Diversity of Colletotrichum species associated with torch ginger anthracnose

LITERATURE CITED

• Barguil BM, Oliveira SMA, Coelho RSB, Beserra Júnior JEA. 2009. Identificação e variabilidade genética de isolados de Colletotrichum causando antracnose em inflorescências de plantas ornamentais tropicais. Cienc Rural. 6:1639–1646. doi:10.1590/S0103-84782009005000126.
   Web of Science ®Google Scholar
• Cai L, Hyde KD, Taylor PWJ, Weir BS, Waller J, Abang MM, Zhang JZ, Yang YL, Phoulivong S, Liu ZY, et al. 2009. A polyphasic approach for studying Colletotrichum. Fungal Divers. 39:183–204.
   Web of Science ®Google Scholar
• Cannon PF, Damm U, Johnston P, Weir BS. 2012. Colletotrichum – current status and future directions. Stud Mycol. 73:181–213. doi:10.3114/sim0014.
   PubMed Web of Science ®Google Scholar
• Cao X, Xu X, Che H, West JS, Luo D. 2019. Three Colletotrichum species, including a new species, are associated to leaf anthracnose of rubber tree in Hainan, China. Plant Dis. 103(1):117–124. doi:10.1094/PDIS-02-18-0374-RE.
   PubMed Web of Science ®Google Scholar
• Crouch JA, Clarke BB, Hillman BI. 2009. What is the value of ITS sequence data in Colletotrichum systematics and species diagnosis? A case study using the falcate-spored graminicolous Colletotrichum group. Mycologia. 101(5):648–656. doi:10.3852/08-231.
   PubMed Web of Science ®Google Scholar
• Damm U, Sato T, Alizadeh A, Groenewald JZ, Crous PW. 2019. The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes. Stud Mycol. 92:1–46. doi:10.1016/j.simyco.2018.04.001.
   PubMed Web of Science ®Google Scholar
• Dettman JR, Jacobson DJ, Taylor JW. 2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution. 57:2703–2720. doi:10.1111/j.0014-3820.2003.tb01514.x.
   PubMed Web of Science ®Google Scholar
• Doyle JJ, Doyle JL. 1990. Isolation of plant DNA from fresh tissue. Focus. 12:13–15.
   Google Scholar
• Doyle VP, Oudemans PV, Rehner SA, Litt A. 2013. Habitat and host indicate lineage identity in Colletotrichum gloeosporioides s.l. from wild and agricultural landscapes in North America. PLoS One. 8:e62394. doi:10.1371/journal.pone.0062394.
   PubMed Web of Science ®Google Scholar
• Duke MM. 1928. The genera Vermicularia Fr. and Colletotrichum Cda. Trans Br Mycol Soc. 13:156–184. doi:10.1016/S0007-1536(28)80016-7.
   Google Scholar
• Ferrari JT. 2008. Antracnose em Bastão do Imperador. São Paulo (BR): Instituto Biológico/APTA. Documento Técnico 003. p. 1–6.
   Google Scholar
• Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307–321. doi:10.1093/sysbio/syq010.
   PubMed Web of Science ®Google Scholar
• Gurgel LMS, Coelho RSB, Oliveira SMA, Silva RLX, Rosa RCT, Assis TC, Andrade DEGT. 2016. Efeito de indutores de resistência no controle da antracnose do bastão do imperador (Etlingera elatior). Anais da Academia Pernambucana de Ciência Agronômica. 13:223–233.
   Google Scholar
• Hyde KD, Cai L, McKenzie EHC, Yang YL, Zhang JZ, Prihastuti H. 2009. Colletotrichum: a catalogue of confusion. Fungal Divers. 39:1–17.
   Web of Science ®Google Scholar
• Johnston PR, Jones D. 1997. Relationship among Colletotrichum isolates from fruit rots assessed using rDNA sequences. Mycologia. 89:420–430. doi:10.1080/00275514.1997.12026801.
   Web of Science ®Google Scholar
• Kalyaanamoorty S, Minh BQ, Wong TKF, Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589. doi:10.1038/nmeth.4285.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 33(7):1870–1874. doi:10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452. doi:10.1093/bioinformatics/btp187.
   PubMed Web of Science ®Google Scholar
• Lima NB, Batista MVA, Morais MA Jr, Barbosa MAG, Michereff SJ, Hyde KD, Câmara MPS. 2013. Five Colletotrichum species are responsible for Mango anthracnose in northeastern Brazil. Fungal Divers. 61:75–88. doi:10.1007/s13225-013-0237-6.
   Web of Science ®Google Scholar
• Lin SR, Lin YH, Ariyawansa HA, Chang YC, Yu SY, Tsai I, Chung CL, Hung TH. 2023. Analysis of the pathogenicity and phylogeny of Colletotrichum species associated with Brown Blight of Tea (Camellia sinensis) in Taiwan. Plant Dis. 107(1):97–106. doi:10.1094/PDIS-03-22-0509-RE.
   PubMed Web of Science ®Google Scholar
• Lins SRO, Coelho RSB. 2003. Antracnose em inflorescências de bastão do imperador (Etlingera elatior): ocorrência e métodos de inoculação. Summa Phytopathol. 29:355–358.
   Google Scholar
• Lins SRO, Coelho RSB. 2004. Ocorrência de doenças em plantas ornamentais tropicais no Estado de Pernambuco. Fitopatol Bras. 29:332–335. doi:10.1590/S0100-41582004000300019.
   Google Scholar
• Liu F, Ma ZY, Hou LW, Diao YZ, Wu WP, Damm U, Song S, Cai L. 2022. Updating species diversity of Colletotrichum, with a phylogenomic overview. Stud Mycol. 101:1–56. doi:10.3114/sim.2022.101.01.
   PubMed Web of Science ®Google Scholar
• Loges V, Castro ACR, Martins LSS, Willadino L, Teixeira MCF, Lira Junior MA, Pinheiro PGL, Souza JWO, Melo MG. 2005. Floriculture research in Pernambuco. Acta Hortic. 638:345–350. doi:10.17660/ActaHortic.2005.683.43.
   Google Scholar
• Marin-Felix Y, Groenewald JZ, Cai L, Chen Q, Marincowitz S, Barnes I, Bensch K, Braun U, Camporesi E, Damm U, et al. 2017. Genera of phytopathogenic fungi: GOPHY 1. Stud Mycol. 86:99–216. doi:10.1016/j.simyco.2017.04.002.
   PubMed Web of Science ®Google Scholar
• Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the Gateway Computing Environments workshop (GCE). p. 1–8. doi:10.1109/GCE.2010.5676129.
   Google Scholar
• Minh BQ, Schimidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. 2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 37(5):1530–1534. doi:10.1093/molbev/msaa015.
   PubMed Web of Science ®Google Scholar
• Nguyen LT, Schmidt HA, Haeseler A, Minh BQ. 2015. IQ–TREE: a fast and effective stochastic algorithm for estimating maximun–likelihood phylogenies. Mol Biol Evol. 32:268–274. doi:10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Nylander JAA. 2004. MrModeltest v2. Program distributed by the author. Sweden: Evolutionary Biology Centre, Uppsala University.
   Google Scholar
• O’Dell TE, Smith JE, Castellano M, Luoma D. 1996. Diversity and conservation of forest fungi. In: Pilz D and Molina R, editors. Managing forest ecosystems to conserve fungus diversity and sustain wild mushroom. Portland (OR): USDA Forest Service – General Technical Report. p. 5–15.
   Google 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
• Prihastuti H, Cai L, Chen H, McKenzie EHC, Hyde KD. 2009. Characterization of Colletotrichum species associated with coffee berries in northern Thailand. Fungal Divers. 39:89–109.
   Web of Science ®Google Scholar
• Rayner RW. 1970. A mycological colour chart. Kew (UK): Commonwealth Mycological Institute and British Mycological Society.
   Google Scholar
• Rojas EI, Rehner SA, Samuels GJ, Van Bael SA, Herre EA, Cannon P, Chen R, Pang J, Wang R, Zhang Y, et al. 2010. Colletotrichum gloeosporioides s.l. associated with Theobroma cacao and other plants in Panama: multilocus phylogenies distinguish host-associated pathogens from asymptomatic endophytes. Mycologia. 102(6):1318–1338. doi:10.3852/09-244.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes v. 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61:539–542. doi:10.1093/sysbio/sys029.
   PubMed Web of Science ®Google Scholar
• Sela I, Ashkenazy H, Katoh K, Pupko T. 2015. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. 43:W7–W14. doi:10.1093/nar/gkv318.
   PubMed Web of Science ®Google Scholar
• Silva DN, Talhinhas P, Várzea V, Cai L, Paulo OS, Batista D. 2012. Application of the Apn2/MAT locus to improve the systematics of the Colletotrichum gloeosporioides complex: an example from coffee (Coffea spp.) hosts. Mycologia. 104:396–409. doi:10.3852/11-145.
   PubMed Web of Science ®Google Scholar
• Staden R, Beal KF, Bonfield JK. 1998. The Staden package. In: Misener S, Krawetz SA, editors. Bioinformatics methods and protocols. New York (US): Humana. p. 115–130.
   Google Scholar
• Statistix. 2013. Statistix 10, version 10. Tallahassee (FL): Analytical Software.
   Google Scholar
• Sutton BC. 1980. The Coelomycetes. Fungi imperfecti with pycnidia, acervuli and stromata. Kew (UK): Commonwealth Mycological Institute. p. 696.
   Google Scholar
• Sutton BC. 1992. The genus Glomerella and its anamorph Colletotrichum. In: Bailey JA, Jeger MJ, editors. Colletotrichum – biology, pathology and control. Wallingford (UK): CAB International. p. 1–26.
   Google Scholar
• Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol. 31(1):21–32. doi:10.1006/fgbi.2000.1228.
   PubMed Web of Science ®Google Scholar
• Vaidya G, Lohman DJ, Meier R. 2011. SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information. Cladistics. 27(2):171–180. doi:10.1111/j.1096-0031.2010.00329.x.
   PubMed Web of Science ®Google Scholar
• Veloso JS, Câmara MP, Lima WL, Michereff SJ, Doyle VP. 2018. Why species delimitation matters for fungal ecology: colletotrichum diversity on wild and cultivated cashew in Brazil. Fungal Biol. 122(7):677–691. doi:10.1016/j.funbio.2018.03.005.
   PubMed Web of Science ®Google Scholar
• Vieira WAS, Bezerra PA, Silva AC, Veloso JS, Câmara MPS, Doyle VP. 2020. Optimal markers for the identification of Colletotrichum species. Mol Phylogenet Evol. 143:106694. doi:10.1016/j.ympev.2019.106694.
   PubMed Web of Science ®Google Scholar
• Vieira WAS, Lima WG, Nascimento ES, Michereff SJ, Câmara MPS. 2017. The impact of phenotypic and molecular data on the inference of Colletotrichum diversity associated with Musa. Mycologia. 109:912–934. doi:10.1080/00275514.2017.1418577.
   PubMed Web of Science ®Google Scholar
• Vieira WAS, Michereff SJ, Morais MA Jr, Hyde KH, Câmara MPS. 2014. Endophytic species of Colletotrichum associated with Mango in northeastern Brazil. Fungal Divers. 67:181–202. doi:10.1007/s13225-014-0293-6.
   Web of Science ®Google Scholar
• Wang W, Silva DD, Moslemi A, Edwards J, Ades PK, Crous PW, Taylor PWJ. 2021. Colletotrichum species causing Anthracnose of Citrus in Australia. J Fungus. 7(1):47. doi:10.3390/jof7010047.
   Google Scholar
• Weir BS, Johnston PR, Damm U. 2012. The Colletotrichum gloeosporioides species complex. Stud Mycol. 73:115–180. doi:10.3114/sim0011.
   PubMed Web of Science ®Google Scholar