Armenteros JJA, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, et al. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37:420–3.
Article
CAS
Google Scholar
Avio L, Cristani C, Strani P, Giovannetti M. Genetic and phenotypic diversity of geographically different isolates of Glomus mosseae. Can J Microbiol. 2009;55:242–53.
Article
CAS
PubMed
Google Scholar
Baroncelli R, Amby DB, Zapparata A, Sarrocco S, Vannacci G, Le Floch G, et al. Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum. BMC Genomics. 2016;17:555.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bartíková M, Brand T, Beltz H, Šafránková I. Host susceptibility and microclimatic conditions influencing the development of blight diseases caused by Calonectria henricotiae. Eur J Plant Pathol. 2020;157:103–17.
Article
CAS
Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST: architecture and applications. BMC Bioinform. 2009;10:1–9.
Article
CAS
Google Scholar
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000;17:540–52.
Article
CAS
PubMed
Google Scholar
Castroagudín VL, Weiland JE, Baysal-Gurel F, Cubeta MA, Daughtrey ML, Gauthier NW, et al. One clonal lineage of Calonectria pseudonaviculata is primarily responsible for the boxwood blight epidemic in the United States. Phytopathology. 2020;110:1845–53.
Article
PubMed
Google Scholar
Castroagudín VL, Yang X, Daughtrey ML, Luster DG, Pscheidt JW, Weiland JE, et al. Boxwood blight disease: a diagnostic guide. Plant Health Progr. 2020;21:291–300.
Article
Google Scholar
Charif D, Lobry JR. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Gerstman BS, editor. Structural approaches to sequence evolution. New York: Springer; 2007. p. 207–32.
Chapter
Google Scholar
Chevanne D, Bastiaans E, Debets A, Saupe SJ, Clavé C, Paoletti M. Identification of the het-r vegetative incompatibility gene of Podospora anserina as a member of the fast evolving HNWD gene family. Curr Genet. 2009;55:93–102.
Article
CAS
PubMed
Google Scholar
Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics. 2017;33:2938–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Couch BC, Fudal I, Lebrun M, Tharreau D, Valent B, Van Kim P, et al. Origins of host-specific populations of the blast pathogen Magnaporthe oryzae in crop domestication with subsequent expansion of pandemic clones on rice and weeds of rice. Genetics. 2005;170:613–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Crous PW. Taxonomy and pathology of Cylindrocladium (Calonectria) and allied genera. St. Paul: American Phytopathological Society Press; 2002.
Google Scholar
Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics. 2011;27:1164–5.
Article
CAS
PubMed
Google Scholar
Daughtrey ML. Boxwood blight: threat to ornamentals. Annu Rev Phytopathol. 2019;57:189–209.
Article
CAS
PubMed
Google Scholar
de Jonge R, van Esse HP, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, et al. Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing. Proc Natl Acad Sci USA. 2012;109:5110–5.
Article
PubMed
PubMed Central
Google Scholar
Demuth JP, Hahn MW. The life and death of gene families. BioEssays. 2009;31:29–39.
Article
PubMed
Google Scholar
Diao Y, Zhang C, Xu J, Lin D, Liu L, Mtung’e OG, et al. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China. Evol Appl. 2015;8:108–18.
Article
PubMed
Google Scholar
Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7: e1002195.
Article
CAS
PubMed
PubMed Central
Google Scholar
Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:1–14.
Article
CAS
Google Scholar
Farr DF, Rossman AY. Fungal Databases, U.S. National Fungus Collections, ARS, USDA. https://nt.ars-grin.gov/fungaldatabases/ accessed 26 July 2021
Feldman D, Yarden O, Hadar Y. Seeking the roles for fungal small-secreted proteins in affecting saprophytic lifestyles. Front Microbiol. 2020;11:455.
Article
PubMed
PubMed Central
Google Scholar
Freitas L, Nery MF. Expansions and contractions in gene families of independently-evolved blood-feeding insects. BMC Evol Biol. 2020;20:1–8.
Article
Google Scholar
Gehesquière B, Crouch JA, Marra RE, Van Poucke K, Rys F, Maes M, et al. Characterization and taxonomic reassessment of the box blight pathogen Calonectria pseudonaviculata, introducing Calonectria henricotiae sp. nov. Plant Pathol. 2016;65:37–52.
Article
CAS
Google Scholar
Grandaubert J, Bhattacharyya A, Stukenbrock EH. RNA-seq-based gene annotation and comparative genomics of four fungal grass pathogens in the genus Zymoseptoria identify novel orphan genes and species-specific invasions of transposable elements. G3-Genes Genom Genet. 2015;5:1323–33.
CAS
Google Scholar
Grandaubert J, Lowe RG, Soyer JL, Schoch CL, Angela P, Fudal I, et al. Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens. BMC Genomics. 2014;15:1–27.
Article
Google Scholar
Hall CR, Hong C, Gouker FE, Daughtrey M. Analyzing the structural shifts in US boxwood production due to boxwood blight. J Environ Hortic. 2021;39:91–9.
Article
Google Scholar
Han MV, Thomas GWC, Lugo-Martinez J, Hahn MW. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013;30:1987–97.
Article
CAS
PubMed
Google Scholar
Henricot B, Sierra AP, Prior C. A new blight disease on Buxus in the UK caused by the fungus Cylindrocladium. Plant Pathol. 2000;49:6.
Article
Google Scholar
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–14.
Article
CAS
PubMed
Google Scholar
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, Von Mering C, et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol. 2017;34:2115–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ivors KL, Lacey LW, Milks DC, Douglas SM, Inman MK, Marra RE, et al. First report of boxwood blight caused by Cylindrocladium pseudonaviculatum in the United States. Plant Dis. 2012;96:1070.
Article
CAS
PubMed
Google Scholar
James TY. Ancient yet fast: rapid evolution of mating genes and mating systems in fungi. In: Singh RS, Xu J, Kulathinal RJ, editors. Rapidly evolving genes and genetic systems. Oxford: Oxford University Press; 2012. p. 187–200.
Chapter
Google Scholar
Kulkarni RD, Kelkar HS, Dean RA. An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins. Trends Biochem Sci. 2003;28:118–21.
Article
CAS
PubMed
Google Scholar
Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: a resource for timelines, timetrees, and divergence times. Mol Biol Evol. 2017;34:1812–9.
Article
CAS
PubMed
Google Scholar
Künzler M. How fungi defend themselves against microbial competitors and animal predators. PLoS Pathog. 2018;14: e1007184.
Article
PubMed
PubMed Central
CAS
Google Scholar
LeBlanc N, Gehesquière B, Salgado-Salazar C, Heungens K, Crouch JA. Limited genetic diversity across pathogen populations responsible for the global emergence of boxwood blight identified using SSRs. Plant Pathol. 2019;68:861–8.
Article
Google Scholar
LeBlanc N, Cubeta MA, Crouch JA. Population genomics trace clonal diversification and intercontinental migration of an emerging fungal pathogen of boxwood. Phytopathology. 2021;111:184–93.
Article
CAS
PubMed
Google Scholar
Lebreton A, Zeng Q, Miyauchi S, Kohler A, Dai Y, Martin FM. Evolution of the mode of nutrition in symbiotic and saprotrophic fungi in forest ecosystems. Annu Rev Ecol Evol S. 2021;52:385–404.
Article
Google Scholar
Liang X, Wang B, Dong Q, Li L, Rollins JA, Zhang R, et al. Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses. PLoS ONE. 2018;13: e0196303.
Article
PubMed
PubMed Central
CAS
Google Scholar
Liu QL, Li J, Wingfield MJ, Duong TA, Wingfield BD, Crous PW, et al. Reconsideration of species boundaries and proposed DNA barcodes for Calonectria. Stud Mycol. 2020;97: 100095.
Article
Google Scholar
Lombard L, Crous PW, Wingfield BD, Wingfield MJ. species concepts in Calonectria (Cylindrocladium). Stud Mycol. 2010;66:1–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lyons R, Stiller J, Powell J, Rusu A, Manners JM, Kazan K. Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS ONE. 2015;10: e0121902.
Article
PubMed
PubMed Central
CAS
Google Scholar
Malapi-Wight M, Veltri D, Gehesquiere B, Heungens K, Rivera Y, Salgado-Salazar C, et al. Global distribution of mating types shows limited opportunities for mating across populations of fungi causing boxwood blight disease. Fungal Genet Biol. 2019;131: 103246.
Article
PubMed
Google Scholar
Martin F, Kohler A, Murat C, Veneault-Fourrey C, Hibbett DS. Unearthing the roots of ectomycorrhizal symbioses. Nat Rev Microbiol. 2016;14:760–73.
Article
CAS
PubMed
Google Scholar
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer EL, et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2021;49:D412–9.
Article
CAS
PubMed
Google Scholar
Mitchell R, Chitanava S, Dbar R, Kramarets V, Lehtijärvi A, Matchutadze I, et al. Identifying the ecological and societal consequences of a decline in Buxus forests in Europe and the Caucasus. Biol Invasions. 2018;20:3605–20.
Article
Google Scholar
Morales-Cruz A, Amrine KC, Blanco-Ulate B, Lawrence DP, Travadon R, Rolshausen PE, et al. Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens. BMC Genomics. 2015;16:1–22.
Article
CAS
Google Scholar
Ochi S, Yoshida M, Nakagawa A, Natsume M. Identification and activity of a phytotoxin produced by Calonectria ilicicola, the causal agent of soybean red crown rot. Can J Plant Pathol. 2011;33:347–54.
Article
CAS
Google Scholar
Pagès H, Aboyoun P, Gentleman R, and DebRoy S. Biostrings: Efficient manipulation of biological strings. R package version 2.48.0. 2020.
Palmer JM. Funannotate: A fungal genome annotation and comparative genomics pipeline. 2017. https://funannotate.readthedocs.io/en/latest/
Paoletti M, Saupe SJ. Fungal incompatibility: evolutionary origin in pathogen defense? BioEssays. 2009;31:1201–10.
Article
CAS
PubMed
Google Scholar
Paoletti M, Saupe SJ, Clavé C. Genesis of a fungal non-self recognition repertoire. PLoS ONE. 2007;2: e283.
Article
PubMed
PubMed Central
CAS
Google Scholar
Powell AJ, Conant GC, Brown DE, Carbone I, Dean RA. Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. BMC Genomics. 2008;9:1–15.
Article
CAS
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2020. https://www.R-project.org/
Rivera Y, Salgado-Salazar C, Veltri D, Malapi-Wight M, Crouch JA. Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola. PeerJ. 2018;6: e5401.
Article
PubMed
PubMed Central
CAS
Google Scholar
Salgado-Salazar C, Skaltsas DN, Phipps T, Castlebury LA. Comparative genome analyses suggest a hemibiotrophic lifestyle and virulence differences for the beech bark disease fungal pathogens Neonectria faginata and Neonectria coccinea. G3-Genes Genom Genet. 2021;11:jkab071.
Google Scholar
Sánchez-Vallet A, Fouché S, Fudal I, Hartmann FE, Soyer JL, Tellier A, et al. The genome biology of effector gene evolution in filamentous plant pathogens. Annu Rev Phytopathol. 2018;56:21–40.
Article
PubMed
CAS
Google Scholar
Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics. 2003;19:301–2.
Article
CAS
PubMed
Google Scholar
Sepúlveda VE, Márquez R, Turissini DA, Goldman WE, Matute DR. Genome sequences reveal cryptic speciation in the human pathogen Histoplasma capsulatum. MBio. 2017;8:1339.
Article
Google Scholar
Sharpton TJ, Stajich JE, Rounsley SD, Gardner MJ, Wortman JR, Jordar VS, et al. Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives. Genome Res. 2009;19:1722–31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shi-Kunne X, Faino L, Grardy CM, Thomma BP, Seidl MF. Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss. Environ Microbiol. 2018;20:1362–73.
Article
CAS
PubMed
Google Scholar
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31:3210–2.
Article
PubMed
CAS
Google Scholar
Sipos G, Prasanna AN, Walter MC, O’Connor E, Bálint B, Krizsán K, et al. Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nat Ecol Evol. 2017;1:1931–41.
Article
PubMed
Google Scholar
Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, et al. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science. 2010;330:1543–6.
Article
CAS
PubMed
Google Scholar
Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. Mol Plant Pathol. 2018;19:2094–110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Swett CL, Kirkpatrick SC, Gordon TR. Evidence for a hemibiotrophic association of the pitch canker pathogen Fusarium circinatum with Pinus radiata. Plant Dis. 2016;100:79–84.
Article
CAS
PubMed
Google Scholar
Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, et al. Comparative genomics of six Juglans species reveals disease-associated gene family contractions. Plant J. 2020;102:410–23.
Article
CAS
PubMed
Google Scholar
Urban M, Cuzick A, Seager J, Wood V, Rutherford K, Venkatesh SY, et al. PHI-base: the pathogen–host interactions database. Nucleic Acids Res. 2020;48:D613–20.
CAS
PubMed
Google Scholar
Wichadakul D, Kobmoo N, Ingsriswang S, Tangphatsornruang S, Chantasingh D, Luangsa-Ard JJ, et al. Insights from the genome of Ophiocordyceps polyrhachis-furcata to pathogenicity and host specificity in insect fungi. BMC Genomics. 2015;16:1–14.
Article
CAS
Google Scholar
Wickham H, Averick M, Bryan J, Chang W, McGowan LD, François R, et al. Welcome to the Tidyverse. J Open Source Softw. 2019;4:1686.
Article
Google Scholar
Yang X, Castroagudín VL, Daughtrey ML, Loyd AL, Weiland JE, Shishkoff N, et al. A diagnostic guide for volutella blight affecting Buxaceae. Plant Health Prog. 2021;22(4):578–90.
Article
Google Scholar
Yang X, McMahon MB, Ramachandran SR, Garrett WM, LeBlanc N, Crouch JA, et al. Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep. 2021;41:BSR20203544.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ye X, Zhong Z, Liu H, Lin L, Guo M, Guo W, et al. Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus. BMC Genomics. 2018;19:1–12.
Article
CAS
Google Scholar
Ye X, Liu H, Jin Y, Guo M, Huang A, Chen Q, et al. Transcriptomic analysis of Calonectria pseudoreteaudii during various stages of Eucalyptus infection. PLoS ONE. 2017;12: e0169598.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yu G, Smith DK, Zhu H, Guan Y, Lam TT. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36.
Article
Google Scholar
Zhang W, Zhang X, Li K, Wang C, Cai L, Zhuang W, et al. Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi. Mycology. 2018;9:176–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao M, Huang C, Chen Q, Wu X, Qu J, Zhang J. Genetic variability and population structure of the mushroom Pleurotus eryngii var. tuoliensis. PLoS ONE. 2013;8:e83253.
Article
PubMed
PubMed Central
Google Scholar