Phylogenetic relationships of Phaeochorellaparinarii and recognition of a new family, Phaeochorellaceae (Diaporthales)

LITERATURE CITED

• Alvarez LV, Groenewald JZ, Crous PW. 2016. Revising the Schizoparmaceae: Coniella and its synonyms Pilidiella and Schizoparme. Studies in Mycology 85:1–34, doi:10.1016/j.simyco.2016.09.001
   PubMed Web of Science ®Google Scholar
• Arx JA von, Müller E. 1954. Die Gattungen der amerosporen Pyrenomyceten. Beiträge zur Kryptogamenflora der Schweiz 11:1–434.
   Google Scholar
• Atlas of Living Australia. 2019. Web site. [ cited 2018 Jan 28]. Available from: https://bie.ala.org.au/species/http://id.biodiversity.org.au/node/apni/2918944
   Google Scholar
• Bardon L, Chamagne J, Dexter KG, Sothers CA, Prance GT, Chave J. 2013. Origin and evolution of Chrysobalanaceae: insights into the evolution of plants in the Neotropics. Botanical Journal of the Linnean Society 171:19–37, doi:10.1111/j.1095-8339.2012.01289.x
   Web of Science ®Google Scholar
• Barr ME. 1978. The Diaporthales in North America with emphasis on Gnomonia and its segregates. Mycologia Memoirs 7:1–232.
   Google Scholar
• Batista AC, Bezerra JL. 1961. Discomycetidae e Pyrenomycetidae novos ou vulgares. Memórias da Sociedade Broteriana 14:29–47.
   Google Scholar
• Batista AC, Peres GEP. 1960. Ascomycetes Fitoparasitos. Publicações do Instituto de Micologia do Recife (IMUR) 277:1–25.
   Google Scholar
• Cannon PF. 1991. A revision of Phyllachora and some similar genera on the host family Leguminosae. Mycological Papers 163:1–302.
   Google Scholar
• Castlebury LA, Rossman AY, Jaklitsch WJ, Vasilyeva LN. 2002. A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences. Mycologia 94:1017–1031, doi:10.1080/15572536.2003.11833157
   PubMed Web of Science ®Google Scholar
• Chadefaud M. 1960. Traité de botanique sistématique. Tome 1. Les Végétaux non vasculaires (Cryptogamie). Paris: Masson. 1018 pp.
   Google Scholar
• Chardón CE, Toro RA. 1930. Mycological explorations of Colombia. Journal of the Department of Agriculture of Porto Rico 14:195–369.
   Google Scholar
• Cheewangkoon R, Groenewald JZ, Verkley GJ M, Hyde KD, Wingfield MJ, Gryzenhout M, Summerell BA, Denman S, Toanun C, Crous PW. 2010. Evaluation of Cryptosporiopsis eucalypti and Cryptosporiopsis-like species occurring on Eucalyptus leaves. Fungal Diversity 44:89–105, doi:10.1007/s13225-010-0041-5
   Web of Science ®Google Scholar
• Crous PW, Summerell BA, Shivas RG, Carnegie AJ, Groenewald JZ. 2012. Aappraisal of Harknessia (Diaporthales), and the introduction of Harknessiaceae fam. nov. Persoonia 28:49–65, doi:10.3767/003158512X639791
   PubMed Web of Science ®Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772, doi:10.1038/nmeth.2109
   Web of Science ®Google Scholar
• de Hoog GS, van den Ende AHG. 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
• Dennis RWG. 1970. Fungus flora of Venezuela and adjacent countries. Kew Bulletin Additional Series 3: 1–531.
   Google Scholar
• Doidge EM. 1942. Revised descriptions of South African species of Phyllachora and related genera. Bothalia 4:421–463.
   Google Scholar
• Doidge EM. 1950. The South African fungi and lichens to the end of 1945. Bothalia 5:1–1094.
   Google Scholar
• Eriksson OE. 2001. Outline of Ascomycota. Myconet 6:1–27.
   Google Scholar
• GBIF.org. 2018. GBIF occurrence download. [ cited 2018 May 18]. Available from: https://www.gbif.org/species/2985023
   Google Scholar
• Gryzenhout M, Myburg H, Wingfield BD. 2006. Cryphonectriaceae (Diaporthales), a new family including Cryphonectria, Chrysoporthe, Endothia and allied genera. Mycologia 98:239–249, doi:10.3852/mycologia.98.2.239
   PubMed Web of Science ®Google Scholar
• Guterres DC, Galvão-Elias S, Souza BCP, Pinho DB, Santos MDM, Miller RNG, Dianese JC. 2018. Taxonomy, phylogeny, and divergence time estimation for Apiosphaeria guaranitica, a Neotropical parasite on bignoniaceous hosts. Mycologia 110:526–545, doi:10.1080/00275514.2018.1465774
   PubMed Web of Science ®Google Scholar
• Hennings P. 1901. Fungi. In: Engler A, ed. Beiträge zur Flora von Afrika XXII. Botanische Jahrbücher für Systematik Pflanzengeschichte und Pflanzengeographie 30:254–257.
   Google Scholar
• Hyde KD, Alcorn JL. 1993. Some disease-associated microorganisms on plants of Cape York Peninsula and Torres Strait Islands. Australasian Plant Pathology 22:73–83, doi:10.1071/APP9930073
   Google Scholar
• Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772–780, doi:10.1093/molbev/mst010
   PubMed Web of Science ®Google Scholar
• Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649, doi:10.1093/bioinformatics/bts199
   PubMed Web of Science ®Google Scholar
• Kim S, Kjer KM, Duckett CN. 2003. Comparison between molecular and morphological-based phylogenies of galerucine/alticine leaf beetles Coleoptera (Chrysomelidae). Insect Systematics and Evolution 34:53–64, doi:10.1163/187631203788964890
   Web of Science ®Google Scholar
• Kirk PM, Cannon PF, Minter DW, Stalpers JA. 2008. Dictionary of the fungi. 10th ed. Wallingford, UK: CAB International. 771 p.
   Google Scholar
• Larsson A. 2014. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30:3276–3278, doi:10.1093/bioinformatics/btu531
   PubMed Web of Science ®Google Scholar
• Liu YJ, Whelen S, Hall BD. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16:1799–1808, doi:10.1093/oxfordjournals.molbev.a026092
   PubMed Web of Science ®Google Scholar
• Maharachchikumbura SSN, Hyde KD, Gareth-Jones EB, McKenzie EHC, Huang S-K, Abdel-Wahab MA, Daranagama DA, Dayarathne M, D’Souza MJ, Goonasekara ID, Hongsanan S, Jayawardena RS, Kirk PM, Konta S, Liu J-K, Liu Z-Y, Norphanphoun C, Pang K-L, Perera RH, Senanayake IC, Shang Q, Shenoy DB, Xiao Y, Bahkali AH, Kang J, Somrothipol S, Suetrong S, Wen T, Xu J. 2015. Towards a natural classification and backbone tree for Sordariomycetes. Fungal Diversity 72:199–301, doi:10.1007/s13225-015-0331-z
   Web of Science ®Google Scholar
• Mardones M, Trampe-Jaschik T, Hofmann TA, Piepenbring M. 2018. Contribution to the phylogeny and a new species of Coccodiella (Phyllachorales). Mycological Progress 17:205–213, doi:10.1007/s11557-017-1353-6
   Web of Science ®Google Scholar
• Mardones M, Trampe-Jaschik T, Oster S, Elliott M, Urbina H, Schmitt I, Piepenbring M. 2017. Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci. Persoonia 39:74–90, doi:10.3767/persoonia.2017.39.04
   PubMed Web of Science ®Google Scholar
• Medeiros RM. 1994. Fungos Phyllachorales associados a plantas nativas do Cerrado [MSc thesis]. Brasília, Brazil: Universidade de Brasília. 150 p.
   Google Scholar
• Mejía LC, Castlebury LA, Rossman AY, Sogonov  MV, White JF. 2011. A systematic account of the genus Plagiostoma (Gnomoniaceae, Diaporthales) based on morphology, host associations, and a four-gene phylogeny. Studies in Mycology 68:211–235, doi:10.3114/sim.2011.68.10
   PubMed Web of Science ®Google Scholar
• Mendes MAS, da Silva VL, Dianese JC, Ferreira MASV, Santos CEN, Gomes Neto E, Urben AF, Castro C. 1998. Fungos em Plantas no Brasil. Brasília, Brazil: Embrapa-SPI/Embrapa-Cenargen. 569 p.
   Google Scholar
• Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES science gateway for inference of large phylogenetic trees. In: Proceedings of the Gateway Computing Environments Workshop; 14 Nov 2010; New Orleans, LA. IEEE. p. 1–8. doi:10.1109/GCE.2010.5676129
   Google Scholar
• Monod M. 1983. Monographie taxonomique des Gnomoniaceae (Ascomycetes) de l‘ordre des Diaporthales) I Beih. Sydowia 9:1–315.
   Google Scholar
• Müller E, Arx JA von. 1973. Pyrenomycetes: Meliolales, Coronophorales, Spaeriales. In: Ainsworth GC, Sparrow FK, Sussman AS, eds. The Fungi. Vol. IV A. New York: Academic Press. p. 87–132.
   Google Scholar
• Nakari T, Alatalo E, Penttilä ME. 1993. Isolation of Trichoderma reesei genes highly expressed on glucose-containing media: characterization of the tef1 gene encoding translation elongation factor 1 alpha. Gene 136:313–318, doi:10.1016/0378-1119(93)90486-M
   PubMed Web of Science ®Google Scholar
• Nannfeldt JA. 1932. Studien über die Morphologie und Systematik der nichlichenisierten inoperculaten Discomyceten. Nova Acta Regiae Societatis Scientiarum Upsaliensis Series 4:1–368.
   Google Scholar
• Norphanphoun C, Hongsanan S, Doilom M, Bhat DJ, Wen TC, Senanayake IC, Bulgakov TS, Hyde KD. 2016. Lamproconiaceae fam. nov. to accommodate Lamproconium desmazieri. Phytotaxa 270:89–102, doi:10.11646/phytotaxa.270.2.2
   Web of Science ®Google Scholar
• Parker EJ. 1978. Causes of damage to some Zambian wild fruit trees. Zambian Jounal of Science and Technology 3:74–83.
   Google Scholar
• Peregrine WTH, Siddiqi MA. 1972. A revised and annotated list of plant diseases in Malawi. Phytopathological Papers 16. Kew, UK: Commonwealth Mycological Institute. 51 p.
   Google Scholar
• Petrak F. 1947. Über die Gattungen Phaeochorella Theiss. et Syd. und Phomachorella n. gen. Sydowia 1:120–126.
   Google Scholar
• Ramakrishnan TS, Ramakrishnan K. 1948. Additions to fungi of Madras IV. Proceedings of the Indian Academy of Sciences Section B 27:33–46.
   Google Scholar
• Ranwez V, Harispe S, Delsuc F, Douzery EJ. 2011. MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS ONE 6:e22594, doi:10.1371/journal.pone.0022594
   PubMed Web of Science ®Google Scholar
• Rede speciesLink. 2019. Web site. [cited 2019 Jan 15]. Available from: http://www.splink.org.br
   Google Scholar
• Rehner SA, Buckley E. 2005. A Beauveria phylogeny inferred from nuclear ITS and EF1-α sequences: evidence for cryptic diversification and links to Cordyceps teleomorphs. Mycologia 97:84–89, doi:10.1080/15572536.2006.11832842
   PubMed Web of Science ®Google Scholar
• Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574, doi:10.1093/bioinformatics/btg180
   PubMed Web of Science ®Google Scholar
• Rossman AY, Farr DF, Castlebury LA. 2007. A review of the phylogeny and biology of the Diaporthales. Mycoscience 48:135–144, doi:10.1007/S10267-007-0347-7
   Google Scholar
• Senanayake IC, Crous PW, Groenewald JZ, Maharachchikumbura SSN, Jeewon J, Phillips AJL, Bhat JD, Perera RH, Li QR, Li WJ, Tangthirasunun N. 2017. Families of Diaporthales based on morphological and phylogenetic evidence. Studies in Mycology 86:217–296, doi:10.1016/j.simyco.2017.07.003
   PubMed Web of Science ®Google Scholar
• Sogonov MV, Castlebury LA, Rossman AY, Mejía LC, White JF. 2008. Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales. Studies in Mycology 62:1–79.
   PubMed Web of Science ®Google Scholar
• Souza BCP. 2017. Ascomicetos associados a plantas da reserva natural da Embrapa Cerrados, Distrito Federal [MSc thesis]. Brasília, Brazil: Universidade de Brasília. 129 p.
   Google Scholar
• Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313, doi:10.1093/bioinformatics/btu033
   PubMed Web of Science ®Google Scholar
• Suetrong S, Klaysuban A, Sakayaroj J, Preedanon S, Rung-areerate P, Phongpaichit S, Pang KL, Gareth Jones EB. 2015. Tirisporellaceae, a new family in the order Diaporthales (Sordariomycetes, Ascomycota). Cryptogamie Mycologie 36:319–330, doi:10.7872/crym/v36.iss3.2015.319
   Web of Science ®Google Scholar
• Sung GH, Sung JM, Hywel-Jones NL, Spatafora JW. 2007. A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach. Molecular Phylogenetics and Evolution 44:1204–1223, doi:10.1016/j.ympev.2007.03.011
   PubMed Web of Science ®Google Scholar
• The Plant List. 2019. Version 1.1. [cited 2019 Jan 14]. Available from: http://www.theplantlist.org/
   Google Scholar
• Theissen F, Sydow H. 1915. Die Dothideales. Kritisch-systematische Originaluntersuchungen. Annales Mycologici 13:147–746.
   Google Scholar
• Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172:4238–4246, doi:10.1128/jb.172.8.4238-4246.1990
   PubMed Web of Science ®Google Scholar
• Voglmayr H, Jaklitsch WM. 2014. Stilbosporaceae resurrected generic reclassification and speciation. Persoonia 33:61–82, doi:10.3767/003158514X684212
   PubMed Web of Science ®Google Scholar
• Voglmayr H, Rossman AY, Castlebury LA, Jaklitsch WM. 2012. Multigene phylogeny and taxonomy of the genus Melanconiella (Diaporthales). Fungal Diversity 57:1–44, doi:10.1007/s13225-012-0175-8
   Web of Science ®Google Scholar
• Walker DM, Castlebury LA, Rossman AY, Sogonov MV, White JF. 2010. Systematics of genus Gnomoniopsis (Gnomoniaceae, Diaporthales) based on a three-gene phylogeny, host associations and morphology. Mycologia 102:1479–1496, doi:10.3852/10-002
   PubMed Web of Science ®Google Scholar
• Walker DM, Castlebury LA, Rossman AY, White JF. 2012. Phylogeny and taxonomy of Ophiognomonia (Gnomoniaceae, Diaporthales), including twenty-five new species in this highly diverse genus. Fungal Diversity 57:85–147, doi:10.1007/s13225-012-0200-y
   Web of Science ®Google Scholar
• Wehmeyer LE. 1975. The Pyrenomycetous Fungi. Mycologia Memoirs 6:1–250.
   Google Scholar
• White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ, eds. PCR protocols: a guide to methods and applications. New York: Academic Press. p. 315–322.
   Google Scholar
• Whiteside JO. 1966. A revised list of plant diseases in Rhodesia. Kirkia 5:87–196.
   Google Scholar
• Wiehe PO. 1953. The plant diseases of Nyasaland. Mycological Papers 53:1–39.
   Google Scholar
• Wijayawardene NN, Hyde KD, Wanasinghe DN, Papizadeh M, Goonasekara ID, Camporesi E, Bhat JD, McKenzie EHC, Phillips AJL, Diederich P, Tanaka K, Li WJing, Tangthirasunun N, Phookamsak R, Dai DQin, Dissanayake AJ, Weerakoon G, Maharachchikumbura SSN, Hashimoto A, Matsumura M, Bahkali AH, Wang Y. 2016. Taxonomy and phylogeny of dematiaceous coelomycetes. Fungal Diversity 77:1–316, doi:10.1007/s13225-016-0360-2
   Web of Science ®Google Scholar
• [WCSP] World Checklist of Selected Plant Families. 2019. Web site. Facilitated by the Royal Botanic Gardens, Kew. [cited 2019 Jan 14]. Available from: http://wcsp.science.kew.org
   Google Scholar
• Yang Q, Fan XL, Du Z, Tian CM. 2018. Diaporthosporellaceae, a novel family of Diaporthales (Sordariomycetes, Ascomycota). Mycoscience 59:229–235, doi:10.1016/j.myc.2017.11.005
   Web of Science ®Google Scholar