{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T03:04:16Z","timestamp":1790651056708,"version":"4.1.0"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T00:00:00Z","timestamp":1478131200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The genus <jats:italic>Aphanomyces<\/jats:italic> (Saprolegniales, Oomycetes) includes species with a variety of ecologies from saprotrophs to plant and animal parasites. Two important species in this genus are <jats:italic>A. astaci,<\/jats:italic> the cause of crayfish plague and its close relative, <jats:italic>A. invadans<\/jats:italic>, which causes the epizootic ulcerative syndrome on fish. In this study, we have assembled and annotated the mitochondrial (mt) genomes of <jats:italic>A. astaci<\/jats:italic> and <jats:italic>A. invadans<\/jats:italic> from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respectively). The assembly was generated from <jats:italic>A. astaci<\/jats:italic> Pc-genotype strain APO3 and <jats:italic>A. invadans<\/jats:italic> strain NJM9701. The sizes of the mtDNAs were 49,489\u2009bp and 49,061\u2009bp for <jats:italic>A. astaci<\/jats:italic> and <jats:italic>A. invadans,<\/jats:italic> respectively. The species shared similar genetic content and organization encoding 35 proteins, two ribosomal RNAs, three putative open reading frames and 33 transfer RNAs of 19 amino acids for peptide synthesis. Both species also had a large inverted repeat region (LIR) of approximately 12\u2009kb, the LIR contained large and small ribosomal RNAs and eight protein coding genes. These annotated mt genomes serve as a valuable genetic backbone for further development of diagnostic methods and phylogenetic and migration studies of the animal parasitic species of <jats:italic>Aphanomyces<\/jats:italic>.<\/jats:p>","DOI":"10.1038\/srep36089","type":"journal-article","created":{"date-parts":[[2016,11,3]],"date-time":"2016-11-03T10:24:01Z","timestamp":1478168641000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans"],"prefix":"10.1038","volume":"6","author":[{"given":"Jenny","family":"Makkonen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arto","family":"Vesterbacka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frank","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Japo","family":"Jussila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Javier","family":"Di\u00e9guez-Uribeondo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raine","family":"Kortet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harri","family":"Kokko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,11,3]]},"reference":[{"key":"BFsrep36089_CR1","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1128\/EC.2.2.191-199.2003","volume":"2","author":"S Kamoun","year":"2003","unstructured":"Kamoun, S. Molecular genetics of pathogenic oomycetes. Eukaryot. Cell. 2(2), 191\u2013199 (2003).","journal-title":"Eukaryot. Cell"},{"key":"BFsrep36089_CR2","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1094\/PDIS-12-11-1036-FE","volume":"96","author":"FN Martin","year":"2012","unstructured":"Martin, F. N., Abad, G. Z., Balci, Y. & Ivors K. Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Dis. 96, 1080\u20131103 (2012).","journal-title":"Plant Dis"},{"key":"BFsrep36089_CR3","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s00709-011-0269-2","volume":"249","author":"GW Beakes","year":"2012","unstructured":"Beakes, G. W., Glockling, S. L. & Sekimoto, S. The evolutionary phylogeny of the oomycete \u201cfungi\u201d. Protoplasma. 249(1), 3\u201319, doi: 10.1007\/s00709-011-0269-2 (2012).","journal-title":"Protoplasma"},{"key":"BFsrep36089_CR4","doi-asserted-by":"crossref","unstructured":"Cerenius, L., Andersson, G. & S\u00f6derh\u00e4ll, K. Aphanomyces astaci and Crustaceans in Oomycete Genetics and Genomics - Diversity, Interactions and Research Tools (eds Lamour, K. & Kamoun, S. ) 425\u2013434 (Wiley-Blackwell, 2009).","DOI":"10.1002\/9780470475898.ch21"},{"key":"BFsrep36089_CR5","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.fgb.2009.02.004","volume":"46","author":"J Di\u00e9guez-Uribeondo","year":"2009","unstructured":"Di\u00e9guez-Uribeondo, J. et al. Phylogenetic relationships among plant and animal parasites, and saprotrophs in Aphanomyces (Oomycetes). Fungal Gen. Biol. 46, 365\u2013376 (2009).","journal-title":"Fungal Gen. Biol"},{"key":"BFsrep36089_CR6","first-page":"529","volume":"9","author":"F Schikora","year":"1906","unstructured":"Schikora, F. Die Krebspest. Fisch. Zeit. 9, 529\u2013532, in German (1906).","journal-title":"Fisch. Zeit."},{"key":"BFsrep36089_CR7","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1111\/j.1365-2761.1995.tb00302.x","volume":"18","author":"LG Willoughby","year":"1995","unstructured":"Willoughby, L. G., Roberts, R. J. & Chinabut, S. Aphanomyces invaderis sp. nov., the fungal pathogen of freshwater tropical fish affected by epizootic ulcerative syndrome. J. Fish Dis. 18(3), 273\u2013275 (1995).","journal-title":"J. Fish Dis"},{"key":"BFsrep36089_CR8","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1111\/j.1865-1682.2011.01241.x","volume":"59","author":"B Oidtmann","year":"2012","unstructured":"Oidtmann, B. Review of biological factors relevant to import risk assessments for Epizootic Ulcerative Syndrome (Aphanomyces invadans). Transbound. Emerg. Dis. 59, 26\u201339 (2012).","journal-title":"Transbound. Emerg. Dis"},{"key":"BFsrep36089_CR9","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1099\/00221287-60-1-77","volume":"60","author":"T Unestam","year":"1970","unstructured":"Unestam, T. & Weiss, D. W. The host-parasite relationship between freshwater crayfish and the crayfish disease fungus Aphanomyces astaci: responses to infection by a susceptible and a resistant species. J. Gen. Microbiol. 60(1), 77\u201390 (1970).","journal-title":"J. Gen. Microbiol."},{"key":"BFsrep36089_CR10","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1038\/icb.1975.40","volume":"53","author":"T Unestam","year":"1976","unstructured":"Unestam, T. Defense reactions in and susceptibility of Australian and New Guinean freshwater crayfish to European crayfish plague fungus. Aust. J. Exp. Biol. Med. Sci. 53(5), 349\u2013359 (1976).","journal-title":"Aust. J. Exp. Biol. Med. Sci."},{"key":"BFsrep36089_CR11","doi-asserted-by":"crossref","first-page":"603","DOI":"10.20506\/rst.15.2.943","volume":"15","author":"DJ Alderman","year":"1996","unstructured":"Alderman, D. J. Geographical spread of bacterial and fungal diseases of crustaceans. Rev. Off. Int. Epizoot. 15(2), 603\u2013632 (1996).","journal-title":"Rev. Off. Int. Epizoot"},{"key":"BFsrep36089_CR12","unstructured":"Souty-Grosset, C., Holdich, D. M., No\u00ebl, P. Y., Reynolds, J. D. & Haffner P. (eds), Atlas of Crayfish in Europe (Mus\u00e9um national d\u2019Histoire naturelle, 2006)."},{"key":"BFsrep36089_CR13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/0044-8486(94)90243-7","volume":"126","author":"TS Huang","year":"1994","unstructured":"Huang, T. S., Cerenius, L. & S\u00f6derh\u00e4ll, K. Analysis of genetic diversity in the crayfish plague fungus, Aphanomyces astaci, by random amplification of polymorphic DNA. Aquaculture 126, 1\u20139 (1994).","journal-title":"Aquaculture"},{"key":"BFsrep36089_CR14","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1016\/S0953-7562(09)80716-8","volume":"99","author":"J Di\u00e9guez-Uribeondo","year":"1995","unstructured":"Di\u00e9guez-Uribeondo, J., Huang, T.-S., Cerenius, L. & S\u00f6derh\u00e4ll, K. Physiological adaptation of an Aphanomyces astaci strain isolated from the freshwater crayfish Procambarus clarkii. Mycol. Res. 99(5), 574\u2013578 (1995).","journal-title":"Mycol. Res."},{"key":"BFsrep36089_CR15","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.jip.2011.08.002","volume":"108","author":"E Kozub\u00edkov\u00e1","year":"2011","unstructured":"Kozub\u00edkov\u00e1, E., Viljamaa-Dirks, S., Heinikainen, S. & Petrusek, A. Spiny-cheek crayfish Orconectes limosus carry a novel genotype of the crayfish plague pathogen Aphanomyces astaci. J. Invert. Pathol. 108, 214\u2013216 (2011).","journal-title":"J. Invert. Pathol"},{"key":"BFsrep36089_CR16","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.fgb.2012.05.014","volume":"49","author":"J Makkonen","year":"2012","unstructured":"Makkonen, J., Jussila, J. & Kokko, H. The diversity of the pathogenic oomycete (Aphanomyces astaci) chitinase genes within the genotypes indicate adaptation to its hosts. Fungal Gen. Biol. 49(8), 635\u2013642 (2012).","journal-title":"Fungal Gen. Biol"},{"key":"BFsrep36089_CR17","doi-asserted-by":"crossref","unstructured":"Jussila, J., Vrezec, A., Makkonen, J., Kortet, R. & Kokko, H. Invasive crayfish and their invasive diseases in Europe with the focus on the virulence evolution of the crayfish plague in Biological invasions in changing ecosystems. Vectors, ecological impacts, management and predictions (ed. Canning-Clode, J. ) Ch. 8, 183\u2013211 (De Gruyter Open Ltd, 2015).","DOI":"10.1515\/9783110438666-013"},{"key":"BFsrep36089_CR18","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1007\/s11160-013-9335-5","volume":"24","author":"D Kamilya","year":"2014","unstructured":"Kamilya, D. & Baruah A. Epizootic ulcerative syndrome (EUS) in fish: history and current status of understanding. Rev. Fish Biol. Fisher. 24, 369\u2013380 (2014).","journal-title":"Rev. Fish Biol. Fisher"},{"key":"BFsrep36089_CR19","doi-asserted-by":"crossref","first-page":"41","DOI":"10.3147\/jsfp.6.41","volume":"6","author":"S Egusa","year":"1971","unstructured":"Egusa, S. & Masuda, N. A new fungal disease of Plecoglossus altivelis. Fish Pathol. 6, 41\u201346 (1971).","journal-title":"Fish Pathol"},{"key":"BFsrep36089_CR20","unstructured":"Food and agriculture organization of the United Nations (FAO). Report of the international emergency disease investigation task force on a serious finfish disease in Southern Africa. Available at: http:\/\/www.fao.org\/3\/a-i0778e.pdf. (Accessed: 30th January 2016) (2009)."},{"key":"BFsrep36089_CR21","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1046\/j.1365-2761.2003.00448.x","volume":"26","author":"JH Lilley","year":"2003","unstructured":"Lilley, J. H. et al. Molecular characterization of the fish-pathogenic fungus Aphanomyces invadans. J. Fish Dis. 26, 263\u2013275 (2003).","journal-title":"J. Fish Dis"},{"key":"BFsrep36089_CR22","doi-asserted-by":"crossref","first-page":"e35568","DOI":"10.1371\/journal.pone.0035568","volume":"7","author":"CA Boys","year":"2012","unstructured":"Boys, C. A. et al. Emergence of epizootic ulcerative syndrome in native fish of the Murray\u2013Darling river system, Australia: hosts, distribution and possible vectors. PLoS One 7, e35568 (2012).","journal-title":"PLoS One"},{"key":"BFsrep36089_CR23","first-page":"11","volume":"12","author":"K S\u00f6derh\u00e4ll","year":"1999","unstructured":"S\u00f6derh\u00e4ll, K. & Cerenius, L. The crayfish plague fungus: history and recent advances. Freshw. Crayfish 12, 11\u201335 (1999).","journal-title":"Freshw. Crayfish"},{"key":"BFsrep36089_CR24","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/0147-5975(90)90058-2","volume":"14","author":"H F\u00f6rster","year":"1990","unstructured":"F\u00f6rster, H. & Coffey, M. D. Mating behavior of Phytophthora parasitica: evidence for sexual recombination in oospores using DNA restriction fragment length polymorphisms as genetic markers. Exp. Mycol. 14, 351\u2013359 (1990).","journal-title":"Exp. Mycol."},{"key":"BFsrep36089_CR25","doi-asserted-by":"publisher","first-page":"e00731","DOI":"10.7554\/eLife.00731","volume":"2","author":"K Yoshida","year":"2013","unstructured":"Yoshida, K. et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. eLife 2, e00731, doi: 10.7554\/eLife.00731 (2013).","journal-title":"eLife"},{"key":"BFsrep36089_CR26","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1038\/ncomms3172","volume":"4","author":"MD Martin","year":"2013","unstructured":"Martin, M. D. et al. Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat. Commun. 4, 2172 (2013).","journal-title":"Nat. Commun."},{"key":"BFsrep36089_CR27","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1093\/molbev\/msu086","volume":"31","author":"MD Martin","year":"2014","unstructured":"Martin, M. D., Ho, S. Y. H., Wales, N., Ristaino, J. B. & Gilbert, T. P. Persistence of the mitochondrial lineage responsible for the Irish potato famine in extant new world Phytophthora infestans. Mol. Biol. Evol. 31, 1414\u20131420 (2014).","journal-title":"Mol. Biol. Evol."},{"key":"BFsrep36089_CR28","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1007\/s002940050220","volume":"31","author":"B Paquin","year":"1997","unstructured":"Paquin, B. et al. The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr. Genet. 31, 380\u2013395 (1997).","journal-title":"Curr. Genet."},{"key":"BFsrep36089_CR29","doi-asserted-by":"publisher","first-page":"R73","DOI":"10.1186\/gb-2010-11-7-r73","volume":"11","author":"CA L\u00e9vesque","year":"2010","unstructured":"L\u00e9vesque, C. A. et al. Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11, R73, doi: 10.1186\/gb-2010-11-7-r73 (2010).","journal-title":"Genome Biol"},{"key":"BFsrep36089_CR30","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1080\/15572536.2005.11832898","volume":"96","author":"WS Grayburn","year":"2004","unstructured":"Grayburn, W. S., Hudspeth, D. S. S., Gane, M. K. & Hudspeth, M. E. S. The mitochondrial genome of Saprolegnia ferax: organization, gene content, and nucleotide sequence. Mycologia 96, 980\u2013987 (2004).","journal-title":"Mycologia"},{"key":"BFsrep36089_CR31","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1007\/s00294-007-0121-6","volume":"51","author":"FN Martin","year":"2007","unstructured":"Martin, F. N., Bensasson, D., Tyler, B. M. & Boore, J. L. Mitochondrial genome sequences and comparative genomics of Phytophthora ramorum and P. sojae. Curr. Genet. 51, 285\u2013296 (2007).","journal-title":"Curr. Genet."},{"key":"BFsrep36089_CR32","first-page":"1550","volume":"61","author":"MA O\u2019Brien","year":"2014","unstructured":"O\u2019Brien, M. A., Misner, I. & Lane, C. E. Mitochondrial genome sequences and comparative genomics of Achlya hypogyna and Thraustotheca clavata. J. Eukaryot. Microbiol. 61(2), 1550\u20137408 (2014).","journal-title":"J. Eukaryot. Microbiol."},{"key":"BFsrep36089_CR33","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1094\/MPMI-05-15-0112-R","volume":"28","author":"L Derevnina","year":"2015","unstructured":"Derevnina, L. et al. Genome sequence and architecture of the tobacco downy mildew pathogen, Peronospora tabacina. Molec. Plant Microbe Interact. 28, 1198\u20132015 (2015).","journal-title":"Molec. Plant Microbe Interact"},{"key":"BFsrep36089_CR34","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1007\/s00294-005-0016-3","volume":"49","author":"C Avila-Adame","year":"2006","unstructured":"Avila-Adame, C. et al. Mitochondrial genome sequences and molecular evolution of the Irish potato famine pathogen, Phytophthora infestans. Curr. Genet. 49(1), 39\u201346 (2006).","journal-title":"Curr. Genet"},{"key":"BFsrep36089_CR35","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1007\/s00294-015-0480-3","volume":"61","author":"ES Lassiter","year":"2015","unstructured":"Lassiter, E. S. et al. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species. Curr. Genet. 61, 567\u2013577 (2015).","journal-title":"Curr. Genet"},{"key":"BFsrep36089_CR36","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.gene.2015.08.036","volume":"575","author":"S Tangphatsornruang","year":"2016","unstructured":"Tangphatsornruang, S. et al. Comparative mitochondrial genome analysis of Pythium insidiosum and related oomycete species provides new insights into genetic variation and phylogenetic relationships. Gene 575(1), 34\u201341 (2016).","journal-title":"Gene"},{"key":"BFsrep36089_CR37","first-page":"3487","volume":"27","author":"WJ Lu","year":"2015","unstructured":"Lu, W. J., Hu, W. G. & Wang, G. P. Complete mitochondrial genome of Pseudoperonospora cubensis. Mitochondr. DNA 27, 3487\u20133488 (2015).","journal-title":"DNA"},{"key":"BFsrep36089_CR38","unstructured":"Russ, C., Tyler, B., Di\u00e9guez-Uribeondo, J. & Van West, P. Aphanomyces WGS initiative. Available at: https:\/\/olive.broadinstitute.org\/projects\/aphanomyces_pathogens. (Accessed: 23th May 2016) (2014)."},{"key":"BFsrep36089_CR39","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/BF00436880","volume":"12","author":"SA McNabb","year":"1987","unstructured":"McNabb, S. A., Boyd, D. A., Belkhiri, A., Dick, M. W. & Klassen, G. R. An inverted repeat comprises more than three-quarters of the mitochondrial genome in two species of Pythium. Curr. Genet. 12(3), 205\u2013208 (1987).","journal-title":"Curr. Genet."},{"key":"BFsrep36089_CR40","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/0147-5975(88)90038-2","volume":"12","author":"SA McNabb","year":"1988","unstructured":"McNabb, S. A. & Klassen, G. R. Uniformity of mitochondrial DNA complexity in oomycetes and the evolution of the inverted repeat. Exp. Mycol. 12(3), 233\u2013242 (1988).","journal-title":"Exp. Mycol."},{"key":"BFsrep36089_CR41","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1073\/pnas.80.1.142","volume":"80","author":"ME Hudspeth","year":"1983","unstructured":"Hudspeth, M. E., Shumard, D. S., Bradford, C. J. & Grossman, L. I. Organization of Achlya mtDNA: A population with two orientations and a large inverted repeat containing the rRNA genes. P. Natl. Acad. Sci. USA 80(1), 142\u2013146 (1983).","journal-title":"P. Natl. Acad. Sci. USA"},{"key":"BFsrep36089_CR42","first-page":"571","volume":"62","author":"DA Boyd","year":"1984","unstructured":"Boyd, D. A., Hobman, T. C., Gruenke, S. A. & Klassen, G. R. Evolutionary stability of mitochondrial DNA organization in Achlya. Can. J. Biochem. Cell B. 62(7), 571\u2013576 (1984).","journal-title":"Cell B"},{"key":"BFsrep36089_CR43","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/s00294-008-0196-8","volume":"54","author":"FN Martin","year":"2008","unstructured":"Martin, F. N. Mitochondrial haplotype determination in the oomycete plant pathogen Phytophthora ramorum. Curr. Genet. 54, 23\u201334 (2008).","journal-title":"Curr. Genet"},{"key":"BFsrep36089_CR44","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1139\/cjb-77-12-1790","volume":"77","author":"A Riethm\u00fcller","year":"1999","unstructured":"Riethm\u00fcller, A., Michael Wei\u03b2, M. & Oberwinkler, F. Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences. Can. J. Bot. 77, 1790\u20131800 (1999).","journal-title":"Can. J. Bot."},{"key":"BFsrep36089_CR45","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1111\/j.1755-0998.2011.03041.x","volume":"11","author":"GP Robideau","year":"2011","unstructured":"Robideau, G. P. et al. DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol. Ecol. Res. 11(6), 1002\u20131011, doi: 10.1111\/j.1755-0998.2011.03041.x (2011).","journal-title":"Mol. Ecol. Res."},{"key":"BFsrep36089_CR46","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1046\/j.1471-8286.2003.00378.x","volume":"3","author":"RAM Wattier","year":"2003","unstructured":"Wattier, R. A. M. et al. Sequence variation of intergenic mitochondrial DNA spacers (mtDNA-IGS) of Phytophthora infestans (Oomycetes) and related species. Mol. Ecol. Notes 3(1), 136\u2013138 (2003).","journal-title":"Mol. Ecol. Notes"},{"key":"BFsrep36089_CR47","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1094\/PHYTO-04-11-0115","volume":"102","author":"FN Martin","year":"2012","unstructured":"Martin, F. N. & Coffey, M. D. Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi. Phytopathology 102(2), 229\u2013239 (2012).","journal-title":"Phytopathology"},{"key":"BFsrep36089_CR48","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.mimet.2013.08.001","volume":"95","author":"Z-H Yang","year":"2013","unstructured":"Yang, Z.-H. et al. Mitochondrial DNA polymorphisms in Phytophthora infestans: New haplotypes are identified and re-defined by PCR. J. Microbiol. Meth. 95(2), 117\u2013121 (2013).","journal-title":"J. Microbiol. Meth."},{"key":"BFsrep36089_CR49","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1016\/j.funbio.2013.10.007","volume":"118","author":"S Rezinciuc","year":"2014","unstructured":"Rezinciuc, S., Galindo, J. & Montserrat, J. & Di\u00e9guez-Uribeondo J. AFLP-PCR and RAPD-PCR evidences of the transmission of the pathogen Aphanomyces astaci (Oomycetes) to wild populations of European crayfish from the invasive crayfish species, Procambarus clarkii. Fungal Biol. 118(7), 612\u2013620 (2014).","journal-title":"Fungal Biol"},{"key":"BFsrep36089_CR50","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1577\/H03-047.1","volume":"16","author":"P Phadree","year":"2004","unstructured":"Phadree, P., Kurata, O., Hatai, K., Hirono, I. & Aoki, T. Detection and identification of fish-pathogenic Aphanomyces piscicida using polymerase chain reaction (PCR) with species-specific primers. J. Aquat. Anim. Health 16(4), 220\u2013230 (2004).","journal-title":"J. Aquat. Anim. Health"},{"key":"BFsrep36089_CR51","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1007\/BF00443081","volume":"64","author":"K S\u00f6derh\u00e4ll","year":"1978","unstructured":"S\u00f6derh\u00e4ll, K., Svensson, E. & Unestam, T. Chinase and protease activities in germinating zoospore cysts of the parasitic fungus, Aphanomyces astaci, Oomycetes. Mycopathologia 64, 9\u201311 (1978).","journal-title":"Mycopathologia"},{"key":"BFsrep36089_CR52","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1089\/cmb.2009.0238","volume":"17","author":"S Boisvert","year":"2010","unstructured":"Boisvert, S., Laviolette, F. & Corbeil, J. Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J. Comput. Biol. 17(11), 1401\u20131415 (2010).","journal-title":"J. Comput. Biol."},{"key":"BFsrep36089_CR53","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","volume":"25","author":"TM Lowe","year":"1997","unstructured":"Lowe, T. M. & Eddy, S. R. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955\u2013964 (1997).","journal-title":"Nucl. Acids Res."},{"key":"BFsrep36089_CR54","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","volume":"28","author":"M Kearse","year":"2012","unstructured":"Kearse, M., et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12), 1647\u20131649 (2012).","journal-title":"Bioinformatics"},{"key":"BFsrep36089_CR55","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1093\/bioinformatics\/bth155","volume":"20","author":"I Milne","year":"2004","unstructured":"Milne, I. et al. TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20, 1806\u20131807 (2004).","journal-title":"Bioinformatics"},{"key":"BFsrep36089_CR56","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","volume":"52","author":"S Guindon","year":"2003","unstructured":"Guindon, S. & Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696\u2013704 (2003).","journal-title":"Syst. Biol."},{"key":"BFsrep36089_CR57","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1093\/bioinformatics\/17.8.754","volume":"17","author":"JP Huelsenbeck","year":"2001","unstructured":"Huelsenbeck, J. P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8), 754\u2013755 (2001).","journal-title":"Bioinformatics"},{"key":"BFsrep36089_CR58","doi-asserted-by":"crossref","first-page":"2620","DOI":"10.1093\/bioinformatics\/btq484","volume":"26","author":"N Darzentas","year":"2010","unstructured":"Darzentas, N. Circoletto: Visualizing sequence similarity with circos. Bioinformatics 26(20), 2620\u20132621 (2010).","journal-title":"Bioinformatics"},{"key":"BFsrep36089_CR59","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25, 3389\u20133402 (1997).","journal-title":"Nucl. Acids Res"},{"key":"BFsrep36089_CR60","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","volume":"19","author":"M Krzywinski","year":"2009","unstructured":"Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Res. 19(9), 1639\u20131645 (2009).","journal-title":"Genome Res"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep36089.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep36089","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep36089.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T00:25:42Z","timestamp":1672878342000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep36089"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,11,3]]},"references-count":60,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12,21]]}},"alternative-id":["BFsrep36089"],"URL":"https:\/\/doi.org\/10.1038\/srep36089","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,11,3]]},"assertion":[{"value":"20 June 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 October 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 November 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"36089"}}