Abstract
A new species of Koorchaloma is described based on morphology and multigene phylogenetic analyses of ITS, LSU and RPB2. Phylogenetic analyses showed our strain clusters with K. europaea with moderate statistical support. Koorchaloma oryzae sp. nov. is morphologically similar to K. europaea, but it can be distinguished by the conidiophores and conidia, while ITS pairwise nucleotide comparison of these two species also revealed differences. Koorchaloma oryzae is compared with all known Koorchaloma species, and a key to Koorchaloma species is provided. Genealogical concordance phylogenetic species recognition analysis (PHI test) results of the new species and closely related species are also given.
References
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Katoh, K., Rozewicki, J. & Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
Kohlmeyer, J. & Volkmann-Kohlmeyer, B. (2001) Fungi on Juncus roemerianus. 16. More new Coelomycetes, including Tetranacriella, gen. nov. Botanica Marina 44: 147–156. https://doi.org/10.1515/BOT.2001.020
Li, W.J., McKenzie, E.H.C, Liu, J.K., Bhat, D.J., Dai, D.Q., Camporesi, E., Tian, Q., Maharachchikumbura, S.S.N, Luo, Z.L. & Shang, Q.J. (2020) Taxonomy and phylogeny of hyaline-spored coelomycetes. Fungal Diversity 100: 279–801. https://doi.org/10.1007/s13225-020-00440-y
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. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 Gateway Computing Environments Workshop (GCE). New Orleans, Louisiana, November 2010. pp. 1–8. https://doi.org/10.1109/GCE.2010.5676129
Nag Raj, T. (1984) Koorchaloma, Koorchalomella, and Kananascus gen. nov. Mycotaxon 19: 167–212.
Nag Raj, T. (1993) Coelomycetous anamorphs with appendage-bearing conidia. Mycologue Publications, Waterloo, pp. 1–1101.
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. https://doi.org/10.3767/003158514X681981
Sarma, V.V., Newell, S. & Hyde, K.D. (2001) Koorchaloma spartinicola sp. nov., a new marine sporodochial fungus from Spartina alterniflora. Botanica Marina 44: 321–326. https://doi.org/10.1515/BOT.2001.041
Senanayake, I., Rathnayake, A., Marasinghe, D., Calabon, M., Gentekaki, E. & Lee, H. (2020) Morphological approaches in studying fungi: collection, examination, isolation, sporulation and preservation. Mycosphere 11: 2678–2754. https://doi.org/10.5943/mycosphere/11/1/20
Species Fungorum (2021). Available online: http://www.speciesfungorum.org/Names/Names.asp (accessed 12 August 2021)
Stamatakis, A., Hoover, P. & Rougemont, J. (2008) A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57: 758–771. https://doi.org/10.1080/10635150802429642
Subramanian, C. (1953) Koorchaloma, a new genus of the Tuberculariaceae. Journal of the Indian Botanical Society 32: 123–126.
Tibpromma, S., Hyde, K.D., McKenzie, E.H.C., Bhat, D.J., Phillips, A.J., Wanasinghe, D.N., Samarakoon, M.C., Jayawardena, R.S., Dissanayake, A.J. & Tennakoon, D.S. (2018) Fungal diversity notes 840–928: micro-fungi associated with Pandanaceae. Fungal Diversity 93: 1–160. https://doi.org/10.1007/s13225-018-0408-6
Treigienë, A. (2006) New species of Kananascus and its anamorph from Lithuania. Mycotaxon 96: 173–180.
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. https://doi.org/10.1128/jb.172.8.4238-4246.1990
White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications 18: 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Wijayawardene, N.N., Hyde, K.D., Al-Ani, L.K.T., Tedersoo, L., Rajeshkumar, K.C., Zhao, R.L., Aptroot, A., Leontyev, D.V., Saxena, R.K., Tokarev, Y.S., Dai, D.Q., Letcher, P.M., Stephenson, S.L., Ertz, D., Lumbsch, H.T., Haelewaters, D., Bensch, K., Madrid, H., Kukwa, M., Issi, I.V., Lateef, A.A., Phillips, A.J.L., Selbmann, L., Pfliegler, W.P., Horváth, E., Pereira, O.L., Kirk, P.M., Kola?íková, Z., Raja, H.A., Radek, R., Papp, V., Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P.B., Triebel, D., Gautam, A.K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S.C., Delgado, G., Réblová, M., Doilom, M., Dolatabadi, S., Paw?owska, J., Humber, R.A., Kodsueb, R., Sánchez-Castro, I., Goto, B.T., Silva, D.K.A., de Souza, F.A., Oehl, F., da Silva, G.A., Silva, I.R., B?aszkowski, J., Jobim, K., Maia, L.C., Barbosa, F.R., Fiuza, P.O., Divakar, P.K., Shenoy, B.D., Castañeda-Ruiz, R.F., Somrithipo, S., Karunarathna, S.C., Tibpromma, S., Mortimer, P.E., Wanasinghe, D.N., Phookamsak, R., Xu, J.C., Wang, Y., Fenghua, T., Alvarado, P., Li, D.W., Kušan, I., Mato?ec, N., Maharachchikumbura, S.S.N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V.P., Lawrey, J.D., Santiago, A.L.C.M.A., Bezerra, J.D.P., Souza-Motta, C.M., Firmino, A.L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A.J., Monteiro, J.S., Grossart, H.P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Kuhnert, E., Vázquez, V., Mungai, P., Damm, U., Li, Q.R., Zhang, H., Boonmee, S., Lu, Y.Z., Becerra, A.G., Kendrick, B., Brearley, F.Q., Motiej?naitë, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D.S.A., Tang, L.Z., He, M.Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M.P., McKenzie, E.H.C., Stadler, M., Bhat, D.J., Liu, J.K., Raza, M., Jeewon, R., Nassonova, E.S., Prieto, M., Jayalal, R.G.U., Erdoðdu, M., Yurkov, A., Schnittler, M., Shchepin, O.N., Novozhilov, Y.K., Silva-Filho, A.G.S., Gentekaki, E., Liu, P., Cavender, J.C., Kang, Y., Mohammad, S., Zhang, L.F., Xu, R.F., Li, Y.M., Dayarathne, M.C., Ekanayaka, A.H., Wen, T.C., Deng, C.Y., Pereira, O.L., Navathe, S., Hawksworth, D.L., Fan, X.L., Dissanayake, L.S., Kuhnert, E., Grossart, H.P. & Thines, M. (2020) Outline of fungi and fungus-like taxa. Mycosphere 11: 1060–1456. https://doi.org/10.5943/mycosphere/11/1/8
Bruen, T.C., Philippe, H. & Bryant, D. (2006) A simple and robust statistical test for detecting the presence of recombination. Genetics 172: 2665–2681. https://doi.org/10.1534/genetics.105.048975
Buchan, A., Newell, S.Y., Moreta, J.I.L. & Moran, M.A. (2002) Analysis of internal transcribed spacer (ITS) regions of rRNA genes in fungal communities in a southeastern U.S. salt marsh. Microbial Ecology 43: 329–340. https://doi.org/10.1007/s00248-001-1062-0
Capella-Gutiérrez, S., Silla-Martínez, J.M. & Gabaldón, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25: 1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Dissanayake, A., Bhunjun, C., Maharachchikumbura, S. & Liu, J.K. (2020) Applied aspects of methods to infer phylogenetic relationships amongst fungi. Mycosphere 11: 2652–2676. https://doi.org/10.5943/mycosphere/11/1/18
Huson, D.H. & Bryant, D. (2006) Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254–267. https://doi.org/10.1093/molbev/msj030
Hyde, K.D. & Goh, T. (1998) Koorchaloma novojournalis sp. nov., a new sporodochial fungus from Hong Kong. Fungal Diversity 1: 193–197.
Hyde, K.D., Norphanphoun, C., Maharachchikumbura, S.S.N., Bhat, D.J., Jones, E.B.G., Bundhun, D., Chen, Y.J., Bao, D.F., Boonmee, S., Calabon, M.S., Chaiwan, N., Chethana, K.W.T., Dai, D.Q., Dayarathne, M.C., Devadatha, B., Dissanayake, A.J., Dissanayake, L.S., Doilom, M., Dong, W., Fan, X.L., Goonasekara, I.D., Hongsanan, S., Huang, S.K., Jayawardena, R.S., Jeewon, R., Karunarathna, A., Konta, S., Kumar, V., Lin, C.G., Liu, J.K., Liu, N.G., Luangsa?ard, J., Lumyong, S., Luo, Z.L., Marasinghe, D.S., McKenzie, E.H.C., Niego, A.G.T., Niranjan, M., Perera, R.H., Phukhamsakda, C., Rathnayaka, A.R., Samarakoon, M.C., Samarakoon, S.M.B.C., Sarma, V.V., Senanayake, I.C., Shang, Q.J., Stadler, M., Tibpromma, S., Wanasinghe, D.N., Wei, D.P., Wijayawardene, N.N., Xiao, Y.P., Yang, J., Zeng, X.Y., Zhang, S.N. & Xiang, M.M. (2020) Refined families of Sordariomycetes. Mycosphere 11: 305–1059. https://doi.org/10.5943/mycosphere/11/1/7
Index Fungorum (2021) Available online: http://www.indexfungorum.org/Names/Names.asp (accessed on 12 August 2021).
Jayasiri, S.C., Hyde, K.D., Ariyawansa, H.A., Bhat, D.J., Buyck, B., Cai, L., Dai, Y.C., Abd-Elsalam, K.A., Ertz, D., Hidayat, I., Jeewon, R., Jones, E.B.G., Bahkali, A.H., Karunarathna, S.C., Liu, J.K., Luangsa-ard, J.J., Lumbsch, H.T., Maharachchikumbura, S.S.N., McKenzie, E.H.C., Moncalvo, J.M., Ghobad-Nejhad, M., Nilsson, H., Pang, K.A., Pereira, O.L., Phillips, A.J.L., Raspé, O., Rollins, A.W., Romero, A.I., Etayo, J., Selçuk, F., Stephenson, S.L., Suetrong, S., Taylor, J.E., Tsui, C.K.M., Vizzini, A., Abdel-Wahab, M.A., Wen, T.C., Boonmee, S., Dai, D.Q., Daranagama, D.A., Dissanayake, A.J., Ekanayaka, A.H., Fryar, S.C., Hongsanan, S., Jayawardena, R.S., Li, W.J., Perera, R.H., Phookamsak, R., de Silva, N.I., Thambugala, K.M., Tian, Q., Wijayawardene, N.N., Zhao, R.L., Zhao, Q., Kang, J.C. & Promputtha, I. (2015) The faces of fungi database: fungal names linked with morphology, phylogeny and human impacts. Fungal Diversity 74: 3–18. https://doi.org/10.1007/s13225-015-0351-8
Katoh, K., Rozewicki, J. & Yamada, K.D. (2019) MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in Bioinformatics 20: 1160–1166. https://doi.org/10.1093/bib/bbx108
Kohlmeyer, J. & Volkmann-Kohlmeyer, B. (2001) Fungi on Juncus roemerianus. 16. More new Coelomycetes, including Tetranacriella, gen. nov. Botanica Marina 44: 147–156. https://doi.org/10.1515/BOT.2001.020
Li, W.J., McKenzie, E.H.C, Liu, J.K., Bhat, D.J., Dai, D.Q., Camporesi, E., Tian, Q., Maharachchikumbura, S.S.N, Luo, Z.L. & Shang, Q.J. (2020) Taxonomy and phylogeny of hyaline-spored coelomycetes. Fungal Diversity 100: 279–801. https://doi.org/10.1007/s13225-020-00440-y
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. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Miller, M.A., Pfeiffer, W. & Schwartz, T. (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: 2010 Gateway Computing Environments Workshop (GCE). New Orleans, Louisiana, November 2010. pp. 1–8. https://doi.org/10.1109/GCE.2010.5676129
Nag Raj, T. (1984) Koorchaloma, Koorchalomella, and Kananascus gen. nov. Mycotaxon 19: 167–212.
Nag Raj, T. (1993) Coelomycetous anamorphs with appendage-bearing conidia. Mycologue Publications, Waterloo, pp. 1–1101.
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. https://doi.org/10.3767/003158514X681981
Sarma, V.V., Newell, S. & Hyde, K.D. (2001) Koorchaloma spartinicola sp. nov., a new marine sporodochial fungus from Spartina alterniflora. Botanica Marina 44: 321–326. https://doi.org/10.1515/BOT.2001.041
Senanayake, I., Rathnayake, A., Marasinghe, D., Calabon, M., Gentekaki, E. & Lee, H. (2020) Morphological approaches in studying fungi: collection, examination, isolation, sporulation and preservation. Mycosphere 11: 2678–2754. https://doi.org/10.5943/mycosphere/11/1/20
Species Fungorum (2021). Available online: http://www.speciesfungorum.org/Names/Names.asp (accessed 12 August 2021)
Stamatakis, A., Hoover, P. & Rougemont, J. (2008) A rapid bootstrap algorithm for the RAxML web servers. Systematic Biology 57: 758–771. https://doi.org/10.1080/10635150802429642
Subramanian, C. (1953) Koorchaloma, a new genus of the Tuberculariaceae. Journal of the Indian Botanical Society 32: 123–126.
Tibpromma, S., Hyde, K.D., McKenzie, E.H.C., Bhat, D.J., Phillips, A.J., Wanasinghe, D.N., Samarakoon, M.C., Jayawardena, R.S., Dissanayake, A.J. & Tennakoon, D.S. (2018) Fungal diversity notes 840–928: micro-fungi associated with Pandanaceae. Fungal Diversity 93: 1–160. https://doi.org/10.1007/s13225-018-0408-6
Treigienë, A. (2006) New species of Kananascus and its anamorph from Lithuania. Mycotaxon 96: 173–180.
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. https://doi.org/10.1128/jb.172.8.4238-4246.1990
White, T.J., Bruns, T., Lee, S. & Taylor, J. (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR protocols: a guide to methods and applications 18: 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Wijayawardene, N.N., Hyde, K.D., Al-Ani, L.K.T., Tedersoo, L., Rajeshkumar, K.C., Zhao, R.L., Aptroot, A., Leontyev, D.V., Saxena, R.K., Tokarev, Y.S., Dai, D.Q., Letcher, P.M., Stephenson, S.L., Ertz, D., Lumbsch, H.T., Haelewaters, D., Bensch, K., Madrid, H., Kukwa, M., Issi, I.V., Lateef, A.A., Phillips, A.J.L., Selbmann, L., Pfliegler, W.P., Horváth, E., Pereira, O.L., Kirk, P.M., Kola?íková, Z., Raja, H.A., Radek, R., Papp, V., Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P.B., Triebel, D., Gautam, A.K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S.C., Delgado, G., Réblová, M., Doilom, M., Dolatabadi, S., Paw?owska, J., Humber, R.A., Kodsueb, R., Sánchez-Castro, I., Goto, B.T., Silva, D.K.A., de Souza, F.A., Oehl, F., da Silva, G.A., Silva, I.R., B?aszkowski, J., Jobim, K., Maia, L.C., Barbosa, F.R., Fiuza, P.O., Divakar, P.K., Shenoy, B.D., Castañeda-Ruiz, R.F., Somrithipo, S., Karunarathna, S.C., Tibpromma, S., Mortimer, P.E., Wanasinghe, D.N., Phookamsak, R., Xu, J.C., Wang, Y., Fenghua, T., Alvarado, P., Li, D.W., Kušan, I., Mato?ec, N., Maharachchikumbura, S.S.N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V.P., Lawrey, J.D., Santiago, A.L.C.M.A., Bezerra, J.D.P., Souza-Motta, C.M., Firmino, A.L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A.J., Monteiro, J.S., Grossart, H.P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Kuhnert, E., Vázquez, V., Mungai, P., Damm, U., Li, Q.R., Zhang, H., Boonmee, S., Lu, Y.Z., Becerra, A.G., Kendrick, B., Brearley, F.Q., Motiej?naitë, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D.S.A., Tang, L.Z., He, M.Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M.P., McKenzie, E.H.C., Stadler, M., Bhat, D.J., Liu, J.K., Raza, M., Jeewon, R., Nassonova, E.S., Prieto, M., Jayalal, R.G.U., Erdoðdu, M., Yurkov, A., Schnittler, M., Shchepin, O.N., Novozhilov, Y.K., Silva-Filho, A.G.S., Gentekaki, E., Liu, P., Cavender, J.C., Kang, Y., Mohammad, S., Zhang, L.F., Xu, R.F., Li, Y.M., Dayarathne, M.C., Ekanayaka, A.H., Wen, T.C., Deng, C.Y., Pereira, O.L., Navathe, S., Hawksworth, D.L., Fan, X.L., Dissanayake, L.S., Kuhnert, E., Grossart, H.P. & Thines, M. (2020) Outline of fungi and fungus-like taxa. Mycosphere 11: 1060–1456. https://doi.org/10.5943/mycosphere/11/1/8