{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T05:05:21Z","timestamp":1790053521929,"version":"4.0.1"},"reference-count":67,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian Science Foundation","award":["25-76-00014"],"award-info":[{"award-number":["25-76-00014"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"crossref"}]},{"award":["25-76-00014"],"award-info":[{"award-number":["25-76-00014"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Colletotrichum coccodes (Wallr.) S. Hughes is an important causal agent of potato black dot, but variation among isolates collected in Russia remains insufficiently characterized. In this study, 68 isolates obtained from potato tubers and stems collected in major potato-producing regions of Russia and Belarus were characterized using morphological, physiological, pathogenic, multilocus, and whole-genome approaches. The collection showed variation in colony pigmentation and sclerotial distribution, together with statistically significant differences in colony growth rate and lesion diameter in a wounded detached tuber-slice assay. Among the six isolates tested for temperature response, mean growth was highest at 25 \u00b0C among the tested temperatures and was strongly reduced at 35 \u00b0C. Multilocus sequence analysis of ITS, act, cal, and his3 loci identified five haplotypes, revealing limited sequence variation in the four loci analyzed and no obvious geographic pattern in this dataset. Comparative genome analysis of two C. coccodes isolates and one C. nigrum isolate revealed high genomic similarity between C. coccodes genomes, conserved repertoires of secreted proteins, effectors, carbohydrate-active enzymes, cytochrome P450 proteins, and secondary metabolite biosynthetic gene clusters, together with 407 orthogroups present in both sequenced C. coccodes isolates and absent from the single C. nigrum genome examined. These findings provide a comprehensive characterization of the collection of C. coccodes isolates from Russia and show that substantial phenotypic variation within the collection was accompanied by limited sequence variation in the analyzed loci, while representatives of two multilocus haplotypes remained highly similar at the whole-genome level.<\/jats:p>","DOI":"10.3390\/plants15182853","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T11:05:53Z","timestamp":1789988753000},"page":"2853","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Morphological, Physiological, Pathogenic, and Molecular Characterization of Colletotrichum coccodes Isolates Associated with Potato Black Dot"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-5018-1265","authenticated-orcid":false,"given":"Konstantin 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Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-1858-1346","authenticated-orcid":false,"given":"Kirill M.","family":"Vorobev","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Russian State Agrarian University\u2014Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5014-8375","authenticated-orcid":false,"given":"Fevzi S.-U.","family":"Dzhalilov","sequence":"additional","affiliation":[{"name":"Department of Plant Protection, Russian State Agrarian University\u2014Moscow Timiryazev Agricultural Academy, Timiryazevskaya Str. 49, 127434 Moscow, 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J. Potato Res."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1007\/s12230-018-9633-5","article-title":"Potato Black Dot\u2014The Elusive Pathogen, Disease Development and Management","volume":"95","author":"Johnson","year":"2018","journal-title":"Am. J. Potato Res."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1094\/PDIS.1999.83.6.561","article-title":"Effect of Colletotrichum coccodes on Potato Yield, Tuber Quality, and Stem Colonization During Spring and Autumn","volume":"83","author":"Tsror","year":"1999","journal-title":"Plant Dis."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1007\/BF02855598","article-title":"Occurrence, Development, and Losses Associated with Silver Scurf and Black Dot on Colorado Potatoes","volume":"56","author":"Hunger","year":"1979","journal-title":"Am. Potato J."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"249","DOI":"10.2298\/ZMSPN1324249S","article-title":"Morphological and Molecular Characterization of Colletotrichum coccodes Isolated from Pepper Cultivated in Bulgaria and Macedonia","volume":"124","author":"Stojanova","year":"2013","journal-title":"Zb. Matice Srp. Za Prir. Nauk."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"573-IN5","DOI":"10.1016\/S0007-1536(65)80035-3","article-title":"Studies on Colletotrichum coccodes: I. The taxonomic significance of variation in isolates from tomato roots","volume":"48","author":"Chesters","year":"1965","journal-title":"Trans. Br. Mycol. Soc."},{"key":"ref_7","first-page":"247","article-title":"Anthracnose of Tomato","volume":"38","author":"Kendrick","year":"1948","journal-title":"Phytopathology"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1094\/PHYTO-98-8-0901","article-title":"Variability in Morphology and Aggressiveness Among North American Vegetative Compatibility Groups of Colletotrichum coccodes","volume":"98","author":"Aqeel","year":"2008","journal-title":"Phytopathology"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1111\/j.1439-0434.1962.tb02045.x","article-title":"Investigations on Tomato Anthracnose.: III. The Influence of Amino Acids on the Growth of Colletotrichum coccodes (Wallr.) Hughes","volume":"45","author":"Loprieno","year":"1962","journal-title":"J. Phytopathol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1094\/PD-69-164","article-title":"Variation of Several Anthracnose Fungi in Virulence to Strawberry and Apple","volume":"69","author":"Maas","year":"1985","journal-title":"Plant Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"902","DOI":"10.1017\/S0043174500083570","article-title":"Colletotrichum coccodes: A Pathogen of Eastern Black Nightshade (Solanum ptycanthum)","volume":"33","author":"Andersen","year":"1985","journal-title":"Weed Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1094\/PDIS-91-7-0805","article-title":"Additional Vegetative Compatibility Groups in Colletotrichum coccodes Subpopulations from Europe and Israel","volume":"91","author":"Shcolnick","year":"2007","journal-title":"Plant Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1094\/PHYTO.2002.92.8.827","article-title":"Vegetative Compatibility Groups in Colletotrichum coccodes, the Causal Agent of Black Dot on Potato","volume":"92","author":"Nitzan","year":"2002","journal-title":"Phytopathology"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.1094\/PD-90-1287","article-title":"Vegetative Compatibility Groups and Aggressiveness of North American Isolates of Colletotrichum coccodes, the Causal Agent of Potato Black Dot","volume":"90","author":"Nitzan","year":"2006","journal-title":"Plant Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1094\/PHYTO-100-3-0271","article-title":"Vegetative Compatibility Groups in Colletotrichum coccodes Subpopulations from Australia and Genetic Links with Subpopulations from Europe\/Israel and North America","volume":"100","author":"Johnson","year":"2010","journal-title":"Phytopathology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1094\/PHYTO-96-1097","article-title":"Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses","volume":"96","author":"Heilmann","year":"2006","journal-title":"Phytopathology"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Alananbeh, K.M., Rivera, V., Bravo, I.A., Secor, G., and Gudmestad, N.C. (2024). Diversity of Genetic and Vegetative Compatibility Group of Colletotrichum coccodes Isolates from Chile Using Amplified Fragment Length Polymorphism Markers. J. Fungi, 10.","DOI":"10.3390\/jof10030200"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"809","DOI":"10.5513\/JCEA01\/21.4.2869","article-title":"Fungal Diversity in Tomato (Solanum lycopersicum) Leaves and Fruits in Russia","volume":"21","author":"Kokaeva","year":"2020","journal-title":"J. Cent. Eur. Agric."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1007\/s41348-017-0138-0","article-title":"Colletotrichum coccodes in Potato and Tomato Leaves in Russia","volume":"125","author":"Belov","year":"2018","journal-title":"J. Plant Dis. Prot."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Yarmeeva, M., Kutuzova, I., Kurchaev, M., Chudinova, E., Kokaeva, L., Belosokhov, A., Belov, G., Elansky, A., Pobedinskaya, M., and Tsindeliani, A. (2023). Colletotrichum Species on Cultivated Solanaceae Crops in Russia. Agriculture, 13.","DOI":"10.3390\/agriculture13030511"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1007\/s10658-024-02891-4","article-title":"Potato Leaf Infection Caused by Colletotrichum coccodes and C. Nigrum","volume":"170","author":"Chang","year":"2024","journal-title":"Eur. J. Plant Pathol."},{"key":"ref_22","first-page":"40","article-title":"Potato Black Dot","volume":"3","author":"Nikitina","year":"1972","journal-title":"Potato Veg."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1046\/j.1365-3059.2002.00690.x","article-title":"Detection of Colletotrichum coccodes from Soil and Potato Tubers by Conventional and Quantitative Real-time PCR","volume":"51","author":"Cullen","year":"2002","journal-title":"Plant Pathol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1094\/PDIS.1998.82.2.235","article-title":"Survival of Colletotrichum coccodes in Infected Tomato Tissue and in Soil","volume":"82","author":"Dillard","year":"1998","journal-title":"Plant Dis."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1007\/BF02883511","article-title":"Colonization of Rotation Crops and Weeds by the Potato Black Dot pathogen Colletotrichum coccodes","volume":"83","author":"Nitzan","year":"2006","journal-title":"Am. J. Potato Res."},{"key":"ref_26","unstructured":"Federal Agency on Technical Regulating and Metrology (2026, September 09). Seed Potatoes. Specifications and Methods of Determining the Quality [GOST 33996-2016]. Available online: https:\/\/gostassistent.ru\/doc\/e66607d0-327a-4dcb-a17a-cb2bd926113e."},{"key":"ref_27","unstructured":"Federal Agency on Technical Regulating and Metrology (2026, September 09). Seed Potatoes. Sampling and Methods of Diagnostics of Phytopathogens. Available online: https:\/\/gostassistent.ru\/doc\/6c266ad5-adb6-48ba-8c51-931bf0380479."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"127","DOI":"10.17660\/ActaHortic.2016.1142.20","article-title":"Isolation and Characterization of Colletotrichum coccodes from Potato in Bulgaria","volume":"1142","author":"Rodeva","year":"2016","journal-title":"Acta Hortic."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e12224","DOI":"10.1002\/ndr2.12224","article-title":"First Report of Colletotrichum coccodes Causing Black Dot on Potato in Mauritius","volume":"48","author":"Takooree","year":"2023","journal-title":"New Dis. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2746","DOI":"10.1094\/PDIS-01-22-0242-PDN","article-title":"First Report of Black Dot Caused by Colletotrichum coccodes on Potato in the Tibet Autonomous Region of China","volume":"106","author":"Zhong","year":"2022","journal-title":"Plant Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1094\/MPMI-22-12-1484","article-title":"Ammonium Secretion by Colletotrichum coccodes Activates Host NADPH Oxidase Activity Enhancing Host Cell Death and Fungal Virulence in Tomato Fruits","volume":"22","author":"Alkan","year":"2009","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.pbi.2009.06.004","article-title":"Fungal Phytotoxins as Mediators of Virulence","volume":"12","author":"Hertweck","year":"2009","journal-title":"Curr. Opin. Plant Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1146\/annurev-phyto-080516-035551","article-title":"Adaptation to the Host Environment by Plant-Pathogenic Fungi","volume":"55","author":"Rep","year":"2017","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/sj.jim.2900534","article-title":"Effects of Carbon Concentration and Carbon-to-Nitrogen Ratio on Growth, Conidiation, Spore Germination and Efficacy of the Potential Bioherbicide Colletotrichum coccodes","volume":"20","author":"Yu","year":"1998","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1111\/j.1365-3059.2004.01045.x","article-title":"Growth in Vitro and Infectivity of Colletotrichum coccodes on Potato Tubers at Different Temperatures","volume":"53","author":"Andrivon","year":"2004","journal-title":"Plant Pathol."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Gostin\u010dar, C. (2020). Towards Genomic Criteria for Delineating Fungal Species. J. Fungi, 6.","DOI":"10.3390\/jof6040246"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"103969","DOI":"10.1016\/j.fgb.2025.103969","article-title":"FungANI, a BLAST-Based Program for Analyzing Average Nucleotide Identity (ANI) between Two Fungal Genomes, Enables Easy Fungal Species Delimitation","volume":"177","author":"Lalanne","year":"2025","journal-title":"Fungal Genet. Biol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Buiate, E.A.S., Xavier, K.V., Moore, N., Torres, M.F., Farman, M.L., Schardl, C.L., and Vaillancourt, L.J. (2017). A Comparative Genomic Analysis of Putative Pathogenicity Genes in the Host-Specific Sibling Species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genom., 18.","DOI":"10.1186\/s12864-016-3457-9"},{"key":"ref_40","first-page":"315","article-title":"Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics","volume":"18","author":"White","year":"1990","journal-title":"PCR Protoc. Guide Methods Appl."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1080\/00275514.1999.12061051","article-title":"A Method for Designing Primer Sets for Speciation Studies in Filamentous Ascomycetes","volume":"91","author":"Carbone","year":"1999","journal-title":"Mycologia"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1094\/PDIS-10-14-1076-RE","article-title":"Investigation of the Colletotrichum gloeosporioides Species Complex Causing Peach Anthracnose in South Carolina","volume":"99","author":"Hu","year":"2015","journal-title":"Plant Dis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"115","DOI":"10.3114\/sim0011","article-title":"The Colletotrichum gloeosporioides Species Complex","volume":"73","author":"Weir","year":"2012","journal-title":"Stud. Mycol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"37","DOI":"10.3114\/sim0010","article-title":"The Colletotrichum acutatum Species Complex","volume":"73","author":"Damm","year":"2012","journal-title":"Stud. Mycol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality Assessment Tool for Genome Assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1186\/s13059-019-1891-0","article-title":"Improved Metagenomic Analysis with Kraken 2","volume":"20","author":"Wood","year":"2019","journal-title":"Genome Biol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e7359","DOI":"10.7717\/peerj.7359","article-title":"MetaBAT 2: An Adaptive Binning Algorithm for Robust and Efficient Genome Reconstruction from Metagenome Assemblies","volume":"7","author":"Kang","year":"2019","journal-title":"PeerJ"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D70","DOI":"10.1093\/nar\/gks1265","article-title":"Dfam: A Database of Repetitive DNA Based on Profile Hidden Markov Models","volume":"41","author":"Wheeler","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: Assessing Genome Assembly and Annotation Completeness with Single-Copy Orthologs","volume":"31","author":"Waterhouse","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1093\/molbev\/msab293","article-title":"eggNOG-Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale","volume":"38","author":"Cantalapiedra","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and Sensitive Protein Alignment Using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btu031","article-title":"InterProScan 5: Genome-Scale Protein Function Classification","volume":"30","author":"Jones","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1038\/s41587-021-01156-3","article-title":"SignalP 6.0 Predicts All Five Types of Signal Peptides Using Protein Language Models","volume":"40","author":"Teufel","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e201900429","DOI":"10.26508\/lsa.201900429","article-title":"Detecting Sequence Signals in Targeting Peptides Using Deep Learning","volume":"2","author":"Salvatore","year":"2019","journal-title":"Life Sci. Alliance"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1094\/MPMI-08-21-0201-R","article-title":"EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes","volume":"35","author":"Sperschneider","year":"2022","journal-title":"Mol. Plant-Microbe Interact."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkad328","article-title":"dbCAN3: Automated Carbohydrate-Active Enzyme and Substrate Annotation","volume":"51","author":"Zheng","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"W32","DOI":"10.1093\/nar\/gkaf334","article-title":"antiSMASH 8.0: Extended Gene Cluster Detection Capabilities and Analyses of Chemistry, Enzymology, and Regulation","volume":"53","author":"Blin","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: Phylogenetic Orthology Inference for Comparative Genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1134\/S002626171204011X","article-title":"Change in the Temperature Preferences of Beauveria Bassiana Sensu Lato Isolates in the Latitude Gradient of Siberia and Kazakhstan","volume":"81","author":"Kryukov","year":"2012","journal-title":"Microbiology"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/S0580-9517(09)70007-8","article-title":"Chapter II Fungal Culture Media","volume":"Volume 4","author":"Booth","year":"1971","journal-title":"Methods in Microbiology"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1080\/02681219180000581","article-title":"Sabouraud(\u2018s) Agar","volume":"29","author":"Odds","year":"1991","journal-title":"Med. Mycol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Ivors, K.L. (2015). Laboratory Protocols for Phytophthora Species, The American Phytopathological Society.","DOI":"10.1094\/9780890544969"}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2853\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T04:32:25Z","timestamp":1790051545000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2853"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":67,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182853"],"URL":"https:\/\/doi.org\/10.3390\/plants15182853","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,18]]}}}