Skip to main content

Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses

World Journal of Microbiology and Biotechnology volume 30, pages 237–243 (2014)Cite this article

Abstract

Species of Diaporthe (anamorph Phomopsis) comprise a diverse and widely distributed group of phytopathogens, saprophytes and endophytes. However, the degree of genetic diversity of endophytic Diaporthe has not yet been fully investigated. In this paper, a survey of endophytes from 28 plants in southeast China yielded 116 Diaporthe isolates, out of which 64 haplotypes were determined using DnaSP ver. 5.1 based on alignment result of internal transcribed spacer of ribosomal nucleotide sequences (ITS rDNA). Many haplotypes turned out to be quite different from known species and displayed high diversity. Among them, 14 strains from 5 discriminating terminal clades were selected to go through further analysis according to partial sequence of translation elongation factor 1-α (tef1-α) and again they got separated from others. The following multi-gene phylogenetic analysis based on ITS rDNA, tef1-α, β tubulin and calmodulin grouped eight most discrepant strains into three distinctive clusters, cluster 1 (Rc001, Eu004 and Eu009), cluster 2 (ZJWCF252, Sjm001 and Ac001) and cluster 3 (Pcs013 and Sfp005) respectively with high support values. These clusters above represent three potentially novel species. This research provides strong evidence of high biodiversity and novelty of Diaporthe endophytes from southeast China, which is thus important not only for better resolving the taxonomy in this genus, but also for further utilization due to their multiple application.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3

References

  • Aly AH, Debbab A, Proksch P (2011) Fungal endophytes: unique plant inhabitants with great promises. Appl Microbiol Biotechnol 90(6):1829–1845

    CAS  Article  Google Scholar 

  • Bills GF, González-Menéndez V, Martín J, Platas G, Fournier J, Peršoh D, Stadler M (2012) Hypoxylon pulicicidum sp. nov. (Ascomycota, Xylariales), a pantropical insecticide-producing endophyte. PLoS ONE. doi:10.1371/journal.pone.0046687

    Google Scholar 

  • Carvalho CR, Goncalves VN, Pereira CB, Johann S, Galliza IV, Alves TMA, Rabello A, Sobral MEG, Zani CL, Rosa CA, Rosa LH (2012) The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian savannah. Symbiosis 57(2):95–107

    Article  Google Scholar 

  • Chandra S (2012) Endophytic fungi: novel sources of anticancer lead molecules. Appl Microbiol Biotechnol 95(1):47–59

    CAS  Article  Google Scholar 

  • Chi MH, Park SY (2009) A quick and safe method for fungal DNA extraction. Plant Pathol J 25(1):108–111

    CAS  Article  Google Scholar 

  • Deshmukh SK, Verekar SA (2012) Fungal endophytes: a potential source of antifungal compounds. Front Biosci (Elite Ed) 4:2045–2070

    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 31:1–41

    Google Scholar 

  • Guo LD, Liew ECY (2000) Identification of endophytic fungi from Livistona chinensis based on morphology and rDNA sequences. New Phytol 147(3):617–630

    CAS  Article  Google Scholar 

  • Iriart X, Binois R, Fior A, Blanchet D, Berry A, Cassaing S, Amazan E, Papot E, Carme B, Aznar C, Couppie P (2011) Eumycetoma caused by Diaporthe phaseolorum (Phomopsis phaseoli): a case report and a mini-review of Diaporthe/Phomopsis spp. invasive infections in humans. Clin Microbiol Infect 17(10):1492–1494

    CAS  Article  Google Scholar 

  • Jiang WM, Yang GM, Zhang CL, Fu CX (2011) Species composition and molecular analysis of symbiotic fungi in roots of Changnienia amoena (Orchidaceae). Afr J Microbiol Res 5(3):222–228

    Google Scholar 

  • Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

    CAS  Article  Google Scholar 

  • Liu YZ, Hu ZY, Zheng ZH, Su WJ (2013) Isolation, Purification and characterization of the secondary metabolites from an endophytic fungus of Camptotheca acuminate. J Xiamen Univ 52(1):127–132

    Google Scholar 

  • Mostert L, Kang JC (2001) Species of Phomopsis and a Libertella sp. occurring on grapevines with specific reference to South Africa: morphological, cultural, molecular and pathological characterization. Mycologia 93(1):146–167

    Article  Google Scholar 

  • Phillips AJL, Crous PW, Alves A (2007) Diplodia seriata, the anamorph of “Botryosphaeria” obtusa. Fungal Divers 25:141–155

    Google Scholar 

  • Pioli R, Prado D (1997) Recent outbreak of stem canker (Diaporthe phaseolorum var. meridionalis) of soybean in Santa Fe, Argentina. Plant Dis 81(10):1215

    Article  Google Scholar 

  • Rodriguez R, Redman R (2007) More than 400 million years of evolution and plants still can’t make it on their own: plant stress tolerance and habitat expansion via fungal symbiosis. Comp Biochem Physiol A-Mol Integr Physiol 146S(4):S221–S221

    Article  Google Scholar 

  • Rodriguez RJ, White-Jr JF, Arnold AE, Redman RS (2009) Fungal endophytes: diversity and functional roles. New Phytol 182(2):314–330

    CAS  Article  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574

    CAS  Article  Google Scholar 

  • Rubini MR, Silva-Ribeiro RT, Pomella AWV, Maki CS, Araujo WL, Dos Santos DR, Azevedo JL (2005) Diversity of endophytic fungal community of cacao (Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of witches’ broom disease. Int J Biol Sci 1(1):24–33

    CAS  Article  Google Scholar 

  • Santos JM, Correia VG, Phillips AJL (2010) Primers for mating-type diagnosis in Diaporthe and Phomopsis: their use in teleomorph induction in vitro and biological species definition. Fungal Biol 114(2–3):255–270

    CAS  Article  Google Scholar 

  • Smit WA, Viljoen CD, Wingfield BD, Wingfield MJ, Calitz FJ (1996) A new canker disease of apple, pear, and plum rootstocks caused by Diaporthe ambigua in South Africa. Plant Dis 80(12):1331–1335

    Article  Google Scholar 

  • Specian V, Sarragiotto MH, Pamphile JA, Clemente E (2012) Chemical characterization of bioactive compounds from the endophytic fungus Diaporthe helianthi isolated from Luehea divaricate. Braz J Microbiol 43(3):1174–1182

    CAS  Article  Google Scholar 

  • Suryanarayanan TS, Thirunavukkarasu N, Govindarajulu MB, Gopalan V (2012) Fungal endophytes: an untapped source of biocatalysts. Fungal Divers 54(1):19–30

    Article  Google Scholar 

  • Thompson JD, Gibson TJ, Jeanmougin F (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882

    CAS  Article  Google Scholar 

  • Udayanga D, Liu XZ, McKenzie EHC, Chukeatirote E, Bahkali AHA, Hyde KD (2011) The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. Fungal Divers 50(1):189–225

    Article  Google Scholar 

  • Udayanga D, Liu XZ, Crous PW, McKenzie EHC, Chukeatirote E, Hyde KD (2012a) A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). Fungal Divers 56(1):157–171

    Article  Google Scholar 

  • Udayanga D, Liu XZ, Mckenzie EHC, Chukeatirote E, Hyde KD (2012b) Multi-locus phylogeny reveals three new species of Diaporthe from Thailand. Cryptogam Mycol 33(3):295–309

    Article  Google Scholar 

  • van Rensburg JCJ, Lamprecht SC, Groenewald JZ, Castlebury LA, Crous PW (2006) Characterisation of Phomopsis spp. associated with die-back of rooibos (Aspalathus linearis) in South Africa. Stud Mycol 55:65–74

    Article  Google Scholar 

  • Vanwarme KT (1972) Phomopsis leptostromiformis-causal fungus of lupinosis, a mycotoxicosis, in sheep. Mycologia 64(2):316–324

    Article  Google Scholar 

  • Wong MKM (2001) Fungi on grasses: new species of Ascotaiwania, Diaporthe and Oxydothis (Ascomycetes). Cryptogam Mycol 22(1):19–28

    Article  Google Scholar 

  • Wu H, Yang HY, You XL, Li YH (2012) Isolation and characterization of saponin-producing fungal endophytes from Aralia elata in Northeast China. Int J Mol Sci 13(12):16255–16266

    CAS  Article  Google Scholar 

  • Xing XK, Chen J, Xu MJ, Lin WH, Guo SX (2011) Fungal endophytes associated with Sonneratia (Sonneratiaceae) mangrove plants on the south coast of China. Forest Pathol 41(4):334–340

    Article  Google Scholar 

  • Yuan ZL, Lin FC, Zhang CL, Kubicek CP (2010) A new species of Harpophora (Magnaporthaceae) recovered from healthy wild rice (Oryza granulata) roots, representing a novel member of a beneficial dark septate endophyte. FEMS Microbiol Lett 307(1):94–101

    CAS  Article  Google Scholar 

  • Yuan ZL, Rao LB, Chen YC, Zhang CL, Wu YG (2011a) From pattern to process: species and functional diversity in fungal endophytes of Abies beshanzuensis. Fungal Biol 115(3):197–213

    Article  Google Scholar 

  • Yuan ZL, Su ZZ, Mao LJ, Peng YQ, Yang GM, Lin FC, Zhang CL (2011b) Distinctive endophytic fungal assemblage in stems of wild rice (Oryza granulata) in China with special reference to two species of Muscodor (Xylariaceae). J Microbiol 49(1):15–23

    CAS  Article  Google Scholar 

  • Zhang CL, Lin FC, Druzhinina IS (2007) Trichoderma taxi sp. nov., an endophytic fungus from Chinese yew Taxus mairei. FEMS Microbiol Lett 270(1):90–96

    CAS  Article  Google Scholar 

  • Zhang CL, Wang GP, Mao LJ, Komon-Zelazowska M, Yuan ZL, Lin FC, Druzhinina IS, Kubicek CP (2010) Muscodor fengyangensis sp. nov. from southeast China: morphology, physiology and production of volatile compounds. Fungal Biol 114(10):797–808

    CAS  Article  Google Scholar 

Download references

Acknowledgments

This work was supported by Special Fund for Agro-scientific Research in the Public Interest (200903052) to Chu-Long Zhang, Program for Changjiang Scholars and Innovative Research Team in University (PCSIRT0943) to Fu-Cheng Lin. We would like to thank Christian P. Kubicek (Vienna University of Technology, Austria) for his comments and linguistic corrections.

Author information

Affiliations

  1. State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China

    Jiaying Wang, Xihui Xu, Jiaping Lao, Fucheng Lin & Chulong Zhang

  2. Analysis Center of Agrobiology and Environmental Science, Zhejiang University, Hangzhou, 310058, China

    Lijuan Mao

  3. Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, Zhejiang Province, China

    Zhilin Yuan

Authors
  1. Jiaying Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xihui Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lijuan Mao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jiaping Lao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Fucheng Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zhilin Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chulong Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chulong Zhang.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 260 kb)

Supplementary material 2 (PDF 115 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Wang, J., Xu, X., Mao, L. et al. Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses. World J Microbiol Biotechnol 30, 237–243 (2014). https://doi.org/10.1007/s11274-013-1446-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11274-013-1446-6

Keywords

  • Diaporthe
  • Endophyte
  • Diversity
  • Phylogeny