An updated phylogenetic classification of Corynespora cassiicola isolates and a practical approach to their identification based on the nucleotide polymorphisms at the ga4 and caa5 loci

LITERATURED CITED

• Alvaro CG, O’Donnell AF, Prosser DC, Augustine AA, Goldman A, Brodsky JL, Cyert MS, Wendland B, Thorner J. 2014. Specific alpha-arrestins negatively regulate Saccharomyces cerevisiae pheromone response by down-modulating the G-protein-coupled receptor Ste2. Molecular and Cellular Biology 34:2660–2681.
   PubMed Web of Science ®Google Scholar
• Aubry L, Guetta D, Klein G. 2009. The arrestin fold: variations on a theme. Current Genomics 10:133–142.
   Web of Science ®Google Scholar
• Banguela-Castillo A, Ramos-González PL, Peña-Marey M, Tanaka FAO, Blassioli-Moraes MC, Hernández-Rodríguez L, Cabrera RI. 2015. The same host but a different Muscodor: a new Muscodor albus isolate from wild pineapple (Ananas ananassoides) with potential application in agriculture. Crop Protection 78:284–292, doi:10.1016/j.cropro.2015.09.022
   Web of Science ®Google Scholar
• Becuwe M, Herrador A, Haguenauer-Tsapis R, Vincent O, Léon S. 2012. Ubiquitin-mediated regulation of endocytosis by proteins of the arrestin family. Biochemistry Research International 2012:1–12.
   Google Scholar
• Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9:1657–1659.
   PubMed Web of Science ®Google Scholar
• Cornet M, Gaillardin C. 2014. pH signaling in human fungal pathogens: a new target for antifungal strategies. Eukaryotic Cell 13:342–352.
   PubMedGoogle Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772–772.
   PubMed Web of Science ®Google Scholar
• Déon M, Bourré Y, Gimenez S, Berger A, Bieysse D, de Lamotte F, Poncet J, Roussel V, Bonnot F, Oliver G, Franchel J, Seguin M, Leroy T, Roeckel-Drevet P, Pujade-Renaud V. 2012. Characterization of a cassiicolin-encoding gene from Corynespora cassiicola, pathogen of rubber tree (Hevea brasiliensis). Plant Science 185: 227–237
   Web of Science ®Google Scholar
• Déon M, Fumanal B, Gimenez S, Bieysse D, Oliveira RR, Shuib SS, Breton F, Elumalai S, Vida JB, Seguin M, Leroy T, Roeckel-Drevet P, Pujade-Renaud V. 2014. Diversity of the cassiicolin gene in Corynespora cassiicola and relation with the pathogenicity in Hevea brasiliensis. Fungal Biology 118:32–47.
   PubMed Web of Science ®Google Scholar
• Dixon LJ, Schlub RL, Pernezny K, Datnoff LE. 2009. Host specialization and phylogenetic diversity of Corynespora cassiicola. Phytopathology 99:1015–1027.
   PubMed Web of Science ®Google Scholar
• Dong B, Xu X, Chen G, Zhang D, Tang M, Xu F, Liu X, Wang H, Zhou B. 2016. Arrestin signaling is required for conidiogenous cell development in Magnaporthe oryzae. Scientific Reports 6:30963.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution. 29:1969–1973.
   Google Scholar
• Farr D, Rossman A. 2018. Fungal Databases. U.S. National Fungus Collections. [cited 2018 Dec 10]. Available from: https://nt.ars-grin.gov/fungaldatabases/
   Google Scholar
• Ferreira AFTAF, Bentes JLS. 2017. Pathogenicity of Corynespora cassiicola on different hosts in Amazonas State, Brazil. Summa Phytopathologica 43:63–65.
   Google Scholar
• Galbieri R, Araújo DCEB, Kobayasti L, Girotto L, Matos JN, Marangoni MS, Almeida WP, Mehta YR, 2014. Corynespora leaf blight of cotton in Brazil and its management. American Journal of Plant Science 5:3805–3811.
   Google Scholar
• Gardner SN, Slezak T, Hall BG. 2015. kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome. Bioinformatics 31:2877–2878.
   Google Scholar
• Hieu ND, Nghia NA, Chi VTQ, Dung PT. 2014. Genetic diversity and pathogenicity of Corynespora cassiicola isolates from rubber trees and other hosts in Vietnam. Journal of Rubber Research 17:187–203.
   Web of Science ®Google Scholar
• Jones S. 1961. A leaf spot of cotton caused by Corynespora cassiicola. Phytopahology 1:305–308.
   Google Scholar
• Kang DS, Tian X, Benovic JL. 2014. Role of β-arrestins and arrestin domain-containing proteins in G protein-coupled receptor trafficking. Current Opinion in Cell Biology 27:63–71.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33:1870–1874.
   PubMed Web of Science ®Google Scholar
• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948.
   Google Scholar
• Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods in Ecology and Evolution 6:1110–1116.
   Web of Science ®Google Scholar
• Looi HK, Toh YF, Yew SM, Na SL. 2017. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola. PeerJ 5: e2841.
   Google Scholar
• Lopez D, Ribeiro S, Label P, Fumanal B, Venisse JS, Kohler A, de Oliveira RR, Labutti K, Lipzen A, Lail K, Bauer D, Ohm RA, Barry KW, Spatafora J, Grigoriev IV, Martin FM, Pujade-Renaud V. 2018. Genome-wide analysis of Corynespora cassiicola leaf fall disease putative effectors. Frontiers in Microbiology 9: 276.
   Web of Science ®Google Scholar
• Nghia NA, Kadir J, Sunderasan E, Abdullah MP, Napis S. 2010. Intraspecific variability of Corynespora cassiicola inferred from single nucleotide polymorphisms in ITS region of ribosomal DNA. Journal of Rubber Research 13:257–264
   Google Scholar
• Nghia NA, Kadir J, Sunderasan E, Abdullah MP, Malik A, Napis S. 2008. Morphological and Inter Simple Sequence Repeat (ISSR) Markers analyses of Corynespora cassiicola isolates from rubber plantations in Malaysia. Mycopathologia 166:189–201.
   PubMed Web of Science ®Google Scholar
• Oktavia F, Kuswanhadi K, Widodo, Sudarsono S, Dinarti D. 2017. Pathogenicity and rDNA-ITS sequence analysis of the Corynespora cassiicola isolates from rubber plantations in Indonesia. Emirates Journal of Food and Agriculture 29:872–883.
   Web of Science ®Google Scholar
• Onesirosan P, Arny D, Durbin R. 1974. Host specificity of Nigerian and North American isolates of Corynespora cassiicola. Phytopahology 64:1364–1367.
   Web of Science ®Google Scholar
• Qi Y, Xie Y, Zhang X, Pu J, Zhang H, Huang S, Zhang H. 2009. Nested PCR assay for detection of Corynespora leaf fall disease caused by Corynespora cassiicola. Australasian Plant Pathology 38:141–148.
   Google Scholar
• Qi Y, Zhang X, Pu J. 2011. Morphological and molecular analysis of genetic variability within isolates of Corynespora cassiicola from different hosts. European Journal of Plant Pathology 130:83–95
   Web of Science ®Google Scholar
• Romruensukharom P, Tragoonrung S, Vanavichit A, Toojinda T. 2005. Genetic variability of Corynespora cassiicola populations in Thailand. Journal of Rubber Research 8:38–49.
   Google Scholar
• Saha T, Kmar A, Sreena A, Joseph A, Jacob C, Kothandaraman R, Nazeer MA. 1988. Genetic variability of Corynespora cassiicola infecting Hevea brasiliensis isolated from the tradicitonal rubber growing areas in India. Indian Journal of Natural Rubber Research 13:1–10.
   Google Scholar
• Schoch CL, Crous PW, Groenewald JZ, Boehm EWA, Burgess TI, de Gruyter J, Boehm EWA, Burgess TI, de Gruyter J, de Hoog GS, Dixon LJ, Grube M, Gueidan C, Harada Y, Hatakeyama S, Hirayama K, Hosoya T, Huhndorf SM, Hyde KD, Jones EBG, Kohlmeyer J, Kruys, Å, Li YM, Lücking R, Lumbsch HT, Marvanová L, Mbatchou JS, McVay AH, Miller AN, Mugambi GK, Muggia L, Nelsen MP, Nelson P, Owensby CA, Phillips AJL, Phongpaichit S, Pointing SB, Pujade-Renaud, V, Raja HA, Plata E, Robbertse B, Ruibal C, Sakayaroj J, Sano T, Selbmann L, Shearer CA, Shirouzu T, Slippers B, Suetrong S, Tanaka K, Volkmann-Kohlmeyer B, Wingfield MJ, Wood AR, Woudenberg JHC, Yonezawa H, Zhang Y, Spatafora JW. 2009. A class-wide phylogenetic assessment of Dothideomycetes. Studies in Mycology 64:1–15.
   PubMed Web of Science ®Google Scholar
• Shimomoto Y, Sato T, Hojo H, Morita Y, Takeuchi S, Mizumoto H, Kiba A, Hikichi Y. 2011. Pathogenic and genetic variation among isolates of Corynespora cassiicola in Japan. Plant Pathology 60:253–260.
   Web of Science ®Google Scholar
• Shrestha SK, Lamour K, Young-Kelly H. 2017. Genome sequences and SNP analyses of Corynespora cassiicola from cotton and soybean in the southeastern United States reveal limited diversity. PLoS ONE 12:e0184908.
   Web of Science ®Google Scholar
• Silva WPK, Deverall BJ, Lyon BR. 2006. Molecular, physiological and pathological characterization of Corynespora leaf spot fungi from rubber plantations in Sri Lanka. Plant Pathology 47:267–277.
   Google Scholar
• Silva WPK, Karunanayake EH, Wijesundera RLC, Priyanka UMS. 2003. Genetic variation in Corynespora cassiicola: a possible relationship between host origin and virulence. Mycology Research 107:567–571.
   PubMed Web of Science ®Google Scholar
• Steel M, McKenzie A. 2001. Properties of phylogenetic trees generated by Yule-type speciation models. Mathematical Bioscience 170:91–112.
   Web of Science ®Google Scholar
• Sumabat LG, Kemerait RC, Brewer M.T. 2018a. Phylogenetic diversity and host specialization of Corynespora cassiicola responsible for emerging target spot disease of cotton and other crops in the southeastern United States. Phytopathology 108:892–901.
   PubMed Web of Science ®Google Scholar
• Sumabat LG, Kemerait RC, Kim DK, Mehta YR, Brewer MT. 2018b. Clonality and geographic structure of host-specialized populations of Corynespora cassiicola causing emerging target spot epidemics in the southeastern United States. PLoS ONE 13:e0205849.
   Web of Science ®Google Scholar
• Tran DM, Clément-Demange A, Déon M, Garcia D, Le Guen V, Clément-Vidal A, Soumahoro M, Masson A, Label P, Tuy-Le M, Pujade-Renaud V. 2016. Genetic determinism of sensitivity to Corynespora cassiicola exudates in rubber tree (Hevea brasiliensis). PLoS ONE 11:e0162807.
   Web of Science ®Google Scholar
• White TJ, Bruns S, Lee S, Taylor JW. 1990. Amplification and direct sequencing of fungal genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to the methods and applications. New York: Academic Press. p. 315–322.
   Google Scholar
• Wu J, Xie X, Shi Y, Chai A, Wang Q, Li B. 2018. Variation of cassiicolin genes among Chinese isolates of Corynespora cassiicola. Journal of Microbiology 56:634–647.
   Web of Science ®Google Scholar