Skip to main content Skip to main navigation menu Skip to site footer
Responsive image
Issue: Vol. 674 No. 3: 28 Nov. 2024
Type: Article
Published: 2024-11-28
DOI: 10.11646/phytotaxa.674.3.1
Page range: 239-251
Abstract views: 27
PDF downloaded: 1

Morpho-molecular analyses reveal Aquadictyospora yunnanensis sp. nov. from coffee (Coffea arabica) in Yunnan Province, China

Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China. School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand. Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand.
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, Yunnan 655011, P.R. China
1 new species, Aquadictyospora yunnanensis, coffee-associated microfungi, multi-gene, phylogeny, taxonomy

Abstract

During a survey of microfungi associated with coffee trees in Jinghong City, Yunnan Province, China, decaying twigs of Arabica coffee with black fungi fruiting bodies were collected, and an interesting fungus was subsequently isolated and identified. Maximum likelihood and Bayesian analyses of combined ITS, LSU, SSU, rpb2, and tef1-α genes showed the fungus belongs to Aquadictyospora (Dictyosporiaceae, Pleosporales) and is well separated from closely related species. Based on morphological comparison with closely related taxa and multigene phylogenetic analyses, Aquadictyospora yunnanensis sp. nov. is introduced, with a description, detailed morphological illustration, and phylogenetic analysis results.

References

  1. Atienza, V., Hawksworth, D.L. & Pérez-Ortega, S. (2021) Verrucoccum (Dothideomycetes, Dictyosporiaceae), a new genus of lichenicolous fungi on Lobaria s. lat. for the Dothidea hymeniicola species complex. Mycologia 113 (6): 1233–1252. https://doi.org/10.1080/00275514.2021.1966281
  2. Berkeley, M.J. & Broome, C.E. (1869) Hemileia vastatrix. Gardeners Chronicle 6: 1157.
  3. Boonmee, S., D’souza, M.J., Luo, Z.L., Pinruan, U., Tanaka, K., Su, H.Y., Bhat, D.J., McKenzie, E.H.C., Jones, E.G.G., Taylor, J.E., Phillips, A.J.L., Hirayama, K., Eungwanichayapant, P.D. & Hyde, K.D. (2016) Dictyosporiaceae fam. nov. Fungal Diversity 80: 457–482. https://doi.org/10.1007/s13225-016-0363-z
  4. 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
  5. Chen, H.Q., Liu, X.G., Xiao, QY., Wu, L., Cheng, M.H., Wang, H.D., Wang, X.L., Hu, D.S., Sun, Z.Q. & Ma, X.D. (2024) Optimizing Split-reduced drip fertigation schemes of Arabica coffee based on soil microcosms, bean yield, quality and flavor in dry-hot region of southwest China. Scientia Horticulturae 336: 113418. https://doi.org/10.1016/j.scienta.2024.113418
  6. do Espírito Santo, B.C., Oliveira, J.A.d.S., Ribeiro, M.A.d., Schoffen, R.P., Polli, A.D., Polonio, J.C., Silva, A.A., Abreu Filho, B.A., Heck, M.C., Meurer, E.C., Constantin, P.P., Pileggi, M., Vicentini, V.E.P., Golias, H.C. & Pamphile, J.A. (2023) Antitumor and antibacterial activity of metabolites of endophytic Colletotrichum siamense isolated from coffee (Coffea arabica L. cv IAPAR-59). Brazilian Journal of Microbiology 54 (4): 2651–2661. https://doi.org/10.1007/s42770-023-01104-0
  7. Dissanayake, A.J., Bhunjun, C.S., Maharachchikumbura, S.S.N. & Liu, J.K. (2020) Applied aspects of methods to infer phylogenetic relationships amongst fungi. Mycosphere 11 (1): 2652–2676. https://doi.org/10.5943/mycosphere/11/1/18
  8. Freitas, V.V., Borges, L.L.R., Vidigal, M.C.T.R., dos Santos, M.H. & Stringheta, P.C. (2024) Coffee: A comprehensive overview of origin, market, and the quality process. Trends in Food Science & Technology 104411. https://doi.org/10.1016/j.tifs.2024.104411
  9. Glez-Peña, D., Gómez-Blanco, D., Reboiro-Jato, M., Fdez-Riverola, F. & Posada, D. (2010) ALTER: program-oriented conversion of DNA and protein alignments. Nucleic acids research 38 (2): W14–W18. https://doi.org/10.1093/nar/gkq321
  10. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series 41 (41): 95–98.
  11. Hyde, K.D., Chaiwan, N., Norphanphoun, C., Boonmee, S., Camporesi, E., Chethana, K.W.T., Dayarathne, M.C., de Silva, N.I., Dissanayake, A.J., Ekanayaka, A.H., Hongsanan, S., Huang, S.K., Jayasiri, S.C., Jayawardena, R.S., Jiang, H.B., Karunarathna, A., Lin, C.G., Liu, J.K., Liu, N.G., Lu, Y.Z., Luo, Z.L., Maharachchimbura, S.S.N., Manawasinghe, I.S., Pem, D., Perera, R.H., Phukhamsakda, C., Samarakoon, M.C., Senwanna, C., Shang, Q.J., Tennakoon, D.S., Thambugala, K.M., Tibpromma, S., Wanasinghe, D.N., Xiao, Y.P., Yang, J., Zeng, X.Y., Zhang, J.F., Zhang, S.N., Bulgakov, T.S., Bhat, D.J., Cheewangkoon, R., Goh, T.K., Jones, E.B.G., Kang, J.C., Jeewon, R., Liu, Z.Y., Lumyong, S., Kuo, C.H., McKenzie, E.H.C., Wen, T.C., Yan, J.Y. & Zhao, Q. (2018) Mycosphere notes169–224. Mycosphere 9: 271–430. https://doi.org/10.5943/mycosphere/9/2/8
  12. Jayasiri, S.C., Hyde, K.D., Ariyawansa, H.A., Bhat, 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.L., 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, phylogenyand human impacts. Fungal Diversity 74: 3–18. https://doi.org/10.1007/s13225-015-0351-8
  13. Jiang, H.B., Jeewon, R., Karunarathna, S.C., Phukhamsakda, C., Doilom, M., Kakumyan, P., Suwannarach, N., Phookamsak, R. & Lumyong, S. (2021) Reappraisal of Immotthia in Dictyosporiaceae, Pleosporales: Introducing Immotthia bambusae sp. nov. and Pseudocyclothyriella clematidis comb. et gen. nov. based on morphology and phylogeny. Frontiers in Microbiology 12: 656235. https://doi.org/10.3389/fmicb.2021.656235
  14. 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. https://doi.org/10.1093/molbev/mst010
  15. Kruys, A., Eriksson, O.E. & Wedin, M. (2006) Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position. Mycological research 110 (5): 527–536. https://doi.org/10.1016/j.mycres.2006.03.002
  16. Li, W.L., Luo, Z.L., Liu, J.K., Bhat, D.J., Bao, D.F., Su, H.Y. & Hyde, K.D. (2017) Lignicolous freshwater fungi from China I: Aquadictyospora lignicola gen. et sp. nov. and new record of Pseudodictyosporium wauense from northwestern Yunnan Province. Mycosphere 8 (10): 1587–1597. https://doi.org/10.5943/mycosphere/8/10/1
  17. Liu, J.K., Hyde, K.D., Jones, E.B.G., Ariyawansa, H.A., Bhat, D.J., Boonmee, S., Maharachchikumbura, S.S.N., McKenzie, E.H.C., Phookamsak, R., Phukhamsakda, C., Shenoy, B.D., Abdel-Wahab, M.A., Buyck, B., Chen, J., Chethana, K.W.T., Singtripop, C., Dai, D.Q., Dai, Y.C., Daranagama, D.A., Dissanayake, A.J., Doilom, M., D’souza, M.J., Fan, X.L., Goonasekara, I.D., Hirayama, K., Hongsanan, S., Jayasiri, S.C., Jayawardena, R.S., Karunarathna, S.C.K., Li, W.J., Mapook, A., Norphanphoun, C., Pang, K.L., Perera, R.H., Peršoh, D., Pinruan, U., Senanayake, I.C., Somrithipol, S., Suetrong, S., Tanaka, K., Thambugala, K.M., Tian, Q., Tibpromma, S., Udayanga, D., Wijayawardene, N.N., Wanasinghe, D., Wisitrassameewong, K., Zeng, X.Y., Abdel-Aziz, F.A., Adamčík, S., Bahkali, A.H., Boonyuen, N., Bulgakov, T., Callac, P., Chomnunti, P., Greiner, K., Hashimoto, A., Hofstetter, V., Kang, J.C., Lewis, D., Li, X.H., Liu, X.Z., Liu, Z.Y., Matsumura, M., Mortimer, P.E., Rambold, G., Randrianjohany, E., Sato, G., Sri-Indrasutdhi, V., Tian, C.M., Verbeken, A., von Brackel, W., Wang, Y., Wen, T.C., Xu, J.C., Yan, J.Y., Zhao, R.L. & Camporesi, E. (2015) Fungal diversity notes 1–110: Taxonomic and phylogenetic contributions to fungal species. Fungal Diversity 72: 1–197. https://doi.org/10.1007/s13225-015-0324-y
  18. 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 (12): 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
  19. Lu, L., Tibpromma, S., Karunarathna, S.C., Thiyagaraja, V., Xu, J.C., Jayawardena, R.S., Lumyong, S. & Hyde, K.D. (2021) Taxonomic and phylogenic appraisal of a novel species and a new record of Stictidaceae from coffee in Yunnan Province, China. Phytotaxa 528: 111–124. https://doi.org/10.11646/phytotaxa.528.2.4
  20. Lu, L., Tibpromma, S., Karunarathna, S.C., Jayawardena, R.S., Lumyong, S., Xu, J. & Hyde, K.D. (2022a) Comprehensive review of fungi on coffee. Pathogens 11 (4): 411. https://doi.org/10.3390/pathogens11040411
  21. Lu, L., Karunarathna, S.C., Hyde, K.D., Bhat, D.J., Dai, D.Q., Jayawardena, R.S. & Tibpromma, S. (2022b) Crassiparies yunnanensis sp. nov. (Neohendersoniaceae, Pleosporales) from dead twigs of Coffea arabica in China. Phytotaxa 543 (4): 244–254. https://doi.org/10.11646/phytotaxa.543.4.4
  22. Lu, L., Karunarathna, S.C., Dai, D.Q., Xiong, Y.R., Suwannarach, N., Stephenson, S.L., Elgorban, A.M., Al-Rejaie, S., Jayawardena, R.S. & Tibpromma, S. (2022c) Description of four novel species in Pleosporales associated with coffee in Yunnan, China. Journal of Fungi 8 (10): 1113. https://doi.org/10.3390/jof8101113
  23. Lu, L., Karunarathna, S.C., Dai, D.Q., Jayawardena, R.S., Suwannarach, N. & Tibpromma, S. (2022d) Three new species of Nigrograna (Dothideomycetes, Pleosporales) associated with Arabica coffee from Yunnan Province, China. MycoKeys 94: 51–71. https://doi.org/10.3897/mycokeys.94.95751
  24. Lu, L., Karunarathna, S.C., Liu, Y., Elgorban, A.M., Tibpromma, S., Jayawardena, R.S. (2024a) Pseudoconiocessia xishuangbannaensis gen. et sp. nov. in Coniocessiaceae, Xylariales from Coffea liberica in China. Phytotaxa 641 (2): 125–137. https://doi.org/10.11646/phytotaxa.641.2.4
  25. Lu, L. et al. (2024b) A polyphasic approach reveals ten novel Ascomycota taxa associated with coffee. Mycology. [in press]
  26. Ma, J., Xiao, X.J., Liu, N.G., Boonmee, S., Xiao, Y.P. & Lu, Y.Z. (2023) Morphological and multi-gene phylogenetic analyses reveal Pseudotubeufia gen. nov. and two new species in Tubeufiaceae from China. Journal of Fungi 9 (7): 742. https://doi.org/10.3390/jof9070742
  27. Ochoa-Henriquez, V.H., Faggioli, V., Gómez-Godínez, L.J., Rivarola, M. & Cristancho, M. (2024) Colombian coffee (Coffea arabica L.) plantations: a taxonomic and functional survey of soil fungi. Frontiers in Sustainable Food Systems 8: 1345383. https://doi.org/10.3389/fsufs.2024.1345383
  28. Phukhamsakda, C., McKenzie, E.H.C., Phillips, A.J.L., Jones, E.B.G., Bhat, D.J., Stadler, M., Bhunjun, C.S., Wanasinghe, D.N., Thongbai, B., Camporesi, E., Ertz, D., Jayawardena, R.S., Perera, R.H., Ekanayake, A.H., Tibpromma, S., Doilom, M., Xu, J.C. & Hyde, K.D. (2020) Microfungi associated with Clematis (Ranunculaceae) with an integrated approach to delimiting species boundaries. Fungal diversity 102: 1–203. https://doi.org/10.1007/s13225-020-00448-4
  29. Poma-Angamarca, R.A., Rojas, J.R., Sánchez-Rodríguez, A. & Ruiz-González, M.X. (2024) Diversity of leaf fungal endophytes from two Coffea arabica varieties and antagonism towards coffee leaf rust. Plants 13 (6): 814. https://doi.org/10.3390/plants13060814
  30. Ramesh, C. (2003) Loculoascomycetes from India. Frontiers of fungal diversity in India 457.
  31. Rathnayaka, A.R., Tennakoon, D.S., Jones, G.E., Wanasinghe, D.N., Bhat, D.J., Priyashantha, A.H., Stephenson, S.L., Tibpromma, S. & Karunarathna, S.C. (2024) Significance of precise documentation of hosts and geospatial data of fungal collections, with an emphasis on plant-associated fungi. New Zealand Journal of Botany. [28 pp.] https://doi.org/10.1080/0028825X.2024.2381734
  32. Rehner, S.A. & Samuels, G.J. (1994) Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences. Mycological Research 98 (6): 625–634. https://doi.org/10.1016/S0953-7562(09)80409-7
  33. Rodríguez, G.A.A., de Abreu, M.S., Pinto, F.A.M.F., Monteiro, A.C.A., Núñez, Á.M.P., de Resende, M.L.V., de Souza, J.T. & de Medeiros, F.H.V. (2016) Phialomyces macrosporus decreases anthracnose severity on coffee seedlings by competition for nutrients and induced resistance. Biological Control 103: 119–128. https://doi.org/10.1016/j.biocontrol.2016.08.009
  34. Samuel, S. (2023) Top 10 Widely Consumed Drinks in The World. Available from: https://besttoppers.com/top-10-widely-consumed-drinks/ (accessed 15 Sept. 2024)
  35. Senanayake, I.C., Rathnayaka, A.R., Marasinghe, D.S., Calabon, M.S., Gentekaki, E., Lee, H.B., Hurdeal, V.G., Pem, D., Dissanayake, L.S., Wijesinghe, S.N., Bundhun, D., Nguyen, T.T., Goonasekara, I.D., Abeywickrama, P.D., Bhunjun, C.S., Jayawardena, R.S., Wanasinghe, D.N., Jeewon, R., Bhat, D.J. & Xiang, M.M. (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
  36. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22 (21): 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
  37. Swindell, S.R. & Plasterer, T.N. (1997) Seqman. In: Swindell, S.R. (Ed.) Sequence Data Analysis Guidebook. Springer, Berlin/Heidelberg, Germany, pp. 75–89.
  38. Talhinhas, P., Batista, D., Diniz, I., Vieira, A., Silva, D.N., Loureiro, A., Tavares, S., Pereira, A.P., Azinheira, H.G., Guerra-Guimarães, L., Várzea, V. & do Céu Silva, M. (2017) The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics. Molecular plant pathology 18 (8): 1039. https://doi.org/10.1111/mpp.12512
  39. Tanaka, K., Hirayama, K., Yonezawa, H., Sato, G., Toriyabe, A., Kudo, H., Hashimoto, A., Matsumura, M., Harada, Y., Kurihara, Y., Shirouzu, T. & Hosoya, T. (2015) Revision of the Massarineae (Pleosporales, Dothideomycetes). Studies in mycology 82: 75–136. https://doi.org/10.1016/j.simyco.2015.10.002
  40. Tanaka, K., Hashimoto, A., Matsumura, M. & Sato, T. (2017) Brevicollum, a new genus in Neohendersoniaceae, Pleosporales. Mycologia 109: 608–619. https://doi.org/10.1080/00275514.2017.1387432
  41. Vilgalys, R. & Hester, M. (1990) Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. Journal of bacteriology 172 (8): 4238–4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
  42. White, T.J., Bruns, T., Lee, S.J.W.T. & Taylor, J. (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. (Ed.) PCR protocols: a guide to methods and applications. San Diego, CA: Academic Press, New York, pp. 315–322.
  43. Wijayawardene, N.N., Hyde, K.D., Dai, D.Q., Sánchez-García, M., Goto, B.T., Saxena, R.K., Erdoğdu, M., Selçuk, F., Rajeshkumar, K.C., Aptroot, A., Błaszkowski, J., Boonyuen, N., da Silva, G.A., de Souza, F.A., Dong, W., Ertz, D., Haelewaters, D., Jones, E.B.G., Karunarathna, S.C., Kirk, P.M., Kukwa, M., Kumla, J., Leontyev, D.V., Lumbsch, H.T., Maharachchikumbura, S.S.N., Marguno, F., Martínez-Rodríguez, P., Mešić, A., Monteiro, J.S., Oehl, F., Pawłowska, J., Pem, D., Pfliegler, W.P., Phillips, A.J.L., Pošta, A., He, M.Q., Li, J.X., Raza, M., Sruthi, O.P., Suetrong, S., Suwannarach, N., Tedersoo, L., Thiyagaraja, V., Tibpromma, S., Tkalčec, Z., Tokarev, Y.S., Wanasinghe, D.N., Wijesundara, D.S.A., Wimalaseana, S.D.M.K., Madrid, H., Zhang, G.Q., Gao, Y., Sánchez-Castro, I., Tang, L.Z., Stadler, M., Yurkov, A. & Thines, M. (2022) Outline of Fungi and fungus-like taxa – 2021. Mycosphere 13 (1): 53–453. https://doi.org/10.5943/mycosphere/13/1/2
  44. Zhang, H., Li, J., Zhou, H., Chen, Z., Song, G., Peng, Z., Pereira, A.P., Silva, M.C. & Varzea, V.M.P. (2014) Arabica coffee production in the Yunnan Province of China. In: 24th International Conference on Coffee Science. pp. 679–684.
  45. Zhang, W.J., Xu, G.P., Liu, Y., Gao, Y., Song, H.Y., Hu, H.J., Zhou, J.P., Chen, M.H., Fan, D.M., Hu, D.M. & Zhai, Z.J. (2024) Multi-gene phylogenetic analyses revealed two novel species and one new record of Trichobotrys (Pleosporales, Dictyosporiaceae) from China. MycoKeys 106: 117–132.
  46. Zhang, Y., Crous, P.W., Schoch, C.L. & Hyde, K.D. (2012) Pleosporales. Fungal diversity 53: 1–221. https://doi.org/10.1007/s13225-011-0117-x