Lifestyle, mating type and mitochondrial genome features of the plant pathogen Calonectria hawksworthii (Hypocreales, Nectriaceae) as revealed by genome analyses

References

• Al-Reedy RM, Malireddy R, Dillman CB, Kennell JC. 2012. Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame. Fungal Genet Biol. 49(1):2–14. doi:10.1016/j.fgb.2011.11.008
   PubMed Web of Science ®Google Scholar
• Alfenas RF, Lombard L, Pereira OL, Alfenas AC, Crous PW. 2015. Diversity and potential impact of Calonectria species in Eucalyptus plantations in Brazil. Stud Mycol. 80:89–103. doi:10.1016/j.simyco.2014.11.002
   PubMed Web of Science ®Google Scholar
• Araki Y, Awakawa T, Matsuzaki M, Cho R, Matsuda Y, Hoshino S, Shinohara Y, Yamamoto M, Kido Y, Inaoka DK, et al. 2019. Complete biosynthetic pathways of ascofuranone and ascochlorin in Acremonium egyptiacum. Proc Natl Acad Sci USA. 116(17):8269–8274. doi:10.1073/pnas.1819254116
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. doi:10.1089/cmb.2012.0021
   PubMed Web of Science ®Google Scholar
• Belyayev A. 2014. Bursts of transposable elements as an evolutionary driving force. J Evol Biol. 27:2573–2584. doi:10.1111/jeb.12513.
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. doi:10.1016/j.ympev.2012.08.023
   PubMed Web of Science ®Google Scholar
• Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, Medema MH, Weber T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acid Res. 47(W1):W81–W87. doi:10.1093/nar/gkz310
   PubMed Web of Science ®Google Scholar
• Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics. 27(4):578–579. doi:10.1093/bioinformatics/btq683
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120. doi:10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Buchfink B, Xie C, Huson DH. 2015. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 12:59–60. doi:10.1038/nmeth.3176
   PubMed Web of Science ®Google Scholar
• Bushley KE, Raja R, Jaiswal P, Cumbie JS, Nonogaki M, Boyd AE, Owensby CA, Knaus BJ, Elser J, Miller D, et al. 2013. The genome of Tolypocladium inflatum: evolution, organization, and expression of the cyclosporin biosynthetic gene cluster. PLoS Genet. 9(6):e1003496. doi:10.1371/journal.pgen.1003496
   PubMed Web of Science ®Google Scholar
• Busk PK, Pilgaard B, Lezyk MJ, Meyer AS, Lange L. 2017. Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. BMC Bioinf. 18:214. doi:10.1186/s12859-017-1625-9
   PubMed Web of Science ®Google Scholar
• Campbell JA, Davies GJ, Bulone V, Henrissat B. 1997. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J. 326(Pt 3):929–939. doi:10.1042/bj3260929u
   PubMedGoogle Scholar
• Carbone I, Kohn LM. 1999. A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia. 91(3):553–556. doi:10.2307/3761358
   Web of Science ®Google Scholar
• Chen W, Lee M-K, Jefcoate C, Kim S-C, Chen F, Yu J-H. 2014. Fungal cytochrome P450 monooxygenases: their distribution, structure, functions, family expansion, and evolutionary origin. Genome Biol Evol. 6(7):1620–1634. doi:10.1093/gbe/evu132
   PubMed Web of Science ®Google Scholar
• Cortázar AR, Aransay AM, Alfaro M, Oguiza JA, Lavín JL. 2014. SECRETOOL: integrated secretome analysis tool for fungi. Amino Acids. 46:471–473. doi:10.1007/s00726-013-1649-z
   PubMed Web of Science ®Google Scholar
• Crouch JA, Dawe A, Aerts A, Barry K, Churchill ACL, Grimwood J, Hillman BI, Milgroom MG, Pangilinan J, Smith M, et al. 2020. Genome sequence of the chestnut blight fungus Cryphonectria parasitica EP155: a fundamental resource for and archetypal invasive plant pathogen. Phytopathology. 110(6):1080–1188. doi:10.1094/PHYTO-12-19-0478-A
   Web of Science ®Google Scholar
• Crous PW. 2002. Taxonomy and pathology of Cylindrocladium (Calonectria) and allied genera. St.Paul (MN): APS Press.
   Google Scholar
• Crous PW, Groenewald JZ, Risede JM, Simoneau P, Hywel-Jones NL. 2004. Calonectria species and their Cylindrocladium anamorphs: species with sphaeropedunculate vesicles. Stud Mycol. 50:415–430.
   Google Scholar
• Crous PW, Wingfield MJ, Cheewangkoon R, Carnegie AJ, Burgess TI, Summerell BA, Edwards J, Taylor PWJ, Groenewald JZ. 2019. Foliar pathogens of eucalypts. Stud Mycol. 94:125–298. doi:10.1016/j.simyco.2019.08.001
   PubMed Web of Science ®Google Scholar
• De Hoog GS, Van den Ende AHGG. 1998. Molecular diagnostics of clinical strains of filamentous Basidiomycetes. Mycoses. 41:183–189. doi:10.1111/j.1439-0507.1998.tb00321.x
   PubMed Web of Science ®Google Scholar
• De Man TJB, Stajich JE, Kubiecek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SSL, Barribeau SM. 2016. Small genome of the fungus Escovopsis weberi a specialized disease agent of ant agriculture. Proc Natl Acad Sci USA. 113(23):3567–3572. doi:10.1073/pnas.1518501113
   PubMedGoogle Scholar
• Druzhinina IS, Shelest E, Kubicek CP. 2012. Novel traits of Trichoderma predicted through the analysis of its secretome. FEMS Microbiol Lett. 337(1):1–9.
   PubMed Web of Science ®Google Scholar
• El-Gebali SJ, Mistry A, Bateman SR, Eddy A, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, et al. 2019. The Pfam protein families database in 2019. Nucleic Acids Res. 47(D1):D427–D432. doi:10.1093/nar/gky995
   PubMed Web of Science ®Google Scholar
• Farr DF, Rossman AY. Fungal databases, U.S. national fungus collections, ARS, USDA. [acessed 2021 May 13]. https://nt.ars-grin.gov/fungaldatabases/.
   Google Scholar
• Flutre T, Duprat E, Fauillet C, Quesneville H. 2011. Considering transposable elements diversification in de novo annotation approaches. PLOS ONE. 6:e16526. doi:10.1371/journal.pone.0016526
   PubMed Web of Science ®Google Scholar
• Gai Y, Pan R, Peng X. 2020. A phylogenomic tree of fungi: evolutionary relationships among Calonectria ilicicola and 586 fungal mitochondrial genomes. Mitochondrial DNA Part B. 5(2):1709–1711. doi:10.1080/23802359.2020.1749163
   Web of Science ®Google Scholar
• Girard V, Dieryckx C, Job C, Job D. 2013. Secretomes: the fungal strike force. Proteomics. 13(3–4):597–608. doi:10.1002/pmic.201200282
   PubMed Web of Science ®Google Scholar
• Godio RP, Martín JF. 2009. Modified oxidosqualene cyclases in the formation of the bioactive secondary metabolites: biosynthesis of the antitumor clavaric acid. Fungal Genet Biol. 46(3):232–242. doi:10.1016/j.fgb.2008.12.002
   PubMed Web of Science ®Google Scholar
• Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, et al. 2011. The iPlant collaborative: cyberinfrastructure for plant biology. Front Plant Sci. 2:34. doi:10.3389/fpls.2011.00034
   PubMed Web of Science ®Google Scholar
• Grant JR, Stothard P. 2008. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36:W181–W184. doi:10.1093/nar/gkn179
   PubMed Web of Science ®Google Scholar
• Hoff KJ, Stanke M. 2013. WebAUGUSTUS – a web service for training AUGUSTUS and predicting genes in eukaryotes. Nucleic Acids Res. 41:W123–W128. doi:10.1093/nar/gkt418
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53(6):904–913. doi:10.1080/10635150490522629
   PubMed Web of Science ®Google Scholar
• Karimi Jasni M, Mehrabi R, Collemare J, Mesarich CH, de Wit PJGM. 2015. The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant-pathogen interactions. Front Plant Sci. 6:584. doi:10.3389/fpls.2015.00584
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi:10.1093/molbev/mst010
   PubMed Web of Science ®Google Scholar
• Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der Hooft JJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, et al. 2020. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res. 48(D1):D454–D458. doi:10.1093/nar/gkz882
   PubMed Web of Science ®Google Scholar
• King R, Urban M, Lauder RP, Hawkins N, Evans M, Plummer A, Halsey K, Lovegrove A, Hammond-Kosack K, Rudd JJ. 2017. A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces. PLoS Pathog. 13(10):e1006672. doi:10.1371/journal.ppat.1006672
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGAX: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 35(6):1547–1549. doi:10.1093/molbev/msy096
   PubMed Web of Science ®Google Scholar
• Levasseur A, Drula E, Lombard V, Coutinho P, Henrissat B. 2013. Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes. Biotechnol Biofuels. 6(1):41. doi:10.1186/1754-6834-6-41
   PubMedGoogle Scholar
• Li JQ, Wingfield BD, Wingfield MJ, Barnes I, Fourie A, Crous PW, Chen SF. 2020. Mating genes in Calonectria and evidence for a heterothallic ancestral state. Persoonia. 45:163–176. doi:10.3767/persoonia.2020.45.06
   PubMed Web of Science ®Google Scholar
• Lin X, Yuan S, Chen S, Chen B, Xu H, Liu L, Li H, Gae Z. 2019. Heterologous expression of ilicicolin H biosynthetic gene cluster and production of a new potent antifungal reagent, ilicicolin. Molecules. 24(12):2267. doi:10.3390/molecules24122267
   Web of Science ®Google Scholar
• Liu F, Chen S, Ferreira MA, Chang R, Sayari M, Kanzi AM, Wingfield WD, Wingfield MJ, Pizarro D, Crespo A, et al. 2019. Draft genome sequences of five Calonectria species from Eucalyptus plantations in China, Celoporthe dispersa, Sporothrix phasma and Alectoria sarmentosa. IMA Fungus. 10:22. doi:10.1186/s43008-019-0023-5
   PubMed Web of Science ®Google Scholar
• Liu QL, Li JQ, Wingfield MJ, Duong TA, Wingfield BD, Crous PW, Chen SF. 2020. Reconsideration of species boundaries and proposed DNA barcodes for Calonectria. Stud Mycol. 97:100106. doi:10.1016/j.simyco.2020.08.001
   PubMedGoogle Scholar
• Lombard L, Crous PW, Wingfield BD, Wingfield MJ. 2010. Phylogeny and systematics of the genus Calonectria. Stud Mycol. 66:31–69. doi:10.3114/sim.2010.66.03
   PubMedGoogle Scholar
• Lombard V, Ramulu HG, Drula E, Coutinho PM, Hensissat B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42:D490–D495. doi:10.1093/nar/gkt1178
   PubMed Web of Science ®Google Scholar
• Lombard L, Wingfield MJ, Alfenas AC, Crous PW. 2016. The forgotten Calonectria collection: pouring old wine into new bags. Stud Mycol. 85:159–198. doi:10.1016/j.simyco.2016.11.004
   PubMedGoogle Scholar
• Makałowski W, Gotea V, Pande A, Makałowska I. 2019. Transposable Elements: Classification, Identification, and Their Use as a Tool for Comparative Genomics. Methods Mol Biol. 177–207.
   PubMedGoogle Scholar
• Malapi-Wight M, Veltri D, Gehesquiere B, Heungens K, Rivera Y, Salgado-Salazar C, Crouch JA. 2019. Global distribution of mating types shows limited opportunities for mating across populations of fungi causing boxwood blight disease. Fungal Genet Biol. 131:103246. doi:10.1016/j.fgb.2019.103246
   PubMed Web of Science ®Google Scholar
• Martinez D, Larrondo LF, Putnam N, Gelpke MD, Huang K, Chapman J, Helfenbein KG, Ramaiya P, Detter JC, Larimer F et al.$3$2 2004. Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol. 22:695–700. doi:10.1038/nbt967.
   PubMed Web of Science ®Google Scholar
• Moktali V, Park J, Fedorova-Abrams ND, Park B, Choi J, Lee Y-H, Kang S. 2012. Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes. BMC Genomics. 13:525. doi:10.1186/1471-2164-13-525
   PubMed Web of Science ®Google Scholar
• Moncalvo JM, Wang HH, Hseu RS. 1995. Phylogenetic relationships in Ganoderma inferred from the internal transcribed spacers and 25S ribosomal DNA sequences. Mycologia. 87(2):223–238. doi:10.2307/3760908
   Web of Science ®Google Scholar
• Muszewska A, Stepniewska-Dziubinska MM, Steczkiewicz K, Pawlowska J, Dziedzic A, Ginalski K. 2017. Fungal lifestyle reflected in serine protease repertoire. Sci Rep. 7(1):9147. doi:10.1038/s41598-017-09644-w
   PubMedGoogle Scholar
• Nelson DR. 2009. The cytochrome p450 homepage. Hum Genomics. 4(1):59–65. doi:10.1186/1479-7364-4-1-59
   PubMedGoogle Scholar
• O’Donnell K, Cigelnik E. 1997. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Phylogenet Evol. 7(1):103–116. doi:10.1006/mpev.1996.0376
   PubMed Web of Science ®Google Scholar
• O’Donnell K, Kistler HC, Cigelnik E, Ploetz RC. 1998. Multiple evolutionary origins of the fungus causing Panama disease of banana: concordant evidence from nuclear and mitochondrial gene genealogies. Proc Natl Acad Sci USA. 95(5):2044–2049. doi:10.1073/pnas.95.5.2044
   PubMed Web of Science ®Google Scholar
• O’Donnell K, Rooney AP, Proctor RH, Brown DW, McCormick SP, Ward TJ, Frandsen RJN, Lysoe E, Rehner SA, Aoki T, et al. 2013. Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria. Fungal Genet Biol. 52:20–31. doi:10.1016/j.fgb.2012.12.004
   PubMed Web of Science ®Google Scholar
• Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, et al. 2012. Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog. 8(12):e1003037. doi:10.1371/journal.ppat.1003037
   PubMed Web of Science ®Google Scholar
• Pantou MP, Kouvelis VN, Typas MA. 2008. The complete mitochondrial genome of Fusarium oxysporum: insights into fungal mitochondrial evolution. Gene. 419(1–2):7–15. doi:10.1016/j.gene.2008.04.009
   PubMed Web of Science ®Google Scholar
• Park J, Lee S, Choi J, Ahn K, Park B, Park J, Kang S, Lee Y-H. 2008. Fungal cytochrome P450 database. BMC Genomics. 9:402. doi:10.1186/1471-2164-9-402
   PubMed Web of Science ®Google Scholar
• Peerally A. 1991. Cylindrocladium hawksworthii sp. nov. pathogenic on water-lilies in Mauritius. Mycotaxon. 40:367–376.
   Web of Science ®Google Scholar
• Qhanya LB, Matowane G, Chen W, Sun Y, Letsimo EM, Parvez M, Yu J-H, Sitheni Mashele S, Syed K. 2015. Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens. Plos One. 10:e0142100. doi:10.1371/journal.pone.0142100.
   PubMed Web of Science ®Google Scholar
• Rambaut A, Suchard M, Drummond A. 2013. Tracer v1.6. http://tree.bio.ed.ac.uk/software/tracer/.
   Google Scholar
• Riko R, Nakamura H, Shindo K. 2014. Studies on pyranonigrins – isolation of pyranonigrin E and biosynthetic studies on pyranonigrin A. J Antibiot. 67(2):179–181. doi:10.1038/ja.2013.91
   PubMed Web of Science ®Google Scholar
• Rivera Y, Salgado-Salazar C, Veltri D, Malapi-Wight M, Crouch JA. 2018. Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola. PeerJ. 6:e5401. doi:10.7717/peerj.5401
   PubMed Web of Science ®Google Scholar
• Salgado-Salazar C, Crouch JA. 2019. Genome resources for the stem and bark canker pathogens Corinectria fuckeliana, Neonectria hederae and N. punicea. Plant Dis. 103(3):389–391. doi:10.1094/PDIS-05-18-0904-A
   PubMed Web of Science ®Google Scholar
• Salgado-Salazar C, Skaltsas DN, Phipps TM, Castlebury LA. 2021. Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3. 11(4):jkab071. doi:10.1093/g3journal/jkab071
   Web of Science ®Google Scholar
• Sello MM, Jafta N, Nelson DR, Chen W, Yu JH, Parvez M, Kgosiemang I, Monyaki R, Raselemane SC, Qhanya LBet al. 2015. Diversity and evolution of cytochrome P450 monooxygenases in Oomycetes. Sci Rep. 5:11572. doi:10.1038/srep11572.
   PubMed Web of Science ®Google Scholar
• Sezutsu H, Le Goff G, Feyereisen R. 2013. Origins of P450 diversity. Phil Trans R Soc Lond B Biol Sci. 368(1612):20120428. doi:10.1098/rstb.2012.0428
   PubMed Web of Science ®Google Scholar
• Silvestro D, Michalak I. 2012. raxmlGUI: a graphical front-end for RAxML. Org Divers Evol. 12:335–337. doi:10.1007/s13127-011-0056-0
   Web of Science ®Google Scholar
• Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 31(19):3210–3212. doi:10.1093/bioinformatics/btv351
   PubMed Web of Science ®Google Scholar
• Skaltsas DN, Salgado-Salazar C. 2020. Genome resources for Thelonectria rubi the causal agent of Nectria canker of caneberry. Phytopathology. 110(4):723–725. doi:10.1094/PHYTO-12-19-0466-A
   PubMed Web of Science ®Google Scholar
• Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. 2018. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol. 19(9):2094–2110. doi:10.1111/mpp.12682
   PubMed Web of Science ®Google Scholar
• Staats CC, Junges A, Guedes RL, Thompson CE, de Morais GL, Boldo JT, de Almeida LG, Andreis FC, Gerber AL, Sbaraini N, et al. 2014. Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. BMC Genomics. 15:822. doi:10.1186/1471-2164-15-822
   PubMed Web of Science ®Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690. doi:10.1093/bioinformatics/btl446
   PubMed Web of Science ®Google Scholar
• Sützl L, Laurent CVFP, Abrera AT, Schütz G, Ludwig R, Haltrich D. 2018. Multiplicity of enzymatic functions in the CAZy AA3 family. Appl Microbiol Biotechnol. 102(6):2477–2492. doi:10.1007/s00253-018-8784-0
   PubMed Web of Science ®Google Scholar
• Syed K, Nelson DR, Riley R, Yadav JS. 2013. Genomewide annotation and comparative genomics of Cytochrome P450 Monooxygenases (P450s) in the polypore species Bjerkandera adusta. Ganoderma Sp. and Phlebia Brevispora. Mycologia. 105:1445–1455. doi:10.3852/13-002.
   PubMed Web of Science ®Google Scholar
• Tzelepis G, Dubey M, Jensen DF, Karlsson M. 2015. Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. Microbiology. 161(7):1407–12419. doi:10.1099/mic.0.000096
   PubMedGoogle Scholar
• Varshney D, Jaiswar A, Adholeya A, Prasad P. 2016. Phylogenetic analyses reveal molecular signatures associated with functional divergence among subtilisin like serine proteases are linked to lifestyle transitions in Hypocreales. BMC Evol Biol. 16(1):220. doi:10.1186/s12862-016-0793-y
   PubMedGoogle Scholar
• Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol. 172(8):4238–4246. doi:10.1128/jb.172.8.4238-4246.1990
   PubMed Web of Science ®Google Scholar
• Wang X-C, Zeng Z-Q, Zhuang W-Y. 2016. The complete mitochondrial genome of the important phytopathogen Nectria cinnabarina (Hypocreales, Ascomycota). Mitochondrial DNA Part A. 27(6):4670–4671. doi:10.3109/19401736.2015.1106495
   PubMed Web of Science ®Google Scholar
• White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protoc. 18:315–322.
   Google Scholar
• Yang M, Li Q, Chen C, Huang W, Liu C. 2019. The complete mitochondrial genome of Ilyonectria sp. (Hypocreales: Hypocreomycetidae). Mitochondrial DNA Part B. 4(2):2385–2386. doi:10.1080/23802359.2018.1536490
   PubMed Web of Science ®Google Scholar
• Yang X, McMahon MB, Ramachandran SR, Garret WM, LeBlanc N, Crouch JA, Shishkoff N, Luster DG. 2021. Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep. 41(3):BSR20203544. doi:10.1042/BSR20203544
   PubMed Web of Science ®Google Scholar
• Ye X, Zhong Z, Liu H, Lin L, Guo M, Guo W, Wang Z, Zhang Q, Feng L, Lu G, et al. 2018. Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus. BMC Genomics. 19(1):358. doi:10.1186/s12864-018-4739-1
   PubMedGoogle Scholar
• Yin Y, Mao Z, Yang J, Chen X, Mao F, Xu Y. 2012. dbCAN: a web resource for automated carbohydrate – active enzyme annotation. Nucleic Acids Res. 40:W445–W451. doi:10.1093/nar/gks479
   PubMed Web of Science ®Google Scholar
• Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, Yin Y. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46(W1):W95–W101. doi:10.1093/nar/gky418
   PubMed Web of Science ®Google Scholar
• Zhao Z, Liu H, Wang C, Xu JR 2013. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics. 14:274. doi:10.1186/1471-2164-14-274
   PubMed Web of Science ®Google Scholar