the extreme arid environment of the Antarctic Dry Valleys. Integrative and Comparative Biology 45: 741–50.10.1093/icb/45.5.74121676825 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. 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution 35: 543–48.10.1093/molbev/msx319585027829220515 Search in Google Scholar

Wharton D. A. and Barclay S. 1993. Anhydrobiosis in the free-living antarctic nematode Panagrolaimus davidi (Nematoda: Rhabditida). Fundamental and Applied Nematology 16: 17–22. Search in Google Scholar

Wiley E. O. 1978. The evolutionary species concept reconsidered. Systematic Zoology 27: 17–26.10.2307/2412809 Search in Google Scholar