Abstract
Alternaria is a widely distributed fungal genus served as saprophytes, endophytes and pathogens. An Alternaria species was isolated from Vigna unguiculata in Inner Mongolia Autonomous Region of China. The strains were determined based on morphological characteristics and multi-locus phylogenetic analyses including the internal transcribed spacer of rDNA region (ITS), glyceraldehydes-3-phosphate dehydrogenase (GAPDH), RNA polymerase second largest subunit (RPB2) and translation-elongation factor 1 alpha (TEF1). The results indicated that it was a new species, which described and illustrated as Alternaria vignae sp. nov. in this study. Phylogenetic analyses showed that the species formed a well-supported clade (sect. Helianthiinficientes) close to A. helianthiinficiens.
References
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Berbee, M.L., Pirseyedi, M. & Hubbard, S. (1999) Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 91: 964–977. https://doi.org/10.2307/3761627
Blagojevi, J., Vukojevi, J., Ivanovi, B. & Ivanovi, A. (2019) Characterization of Alternaria species associated with leaf spot disease of Armoracia rusticana in serbia. Plant Disease 104: 1378–1389. https://doi.org/10.1094/PDIS-02-19-0289-RE
Cai, Z.Y., Liu, Y.X., Shi, Y.-P., Dai, L.M., Li, L.L., Mu, H.J., Lv, M.L. & Liu, X.Y. (2019) Alternaria yunnanensis sp. nov., a new Alternaria species causing foliage spot of rubber tree in China. Mycobiology 47: 66–75. https://doi.org/10.1080/12298093.2019.1575584
Carbone, I. & Kohn, L.M. (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553–556. https://doi.org/10.1016/10.2307/3761358
Cenis, J. (1992) Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Research 20: 2380. https://doi.org/10.1093/nar/20.9.2380
Cheng, H., Zhao, L., Wei, X., Liu, X., Gao, G.Y. & Deng, J.X. (2022) Alternaria species causing leaf spot on hemp (Cannabis sativa) in northern China. European Journal of Plant Pathology 162: 957–970. https://doi.org/10.1007/s10658-021-02450-1
Cho, H.S & Yu, S.H. (2000) Three Alternaria species pathogenic to sunflower. Plant Pathology Journal 16: 331–334.
Deng, J.X., Cho, H.S., Paul, N.C., Lee, H.B. & Yu, S.H. (2014) A novel Alternaria species isolated from Peucedanum japonicum in korea. Mycobiology 42: 12–16. https://doi.org/10.5941/MYCO.2014.42.1.12
Deng, J.X., Li, M.J., Paul, N.C., Oo, M.M. & Yu, S.H. (2018) Alternaria brassicifolii sp. nov. isolated from Brassica rapa subsp. pekinensis in korea. Mycobiology 46: 172–176. https://doi.org/10.1080/12298093.2018.1468054
Gannibal, P.B., Orina, A.S. & Gasich, E.L. (2022) A new section for Alternaria helianthiinficiens found on sunflower and new asteraceous hosts in Russia. Mycological Progress 21: 34. https://doi.org/10.1007/s11557-022-01780-6
Ghafri, A.A., Maharachchikumbura, S., Hyde, K.D., Al-Saady, N.A. & Al-Sadi, A.M. (2019) A new section and a new species of Alternaria encountered from Oman. Phytotaxa 405: 279–289. https://doi.org/10.11646/phytotaxa.405.6.1
Grange, N.L. & Aveling, T.A.S. (1998) First Report of Alternaria cassiae on Cowpea. Plant Disease 82: 1171–1171. https://doi.org/10.1094/PDIS.1998.82.10.1171A
Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
He, L., Liu, H.F., Cui, M.J., Pei, D.F. & Deng, J.X. (2020) Alternaria vicatiae sp. nov. (Ascomycota: Pleosporaceae) Isolated from Vicatia thibetica in China. Phytotaxa 439: 255–264. https://doi.org/10.11646/phytotaxa.439.3.7
Hong, S.G., Cramer, R.A., Lawrence, C.B. & Pryor, B.M. (2005) Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure. Fungal Genetics & Biology 42: 119–129. https://doi.org/10.1016/j.fgb.2004.10.009
Index Fungorum. (2022) Available at: http://www.indexfungorum.org/names/Names.asp (accessed 5 August 2022)
Lawrence, D.P., Rotondo, F. & Gannibal, P.B. (2016) Biodiversity and taxonomy of the pleomorphic genus Alternaria. Mycological 15: 3. https://doi.org/10.1007/s11557-015-1144-x
Li, L., Yang, T., Liu, R., Redden, B., Maalouf, F. & Zong, X.X. (2017) Food legume production in China. The Crop Journal 5: 115–126. https://doi.org/10.1016/j.cj.2016.06.001
Liu, H.F., Liao, J., Chen, X.Y., Liu, Q.K. & Deng, J.X. (2019) A novel species and a new record of Alternaria isolated from two solanaceae plants in China. Mycological Progress 18: 1005–1012. https://doi.org/10.1007/s11557-019-01504-3
Liu, Y.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution l16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Luo, H., Jia, G.G., Fan, X.Y., Liu, H.F., Pei, D.F. & Deng, J.X. (2017) Isolation and identification of a new pathogen causing leaf blight on Cosmos bipinnatus. Plant Protection 43: 182–186. https://doi.org/10.1093/bioinfo10.3969/j.issn.0529-1542.2017.06.032
Marin-Felix, Y., Hernández-Restrepo, M., Iturrieta-González, I., Garcia, D., Gene, J., Groenewald, J.Z., Cai, L., Chen, Q., Quaedvlieg, W., Schumacher, R.K., Taylor, P.W.J., Ambers, C., Bonthond, G., Edwards, J., Krueger-Hadfield, S.A., Luangsa-ard, J.J., Morton, L., Moslemi, A., Sandoval-Denis, M., Tan, Y.P., Thangavel, R., Vaghefi, N., Cheewangkoon, R. & Crous, P.W. (2019) Genera of phytopathogenic fungi: GOPHY 3. Studies in Mycology 94: 1–124. https://doi.org/10.1016/j.simyco.2019.05.001
Nishikawa, J. & Nakashima, C. (2020) Japanese species of Alternaria and their species boundaries based on host range. Fungal Systematics and Evolution 5: 197–282. https://doi.org/10.3114/fuse.2020.05.13
Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author, Evolutionary Biology Centre. Uppsala University.
Pinto, V. & Patriarca, A. (2017) Alternaria species and their associated mycotoxins. Mycotoxigenic Fungi 1542: 13–32. https://doi.org/10.1007/978-1-4939-6707-0_2
Pitt, J.I. & Hocking, A.D. (2009) Fungi and Food Spoilage. Springer US. XVI, 520 pp. https://doi.org/10.1007/978-0-387-92207-2
Rambaut, A. & Drummond, A. (2010) FigTree v.1.3.1. Institute of Evolutionary Biology. University of Edinburgh, Edinburgh, UK.
Romain, B.B.N.D., Hassan, O., Kim, J.S. & Chang, T. (2022) Alternaria koreana sp. nov., a new pathogen isolated from leaf spot of ovate-leaf Atractylodes in South Korea. Molecular Biology Reports 49: 413–420. https://doi.org/10.3114/fuse.2020.05.13
Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. https://doi.org/10.1093/bioinformatics/btg180
Simmons, E.G. (2007) Alternaria: An identification manual. American Society of Microbiology, Wash-ington D.C., USA 775 pp. https://doi.org/10.1093/molbev/msr121
Simmons, E.G. (1986) Alternaria themes and variations (17–21). Mycotaxon 25: 203–216.
Stamatakis, A. & Alachiotis, N. (2010) Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinformatics 26: i132–i139. https://doi.org/10.1093/bioinformatics/btq205
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood–basedphy-logenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
Sung, G.H., Sung, J.M., Hywel-Jones, N.L. & Spatafora, J.W. (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. https://doi.org/10.1016/j.ympev.2007.03.011
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution l30: 2725–2729.
Thomma, B. (2003) Alternaria spp.: from general saprophyte to specific parasite. Molecular Plant Pathology 4: 225–236. https://doi.org/10.1046/j.1364-3703.2003.00173.x
White, T.J., Bruns, T. & Lee, S. (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, SanDiego, ifornia, USA, pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Woudenberg, J., Groenewald, J.Z., Binder, M. & Crous, P.W. (2013) Alternaria redefined. Studies in Mycology 75: 171–212.
htps://doi.org/10.3114/sim0015
Woudenberg, J., Truter, M., Groenewald, J.Z. & Crous, P.W. (2014) Large-spored Alternaria pathogens in section Porri disentangled. Studies in Mycology 79: 1–47. https://doi.org/10.1016/j.simyco.2014.07.003
Zhang, T.Y. (2003) Flora fungorum sinicorum, Alternaria, vol 16, 1st edn. Beijing, pp. 55–61.
A?imovi?, M & La?ok, N. (1991) Alternaria helianthiinficiens Simmons, Walcz and R. Roberts sp. Nov.: The 248 causals agent of brown-red spot, a new sunflower disease. Helia 14: 129–145.
Berbee, M.L., Pirseyedi, M. & Hubbard, S. (1999) Cochliobolus phylogenetics and the origin of known, highly virulent pathogens, inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences. Mycologia 91: 964–977. https://doi.org/10.2307/3761627
Blagojevi, J., Vukojevi, J., Ivanovi, B. & Ivanovi, A. (2019) Characterization of Alternaria species associated with leaf spot disease of Armoracia rusticana in serbia. Plant Disease 104: 1378–1389. https://doi.org/10.1094/PDIS-02-19-0289-RE
Cai, Z.Y., Liu, Y.X., Shi, Y.-P., Dai, L.M., Li, L.L., Mu, H.J., Lv, M.L. & Liu, X.Y. (2019) Alternaria yunnanensis sp. nov., a new Alternaria species causing foliage spot of rubber tree in China. Mycobiology 47: 66–75. https://doi.org/10.1080/12298093.2019.1575584
Carbone, I. & Kohn, L.M. (1999) A method for designing primer sets for speciation studies in filamentous ascomycetes. Mycologia 91: 553–556. https://doi.org/10.1016/10.2307/3761358
Cenis, J. (1992) Rapid extraction of fungal DNA for PCR amplification. Nucleic Acids Research 20: 2380. https://doi.org/10.1093/nar/20.9.2380
Cheng, H., Zhao, L., Wei, X., Liu, X., Gao, G.Y. & Deng, J.X. (2022) Alternaria species causing leaf spot on hemp (Cannabis sativa) in northern China. European Journal of Plant Pathology 162: 957–970. https://doi.org/10.1007/s10658-021-02450-1
Cho, H.S & Yu, S.H. (2000) Three Alternaria species pathogenic to sunflower. Plant Pathology Journal 16: 331–334.
Deng, J.X., Cho, H.S., Paul, N.C., Lee, H.B. & Yu, S.H. (2014) A novel Alternaria species isolated from Peucedanum japonicum in korea. Mycobiology 42: 12–16. https://doi.org/10.5941/MYCO.2014.42.1.12
Deng, J.X., Li, M.J., Paul, N.C., Oo, M.M. & Yu, S.H. (2018) Alternaria brassicifolii sp. nov. isolated from Brassica rapa subsp. pekinensis in korea. Mycobiology 46: 172–176. https://doi.org/10.1080/12298093.2018.1468054
Gannibal, P.B., Orina, A.S. & Gasich, E.L. (2022) A new section for Alternaria helianthiinficiens found on sunflower and new asteraceous hosts in Russia. Mycological Progress 21: 34. https://doi.org/10.1007/s11557-022-01780-6
Ghafri, A.A., Maharachchikumbura, S., Hyde, K.D., Al-Saady, N.A. & Al-Sadi, A.M. (2019) A new section and a new species of Alternaria encountered from Oman. Phytotaxa 405: 279–289. https://doi.org/10.11646/phytotaxa.405.6.1
Grange, N.L. & Aveling, T.A.S. (1998) First Report of Alternaria cassiae on Cowpea. Plant Disease 82: 1171–1171. https://doi.org/10.1094/PDIS.1998.82.10.1171A
Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
He, L., Liu, H.F., Cui, M.J., Pei, D.F. & Deng, J.X. (2020) Alternaria vicatiae sp. nov. (Ascomycota: Pleosporaceae) Isolated from Vicatia thibetica in China. Phytotaxa 439: 255–264. https://doi.org/10.11646/phytotaxa.439.3.7
Hong, S.G., Cramer, R.A., Lawrence, C.B. & Pryor, B.M. (2005) Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure. Fungal Genetics & Biology 42: 119–129. https://doi.org/10.1016/j.fgb.2004.10.009
Index Fungorum. (2022) Available at: http://www.indexfungorum.org/names/Names.asp (accessed 5 August 2022)
Lawrence, D.P., Rotondo, F. & Gannibal, P.B. (2016) Biodiversity and taxonomy of the pleomorphic genus Alternaria. Mycological 15: 3. https://doi.org/10.1007/s11557-015-1144-x
Li, L., Yang, T., Liu, R., Redden, B., Maalouf, F. & Zong, X.X. (2017) Food legume production in China. The Crop Journal 5: 115–126. https://doi.org/10.1016/j.cj.2016.06.001
Liu, H.F., Liao, J., Chen, X.Y., Liu, Q.K. & Deng, J.X. (2019) A novel species and a new record of Alternaria isolated from two solanaceae plants in China. Mycological Progress 18: 1005–1012. https://doi.org/10.1007/s11557-019-01504-3
Liu, Y.J., Whelen, S. & Hall, B.D. (1999) Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Molecular Biology and Evolution l16: 1799–1808. https://doi.org/10.1093/oxfordjournals.molbev.a026092
Luo, H., Jia, G.G., Fan, X.Y., Liu, H.F., Pei, D.F. & Deng, J.X. (2017) Isolation and identification of a new pathogen causing leaf blight on Cosmos bipinnatus. Plant Protection 43: 182–186. https://doi.org/10.1093/bioinfo10.3969/j.issn.0529-1542.2017.06.032
Marin-Felix, Y., Hernández-Restrepo, M., Iturrieta-González, I., Garcia, D., Gene, J., Groenewald, J.Z., Cai, L., Chen, Q., Quaedvlieg, W., Schumacher, R.K., Taylor, P.W.J., Ambers, C., Bonthond, G., Edwards, J., Krueger-Hadfield, S.A., Luangsa-ard, J.J., Morton, L., Moslemi, A., Sandoval-Denis, M., Tan, Y.P., Thangavel, R., Vaghefi, N., Cheewangkoon, R. & Crous, P.W. (2019) Genera of phytopathogenic fungi: GOPHY 3. Studies in Mycology 94: 1–124. https://doi.org/10.1016/j.simyco.2019.05.001
Nishikawa, J. & Nakashima, C. (2020) Japanese species of Alternaria and their species boundaries based on host range. Fungal Systematics and Evolution 5: 197–282. https://doi.org/10.3114/fuse.2020.05.13
Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author, Evolutionary Biology Centre. Uppsala University.
Pinto, V. & Patriarca, A. (2017) Alternaria species and their associated mycotoxins. Mycotoxigenic Fungi 1542: 13–32. https://doi.org/10.1007/978-1-4939-6707-0_2
Pitt, J.I. & Hocking, A.D. (2009) Fungi and Food Spoilage. Springer US. XVI, 520 pp. https://doi.org/10.1007/978-0-387-92207-2
Rambaut, A. & Drummond, A. (2010) FigTree v.1.3.1. Institute of Evolutionary Biology. University of Edinburgh, Edinburgh, UK.
Romain, B.B.N.D., Hassan, O., Kim, J.S. & Chang, T. (2022) Alternaria koreana sp. nov., a new pathogen isolated from leaf spot of ovate-leaf Atractylodes in South Korea. Molecular Biology Reports 49: 413–420. https://doi.org/10.3114/fuse.2020.05.13
Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. https://doi.org/10.1093/bioinformatics/btg180
Simmons, E.G. (2007) Alternaria: An identification manual. American Society of Microbiology, Wash-ington D.C., USA 775 pp. https://doi.org/10.1093/molbev/msr121
Simmons, E.G. (1986) Alternaria themes and variations (17–21). Mycotaxon 25: 203–216.
Stamatakis, A. & Alachiotis, N. (2010) Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. Bioinformatics 26: i132–i139. https://doi.org/10.1093/bioinformatics/btq205
Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood–basedphy-logenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688–2690. https://doi.org/10.1093/bioinformatics/btl446
Sung, G.H., Sung, J.M., Hywel-Jones, N.L. & Spatafora, J.W. (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. https://doi.org/10.1016/j.ympev.2007.03.011
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution l30: 2725–2729.
Thomma, B. (2003) Alternaria spp.: from general saprophyte to specific parasite. Molecular Plant Pathology 4: 225–236. https://doi.org/10.1046/j.1364-3703.2003.00173.x
White, T.J., Bruns, T. & Lee, S. (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, SanDiego, ifornia, USA, pp. 315–322. https://doi.org/10.1016/B978-0-12-372180-8.50042-1
Woudenberg, J., Groenewald, J.Z., Binder, M. & Crous, P.W. (2013) Alternaria redefined. Studies in Mycology 75: 171–212.
htps://doi.org/10.3114/sim0015
Woudenberg, J., Truter, M., Groenewald, J.Z. & Crous, P.W. (2014) Large-spored Alternaria pathogens in section Porri disentangled. Studies in Mycology 79: 1–47. https://doi.org/10.1016/j.simyco.2014.07.003
Zhang, T.Y. (2003) Flora fungorum sinicorum, Alternaria, vol 16, 1st edn. Beijing, pp. 55–61.