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Diaporthe from walnut tree (Juglans regia) in China, with insight of the Diaporthe eres complex

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Abstract

Species of Diaporthe are important plant pathogenic fungi that commonly occur on a wide range of hosts. They are relatively difficult to identify due to their extreme similarity in morphology and confusing multigene phylogeny, especially in the Diaporthe eres complex. In the present study, isolates were collected from diseased branches of Juglans regia in China. Most strains were clustered into the D. eres species complex based on the combined internal transcribed spacer (ITS) region, partial calmodulin (CAL), histone H3 (HIS), translation elongation factor 1-alpha (TEF1-α) and beta-tubulin (TUB) genes. To focus on this complex, CAL, TEF1-α and TUB were selected in further phylogenetic analyses that showed a better topology compared with combined five-gene phylogeny. Results revealed that all strains which clustered in the Diaporthe eres complex from Juglans regia in China were Diaporthe eres. Results suggested a revised species criterion in the Diaporthe eres complex. The current study uncovered a new species here described as Diaporthe. tibetensis.

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References

  • Anagnostakis SL (2007) Diaporthe eres (Phomopsis oblonga) as a pathogen of butternut (Juglans cinerea) in Connecticut. Plant Dis 91:1198

    Article  PubMed  Google Scholar 

  • Bickford D, Lohman DJ, Sodhi NS, Ng PK, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155

    Article  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Castlebury LA, Rossman AY, Jaklitsch WJ, Vasilyeva LN (2002) A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences. Mycologia 94:1017–1031

    Article  PubMed  CAS  Google Scholar 

  • Chepkirui C, Stadler M (2017) The genus Diaporthe: a rich source of diverse and bioactive metabolites. Mycol Prog 16:477–494

    Article  Google Scholar 

  • Crous PW, Groenewald JZ, Risède JM, Simoneau P, Hywel-Jones NL (2004a) Calonectria species and their Cylindrocladium anamorphs: species with sphaeropedunculate vesicles. Stud Mycol 50:415–430

    Google Scholar 

  • Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G (2004b) MycoBank: an online initiative to launch mycology into the 21st century. Stud Mycol 50:19–22

    Google Scholar 

  • Desjardins P, Hansen JB, Allen M (2009) Microvolume protein concentration determination using the NanoDrop 2000c spectrophotometer. J Vis Exp (33):1–3

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Du Z, Fan XL, Hyde KD, Yang Q, Liang YM, Tian CM (2016) Phylogeny and morphology reveal two new species of Diaporthe from Betula spp. in China. Phytotaxa 269:90–102

    Article  Google Scholar 

  • Fan XL, Hyde KD, Udayanga D, Wu XY, Tian CM (2015a) Diaporthe rostrata, a novel ascomycete from Juglans mandshurica associated with walnut dieback. Mycol Prog 14:1–8

    Article  Google Scholar 

  • Fan XL, Hyde KD, Liu M, Liang YM, Tian CM (2015b) Cytospora species associated with walnut canker disease in China, with description of a new species C. gigalocus. Fungal Biology 119:310–319

    Article  PubMed  Google Scholar 

  • Gandev S (2007) Budding and grafting of the walnut (Juglans regia L.) and their effectiveness in Bulgaria (review). Bulgarian J Agric Sci 13:683–689

    Google Scholar 

  • Gao YH, Liu F, Cai L (2016) Unravelling Diaporthe species associated with Camellia. Syst Biodivers 14:102–117

    Article  Google Scholar 

  • Gao YH, Liu F, Duan WJ, Crous PW, Cai L (2017) Diaporthe is paraphyletic. IMA Fungus 8:153–187

    Article  PubMed  PubMed Central  Google Scholar 

  • Gao YH, Sun W, Su YY, Cai L (2014) Three new species of Phomopsis in Gutianshan Nature Reserve in China. Mycol Prog 13:111–121

    Article  Google Scholar 

  • Gao YH, Su Y, Sun W, Cai L (2015) Diaporthe species occurring on Lithocarpus glabra in China, with descriptions of five new species. Fungal Biology 119:295–309

    Article  PubMed  Google Scholar 

  • Glass NL, Donaldson GC (1995) Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323–1330

    PubMed  PubMed Central  CAS  Google Scholar 

  • Gomes RR, Glienke C, Videira SIR, Lombard L, Groenewald JZ, Crous PW (2013) Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi. Persoonia: Mol Phylogeny Evol Fungi 31:1–41

    Article  CAS  Google Scholar 

  • Guarnaccia V, Groenewald JZ, Woodhall J et al (2018) Diaporthe diversity and pathogenicity revealed from a broad survey of grapevine diseases in Europe. Persoonia 40:135–153

    Article  PubMed  PubMed Central  Google Scholar 

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321

    Article  PubMed  CAS  Google Scholar 

  • Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42:182–192

    Article  Google Scholar 

  • Huang F, Udayanga D, Wang X, Hou X, Mei X, Fu Y, Hyde KD, Li H (2015) Endophytic Diaporthe associated with Citrus: a phylogenetic reassessment with seven new species from China. Fungal Biol 119:331–347

    Article  PubMed  Google Scholar 

  • Katoh K, Toh H (2010) Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 26:1899–1900

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Martínez ML, Labuckas DO, Lamarque AL, Maestri DM (2010) Walnut (Juglans regia L.): genetic resources, chemistry, by-products. J Sci Food Agric 90:1959–1967

    PubMed  Google Scholar 

  • Nitschke T (1870) Pyrenomycetes Germanici 2. Breslau, Eduard Trewendt, Germany

    Google Scholar 

  • Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818

    Article  PubMed  CAS  Google Scholar 

  • Rambaut A, Drummond A (2010) FigTree v.1.3.1. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK

  • Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311

    Article  PubMed  CAS  Google Scholar 

  • Rayner RW (1970) A mycological colour chart. Commonwealth Mycological Institute, London

    Google Scholar 

  • Rehner SA, Uecker FA (1994) Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can J Bot 72:1666–1674

    Article  CAS  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  PubMed  CAS  Google Scholar 

  • Santos JM, Correia VG, Phillips AJ (2010) Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biol 114:255–270

    Article  PubMed  CAS  Google Scholar 

  • Santos JM, Phillips AJL (2009) Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal. Fungal Divers 34:111–125

    Google Scholar 

  • Santos L, Alves A, Alves R (2017) Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ. https://doi.org/10.7717/peerj.3120

  • Swofford DL (2003) PAUP*: Phylogenetic analysis using parsimony (* and other methods). Version 4.0b10. Sunderland, England, UK

  • Taha NA, Al-wadaan MA (2011) Utility and importance of walnut, Juglans regia Linn: a review. Afr J Microbiol Res 5:5796–5805

    Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tanney JB, Mcmullin DR, Green BD, Miller JD, Seifert KA (2016) Production of antifungal and antiinsectan metabolites by the Picea endophyte Diaporthe maritima sp. nov. Fungal Biol 120:1448–1457

    Article  PubMed  CAS  Google Scholar 

  • Tan YP, Edwards J, Grice KRE, Shivas RG (2013) Molecular phylogenetic analysis reveals six new species of Diaporthe from Australia. Fungal Divers 61:251–260

    Article  Google Scholar 

  • Taylor JW, Jacobson DJ, Kroken S, Kasuga T, Geiser DM, Hibbett DS, Fisher MC (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genet Biol 31:21–32

    Article  PubMed  CAS  Google Scholar 

  • Uecker FA (1988) A world list of Phomopsis names with notes on nomenclature, morphology and biology. Mycological Memoirs 13:1–231

    Google Scholar 

  • Udayanga D, Liu X, McKenzie EH, Chukeatirote E, Bahkali AH, Hyde KD (2011) The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fungal Divers 50:189–225

    Article  Google Scholar 

  • Udayanga D, Liu X, Crous PW, McKenzie EH, Chukeatirote E, Hyde KD (2012a) A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Divers 56:157–171

    Article  Google Scholar 

  • Udayanga D, Liu X, Mckenzie EH, Chukeatirote E, Hyde KD (2012b) Multi-locus phylogeny reveals three new species of Diaporthe from Thailand. Cryptogam Mycol 33:295–309

    Article  Google Scholar 

  • Udayanga D, Castlebury LA, Rossman AY, Hyde KD (2014a) Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis. Persoonia: Mol Phylogeny Evol Fungi 32:83–101

    Article  CAS  Google Scholar 

  • Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD (2014b) Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. Fungal Divers 67:203–229

    Article  Google Scholar 

  • Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD (2015) The Diaporthe sojae species complex: phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biology 119:383–407

    Article  PubMed  Google Scholar 

  • Voglmayr H, Castlebury LA, Jaklitsch WM (2017) Juglanconis gen. nov. on Juglandaceae, and the new family Juglanconidaceae (Diaporthales). Persoonia 38:136–155

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wehmeyer LE (1933) The genus Diaporthe Nitschke and its segregates. Univ Mich Student Sci Serv 9:1–349

    Google Scholar 

  • White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Snisky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. San Diego, USA

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Acknowledgements

This study is financed by Fundamental Research Funds for the Central Universities (Project No.: BLX201613) and National Natural Science Foundation of China (Project No.: 31670647). CM Tian and XL Fan thank Chungen Piao, Minwei Guo (China Forestry Culture Collection Center (CFCC), Chinese Academy of Forestry, Beijing. JDP Bezerra thanks Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and the Fundação de Amparo à Ciência e Tecnologia de Pernambuco (FACEPE) of Brazil for scholarships.

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Authors and Affiliations

  1. The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, 100083, China

    XinLei Fan, Qin Yang & ChengMing Tian

  2. Departamento de Micologia Prof. Chaves Batista, Universidade Federal de Pernambuco, Av. Prof. Moraes Rego, s/n, Centro de Biociências, Cidade Universitária, CEP, Recife, PE, 50670-901, Brazil

    Jadson D. P. Bezerra

  3. Department of Biology, College of Science, Polytechnic University of the Philippines, Sta. Mesa, Manila, Philippines

    Lourdes V. Alvarez

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  1. XinLei Fan
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Correspondence to ChengMing Tian.

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Fan, X., Yang, Q., Bezerra, J.D.P. et al. Diaporthe from walnut tree (Juglans regia) in China, with insight of the Diaporthe eres complex. Mycol Progress 17, 841–853 (2018). https://doi.org/10.1007/s11557-018-1395-4

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  • DOI: https://doi.org/10.1007/s11557-018-1395-4

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