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Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan



The genus Coniochaeta is an important ascomycete because its members live in diversified habitats and nutritional modes. In this study, two new species, C. acaciae and C. coluteae, are introduced from dead branches of Acacia sp. and Colutea paulsenii Freyn (both Fabaceae) respectively from Uzbekistan, based on morphological and phylogenetic studies. Analyses of combined ITS and LSU sequence data with Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and comparison of similar taxa, provide evidences for placement of these new species in Coniochaeta, as distinct lineages.


ascomycetous microfungi, Central Asia, Coniochaetales, Fabaceae, phylogenetic analyses, Fungi

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Alves, A., Correia, A., Luque, J. & Phillips, A.J.L. (2004) Botryosphaeria corticola, sp. nov. on Quercus species, with notes and description of Botryosphaeria stevensii and its anamorph, Diplodia mutila. Mycologia 96: 598–613.

Asgari, B., Zare, R. & Gams, W. (2007) Coniochaeta ershadii, a new species from Iran, and a key to well-documented Coniochaeta species. Nova Hedwigia 84: 175−187.

Bruen, T.C., Philippe, H. & Bryant, D. (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665–2681.

Carbone, I. & Kohn, L.M. (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553–556.

Chang, J.H. & Wang, Y.Z. (2011) Taxonomy of Coniochaeta leucoplaca and C. velutina: morphological and molecular studies based on LSU rDNA of isolates from Taiwan. Nova Hedwigia 92: 57−67.

Checa, J. (1988) The genus Coniochaeta (Sacc.) Cooke (Coniochaetaceae, Ascomycotina) in Spain. Cryptogamie Mycologie 9: 1−34.

Choi, Y.W., Hyde, K.D. & Ho, W.H. (1999) Single spore isolation of fungi. Fungal Diversity 3: 2938.

Chomnunti, P., Hongsanan, S., Hudson, B.A., Tian, Q., Peršoh, D., Dhami, M.K., Alias, A.S., Xu, J., Liu, X., Stadler, M. & Hyde, K.D. (2014) The Sooty Moulds. Fungal Diversity 66: 1–36.

Cooke, M.C. (1887) New Australian fungi. Grevillea 16: 1–6.

Damm, U., Fourie, P.H. & Crous, P.W. (2010) Coniochaeta (Lecythophora), Collophora gen. nov. and Phaeomoniella species associated with wood necroses of Prunus trees. Persoonia 24: 60–80.

Friebes, G., Jaklitsch, W.M., García, S. & Voglmayr, H. (2016) Lopadostoma taeniosporum revisited and a new species of Coniochaeta. Sydowia 68: 87–97.

Gafforov, Y.S. (2017) A preliminary checklist of Ascomycetous microfungi from Southern Uzbekistan. Mycosphere 8: 660–696.

García, D., Stchigel, A.M., Cano, J., Calduch, M., Hawksworth, D.L. & Guarro, J. (2006) Molecular phylogeny of Coniochaetales. Mycological Research 110: 1271–1289.

Gulyamova, M.G., Kuchmi, N.P., Ramazanova, S.S., Sagdullaeva, M.S.H. & Kirgizbaeva, K.H.M. (1990) Fungal Flora of Uzbekistan. vol. 7. Ascomycete fungi. Fan Publishing House, Tashkent, pp. 1–196. [In Russian]

GBIF (2017) Available from: org (accessed 21 September 2017)

Greville, K.R. (1823–1824) Scottish cryptogamic flora 2: 82–83.

Hall, T.A. (2004) BioEdit Sequence Alignment Editor 7.0. 1. Carlsbad, CA, USA: Isis Pharmaceuticals.

Hernández-Restrepo, M., Groenewald, J.Z. & Crous, P.W. (2015) Neocordana gen. nov., the causal organism of Cordana leaf spot on banana. Phytotaxa 205: 229–238.

Hawksworth, D.L. & Yip, H.Y. (1981) Coniochaeta angustispora sp. nov. from roots in Australia, with a key to the species known in culture. Australian Journal of Botany 29: 377–384.

Hongsanan, S., Maharachchikumbura, S.S.N., Hyde, K.D., Samarakoon, M.C., Jeewon, R., Zhao, Q., Al-Sadi, A.M. & Bahkali, A.H. (2017) An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence. Fungal Diversity 84: 25–41.

Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755.

Huhndorf, S.M., Miller, A.N. & Fernández, F.A. (2004) Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia 96: 368–387.

Huson, D.H. & Bryant, D. (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267.

Huson, D.H. (1998) Splits Tree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68–73.

Index Fungorum (2017) Available from: (accessed 21 September 2017)

Jayasiri, S.C., Hyde, K.D., Abd-Elsalam, K.A., Abdel-Wahab, M.A., Ariyawansa, H.A., Bhat, J., Buyck, B., Dai, Y.C., Ertz, D., Hidayat, I., Jeewon, R., Jones, E.B.G., Karunarathna, S.C., Kirk, P., Lei, C., Liu, J.K., Maharachchikumbura, S.S.N., McKenzie, E., Ghobad-Nejhad, M., Nilsson, H., Pang, K.L., Phookamsak, R., Rollins, A.W., Romero, A.I., Stephenson, S., Suetrong, S., Tsui, C.K.M., Vizzini, A., Wen, T.C., De Silva, N.I., Promputtha, I. & Kang, J.C. (2015) The faces of fungi database: fungal names linked with morphology, molecular and human attributes. Fungal Diversity 74: 18–357.

Jaklitsch, W.M., Komon, M., Kubicek, C.P. & Druzhinina, I.S. (2005) Hypocrea voglmayrii sp. nov. from the Austrian Alps represents a new phylogenetic clade in Hypocrea/ Trichoderma. Mycologia 97: 1365–1378.

Kamiya, S., Uchiyama, S. & Udagawa, S.I. (1995) Two new species of Coniochaeta with a cephalothecoid peridium wall. Mycoscience 36: 377–383.

Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30: 772–780.

Khan, Z., Gené, J., Ahmad, S., Cano, J., Al-Sweih, N., Joseph, L., Chandy, R. & Guarro, J. (2013) Coniochaeta polymorpha, a new species from endotracheal aspirate of a preterm neonate, and transfer of Lecythophora species to Coniochaeta. Antonie van Leeuwenhoek 104: 243–252.

Kirk, P.M., Cannon, P.F., Minter, D.W. & Stalpers, J.A. (2008) Dictionary of the fungi, 10th edn. CABI, Wallingford.

Kumar, S. & Hedges, S.B. (1998) A molecular time scale for vertebrate evolution. Nature 392: 917–920.

Liu, Y.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution 16: 1799–1808.

Maharachchikumbura, S.S.N., Hyde, K.D., Jones, E.B.G., McKenzie, E.H.C., Bhat, J.D., Dayarathne, M.C., Huang, S.K., Norphanphoun, C., Senanayake, I.C., Perera, R.H., Shang, Q.J., Xiao, Y., D’souza, M.J., Hongsanan, S., Jayawardena, R.S., Daranagama, D.A., Konta, S., Goonasekara, I.D., Zhuang, W.Y., Jeewon, R., Phillips, A.J.L., Abdel-Wahab, M.A., Al-Sadi, A.M., Bahkali, A.H., Boonmee, S., Boonyuen, N., Cheewangkoon, R., Dissanayake, A.J., Kang, J., Li, Q.R., Liu, J.K., Liu, X.Z., Liu, Z.Y., Luangsa-ard, J.J., Pang, K.L., Phookamsak, R., Promputtha, I., Suetrong, S., Stadler, M., Wen, T. & Wijayawardene, N.N. (2016) Families of Sordariomycetes. Fungal Diversity 79: 1–317.

Maharachchikumbura, S.S.N., Hyde, K.D., Jones, E.B.G., McKenzie, E.H.C., Huang, S-K., Abdel-Wahab, M.A., Daranagama, D.A., Dayarathne, M., D’souza, M.J., Goonasekara, I.D., Hongsanan, S., Jayawardena, R.S., Kirk, P.M., Konta, S., Liu, J-K., Liu, Z-Y., Norphanphoun, C., Shenoy, B.D., Xiao, Y., Bahkali, A.H., 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.

Malloch, D. & Cain, R.F. (1971) New cleistothecial Sordariaceae and a new family, Coniochaetaceae. Canadian Journal of Botany 49: 869–880.

Miller, A.N., Huhndorf, S.M. & Fournier, J. (2014) Phylogenetic relationships of five uncommon species of Lasiosphaeria and three new species in the Helminthosphaeriaceae (Sordariomycetes). Mycologia 106: 505–524.

Nylander, J.A.A. (2004) MrModeltest 2.0. Program distributed by author. Evolutionary Biology Centre, Uppsala University.

Perdomo, H., García, D., Gené, J., Cano, J., Sutton, D.A., Summerbell, R. & Guarro, J. (2013) Phialemoniopsis, a new genus of Sordariomycetes, and new species of Phialemonium and Lecythophora. Mycologia 105: 398–421.

Perera, R.H., Maharachchikumbura, S.S.N., Bhat, J.D., Al-Sadi, A.M., Liu, J.K., Hyde, K.D. & Liu, Z.Y. (2016) New species of Thozetella and Chaetosphaeria and new records of Chaetosphaeria and Tainosphaeria from Thailand. Mycosphere 7: 1301–1321.

Quaedvlieg, W., Binder, M., Groenewald, J.Z., Summerell, B.A., Carnegie, A.J., Burgess, T.I. & Crous, P.W. (2014) Introducing the consolidated species concept to resolve species in the Teratosphaeriaceae. Persoonia 33: 1–40.

Raja, H.A., Fournier, J., Shearer, C.A. & Miller, A.N. (2012) Freshwater ascomycetes: Coniochaeta gigantospora sp. nov. based on morphological and molecular data. Mycoscience 53: 373–380.

Raju, N.B. & Perkins, D.D. (2000) Programmed ascospore death in the homothallic ascomycete Coniochaeta tetraspora. Fungal Genetics and Biology 30: 213–221.

Ramaley, A.W. (1997) Barrina, a new genus with polysporous asci. Mycologia 89: 962–966.

Rambaut, A. & Drummond, A.J. (2003) Tracer: MCMC trace analysis tool. University of Oxford, Oxford.

Rambaut, A. (2006) FigTree. Tree figure drawing tool version 1.3.1, Institute of Evolutionary Biology, University of Edinburgh. Available from: (accessed 1 January 2018)

Sanderson, M.J., Donoghue, M.J., Piel, W. & Eriksson, T. (1994) TreeBase: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. The Journal of the Botany American 81: 6.

Silvestro, D. & Michalak, I. (2012) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity and Evolution 12: 335−337.

Spatafora, J.W., Sung, G-H., Johnson, D., Hesse, C., O’Rourke, B., Serdani, M., Spotts, R., Lutzoni, F., Hofstetter, V., Miadlikowska, J., Reeb, V., Gueidan, C., Fraker, E., Lumbsch, T., Lücking, R., Schmitt, I., Hosaka, K., Aptroot, A., Roux, C., Miller, A.N., Geiser, D.M., Hafellner, J., Hestmark, G., Arnold, A.E., Büdel, B., Rauhut, A., Hewitt, D., Untereiner, W.A., Cole, M.S., Scheidegger, C., Schultz, M., Sipman, H. & Schoch, C.L. (2006) A five-gene phylogeny of Pezizomycotina. Mycologia 98: 1018−1028.

Swofford, D.L. (2002) PAUP*: phylogenetic analysis using parsimony, version 4.0 b10. Sinauer Associates, Sunderland.

Troy, G.C., Panciera, D.L., Pickett, J.P., Sutton, D.A., Gene, J., Cano, J.F., Guarro, J., Thompson, E.H. & Wickes, B.L. (2013) Mixed infection caused by Lecythophora canina sp. nov. and Plectosphaerella cucumerina in a German shepherd dog. Medical Mycology 51: 455−460.

van Heerden, A., van Zyl, W.H., Cruywagen, C.W., Mouton, M. & Botha, A. (2011) The lignicolous fungus Coniochaeta pulveracea and its interactions with syntrophic yeasts from the woody phylloplane. Microbial Ecology 62: 609.

Vázquez-Campos, X., Kinsela, A.S., Waite, T.D., Collins, R.N. & Neilan, B.A. (2014) Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta fodinicola sp. nov., two uranium mine-inhabiting Ascomycota fungi from northern Australia. Mycologia 106: 1073–1089.

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.

Weber, E. (2002) The Lecythophora-Coniochaeta complex I. Morphological studies on Lecythophora species isolated from Picea abies. Nova Hedwigia 74: 159–185.

Weber, E., Görke, C. & Begerow, D. (2002) The Lecythophora-Coniochaeta complex: II. Molecular studies based on sequences of the large subunit of ribosomal DNA. Nova Hedwigia 74: 187–200.

White, T.J., Bruns, T., Lee, J. & Taylor, S.B. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J. & White, T.J. (Eds.) PCR protocols: a guide to methods and applications. Academic Press, San Diego, California, USA, pp. 315–322.

Wijayawardene, N.N., Hyde, K.D., Rajeshkumar, K.C., Hawksworth, D.L., Madrid, H., Kirk, P.M., Braun, U., Singh, R.V., Crous, P.W., Kukwa, M., Lücking, R., Kurtzman, C.P., Yurkov, A., Haelewaters, D., Aptroot, A., Lumbsch, H.T., Timdal, E., Ertz, D., Etayo, J., Phillips, A.J.L., Groenewald, J.Z., Papizadeh, M., Selbmann, L., Dayarathne, M.C., Weerakoon, G., Jones, E.B.G., Suetrong, S., Tian, Q., Castañeda-Ruiz, R.F., Bahkali, A.H., Pang, K-L., Tanaka, K., Dai, D.Q., Sakayaroj, J., Hujslová, M., Lombard, L., Shenoy, B.D., Suija, A., Maharachchikumbura, S.S.N., Thambugala, K.M., Wanasinghe, D.N., Sharma, B.O., Gaikwad, S., Pandit, G., Zucconi, L., Onofri, S., Egidi, E., Raja, H.A., Kodsueb, R., Cáceres, M.E.S., Pérez-Ortega, S., Fiuza, P.O., Monteiro, J.S., Vasilyeva, L.N., Shivas, R.G., Prieto, M., Wedin, M., Olariaga, I., Lateef, A.A., Agrawal, Y., Fazeli, S.A.S., Amoozegar, M.A., Zhao, G.Z., Pfliegler, W.P., Sharma, G., Oset, M., Abdel-Wahab, M.A., Takamatsu, S., Bensch, K., de Silva, N.I., De Kese, A., Karunarathna, A., Boonmee, S., Pfister, D.H., Lu, Y-Z., Luo, Z-L., Boonyuen, N., Daranagama, D.A., Senanayake, I.C., Jayasiri, S.C., Samarakoon, M.C., Zeng, X-Y., Doilom, M., Quijada, L., Rampadarath, S., Heredia, G., Dissanayake, A.J., Jayawardana, R.S., Perera, R.H., Tang, L.Z., Phukhamsakda, C., Hernández-Restrepo1, M., Ma, X., Tibpromma, S., Gusmao, L.F.P., Weerahewa, D. & Karunarathna, S.C. (2017) Notes for genera-Ascomycota. Fungal Diversity 86: 1–594.

Zhaxybayeva, O. & Gogarten, J.P. (2002) Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses. Genomics 3: 1–15.


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