New molecular markers for distinguishing the main phylogenetic lineages within Alternaria section Alternaria

References

• Aichinger G, Del Favero G, Warth B, Marko D. 2021. Alternaria toxins—still emerging? Compr Rev Food Sci Food Saf. 20:4390–4406. doi:10.1111/1541-4337.12803.
   PubMed Web of Science ®Google Scholar
• Andrew M, Peever TL, Pryor BM. 2009. An expanded multilocus phylogeny does not resolve morphological species within the small-spored Alternaria species complex. Mycologia. 101:95–109. doi:10.3852/08-135.
   PubMed Web of Science ®Google Scholar
• Armitage AD, Barbara DJ, Harrison RJ, Lane CR, Sreenivasaprasad S, Woodhall JW, Clarkson JP. 2015. Discrete lineages within Alternaria alternata species group: identification using new highly variable loci and support from morphological characters. Fungal Biol. 119:994–1006. doi:10.1016/j.funbio.2015.06.012.
   PubMed Web of Science ®Google Scholar
• Armitage AD, Cockerton HM, Sreenivasaprasad S, Woodhall J, Lane CR, Harrison RJ, Clarkson JP. 2020. Genomics evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes. Front Microbiol. 10:3124. doi:10.3389/fmicb.2019.03124.
   PubMed Web of Science ®Google Scholar
• Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. 2015. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci USA. 112:5756–5761. doi:10.1073/pnas.1420815112.
   PubMed Web of Science ®Google Scholar
• Borowiec ML. 2016. AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ. 4:e1660. doi:10.7717/peerj.1660.
   PubMed Web of Science ®Google Scholar
• da Cruz Cabral L, Rodriguero M, Stenglein S, Fog Nielsen K, Patriarca A. 2017. Characterization of small-spored Alternaria from Argentinean crops through a polyphasic approach. Int J Food Microbiol. 257:206–215. doi:10.1016/j.ijfoodmicro.2017.06.026.
   PubMed Web of Science ®Google Scholar
• Dettman JR, Eggertson Q. 2021. Phylogenomic analyses of Alternaria section Alternaria: a high-resolution, genome-wide study of lineage sorting and gene tree discordance. Mycologia. 113:1218–1232. doi:10.1080/00275514.2021.1950456.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797. doi:10.1093/nar/gkh340.
   PubMed Web of Science ®Google Scholar
• Gao J, Yang MJ, Xie Z, Lu BH, Hsiang T, Liu LP. 2021. Morphological and molecular identification and pathogenicity of Alternaria spp. associated with ginseng in Jilin province, China. Can J Plant Pathol. 43:537–550. doi:10.1080/07060661.2020.1858167.
   Web of Science ®Google Scholar
• Gonçalves VN, Cantrell CL, Wedge DE, Ferreira MC, Soares MA, Jacob MR, Oliveira FS, Galante D, Rodrigues F, Alves TMA, et al. 2016. Fungi associated with rocks of the Atacama Desert: taxonomy, distribution, diversity, ecology and bioprospection for bioactive compounds. Environ Microbiol. 18:232–245. doi:10.1111/1462-2920.13005.
   PubMed Web of Science ®Google Scholar
• Lawrence DP, Gannibal PB, Peever TL, Pryor BM. 2013. The sections of Alternaria: formalizing species-group concepts. Mycologia. 105:530–546. doi:10.3852/12-249.
   PubMed Web of Science ®Google Scholar
• Lin CH, Chung KR. 2010. Specialized and shared functions of the histidine kinase- and HOG1 MAP kinase-mediated signaling pathways in Alternaria alternata, a filamentous fungal pathogen of citrus. Fungal Genet Biol. 47:818–827. doi:10.1016/j.fgb.2010.06.009.
   PubMed Web of Science ®Google Scholar
• Lin C-H, Yang SL, Chung K-R. 2009. The YAP1 homolog–mediated oxidative stress tolerance is crucial for pathogenicity of the necrotrophic fungus Alternaria alternata in citrus. Mol Plant-Microbe Interact. 22:942–952. doi:10.1094/MPMI-22-8-0942.
   PubMed Web of Science ®Google Scholar
• Liu YJ, Whelen S, Hall BD. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit. Mol Biol Evol. 12:1799–1808. doi:10.1093/oxfordjournals.molbev.a026092.
   Google Scholar
• Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, et al. 2020. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus. 11:14. doi:10.1186/s43008-020-00033-z.
   PubMed Web of Science ®Google Scholar
• Luis P, Saint-Genis G, Vallon L, Bourgeois C, Bruto M, Marchand C, Record E, Hugoni M. 2019. Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments. Environ Microbiol. 21:1407–1424. doi:10.1111/1462-2920.14571.
   PubMed Web of Science ®Google Scholar
• Meena M, Gupta SK, Swapnil P, Zehra A, Dubey MK, Upadhyay RS. 2017. Alternaria toxins: potential virulence factors and genes related to pathogenesis. Front Microbiol. 8:1451. doi:10.3389/fmicb.2017.01451.
   PubMed Web of Science ®Google Scholar
• Mujahid C, Savoy MC, Baslé Q, Woo PM, Ee ECY, Mottier P, Bessaire T. 2020. Levels of Alternaria toxins in selected food commodities including green coffee. Toxins (Basel). 12:595. doi:10.3390/toxins12090595.
   PubMed Web of Science ®Google Scholar
• Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32:268–274. doi:10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Nishikawa J, Nakashima C. 2020. Japanese species of Alternaria and their species boundaries based on host range. Fungal Syst Evol. 5:197–282. doi:10.3114/fuse.2020.05.13.
   PubMedGoogle Scholar
• Peever TL, Su G, Carpenter-Boggs L, Timmer LW. 2004. Molecular systematics of citrus-associated Alternaria species. Mycologia. 96:119–134. doi:10.2307/3761993.
   PubMed Web of Science ®Google Scholar
• Robideau GP, De Cock AW, Coffey MD, Voglmayr H, Brouwer H, Bala K, Chitty DW, Désaulniers N, Eggertson QA, Gachon CM, et al. 2011. DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour. 6:1002–1011. doi:10.1111/j.1755-0998.2011.03041.x.
   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
• Rotem J. 1994. The genus Alternaria. Biology, epidemiology and pathogenicity. St. Paul (MN): APS Press.
   Google Scholar
• Rotondo F, Collina M, Brunelli A, Pryor BM. 2012. Comparison of Alternaria spp. collected in Italy from apple with A. Mali and other AM-toxin producing strains. Phytopathology. 102:1130–1142. doi:10.1094/PHYTO-04-12-0076-R.
   PubMed Web of Science ®Google Scholar
• Simmons EGS. 1993. Alternaria themes and variations (63-72). Mycotaxon. 47:91–107.
   Google Scholar
• Simmons EGS, Roberts R. 1993. Alternaria themes and variations (73). Mycotaxon. 47:109–140.
   Google Scholar
• Somma S, Amatulli MT, Masiello M, Moretti A, Logrieco AF. 2019. Alternaria species associated to wheat black point identified through a multilocus sequence approach. Int J Food Microbiol. 293:34–43. doi:10.1016/j.ijfoodmicro.2019.01.001.
   PubMed Web of Science ®Google Scholar
• Thomma BPHJ. 2003. Alternaria spp.: from general saprophyte to specific parasite. Mol Plant Pathol. 4:225–236. doi:10.1046/j.1364-3703.2003.00173.x.
   PubMed Web of Science ®Google Scholar
• Tralamazza SM, Piacentini KC, Iwase CHT, Rocha LDO. 2018. Toxigenic Alternaria species: impact in cereals worldwide. Curr Opin Food Sci. 23:57–63. doi:10.1016/j.cofs.2018.05.002.
   Web of Science ®Google Scholar
• Woudenberg JHC, Seidl MF, Groenewald JZ, de Vries M, Stielow JB, Thomma BPHJ, Crous PW. 2015. Alternaria section Alternaria: species, formae speciales or pathotypes? Stud Mycol. 82:1–21. doi:10.1016/j.simyco.2015.07.001.
   PubMed Web of Science ®Google Scholar
• Zhang C, Rabiee M, Sayyari E, Mirarab S. 2018. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19(Suppl 6):153. doi:10.1186/s12859-018-2129-y.
   PubMedGoogle Scholar