Antonie van Leeuwenhoek

, Volume 111, Issue 6, pp 897–904 | Cite as

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

  • Christopher A. Dunlap
  • José Luis Ramirez
  • Gabriel Moura Mascarin
  • David P. Labeda
Original Paper
First Online:
Received:
Accepted:

Abstract

We report the development of a publicly accessible, curated nucleotide sequence database of hypocrealean entomopathogenic fungi. The goal is to provide a platform for users to easily access sequence data from taxonomic reference strains. The database can be used to accurately identify unknown entomopathogenic fungi based on sequence data for a variety of phylogenetically informative loci. The database provides full multi-locus sequence alignment capabilities. The initial release contains data compiled for 525 strains covering the phylogenetic diversity of three important entomopathogenic families: Clavicipitaceae, Cordycipitaceae, and Ophiocordycipitaceae. Furthermore, Entomopathogen ID can be expanded to other fungal clades of insect pathogens, as sequence data becomes available. The database will allow isolate characterisation and evolutionary analyses. We contend that this freely available, web-accessible database will facilitate the broader community to accurately identify fungal entomopathogens, which will allow users to communicate research results more effectively.

Keywords

Beauveria Cordyceps Isaria Metacordyceps Metarhizium MLSA 
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Notes

Acknowledgements

The authors would like to thank Heather Walker for data entry assistance. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture. The mention of firm names or trade products does not imply that they are endorsed or recommended by the USDA over other firms or similar products not mentioned. USDA is an equal opportunity provider and employer.

Funding

This project was funded by the U.S. Department of Agriculture, Agriculture Research Service, Project No. 5010-22410-017-00-D.

Conflict of interest

The authors declare no conflicts of interests.

Supplementary material

10482_2017_988_MOESM1_ESM.pdf (1.7 mb)
Supplementary material 1 (PDF 1755 kb)

References

  1. Agrawal Y, Mual P, Shenoy BD (2014) Multi-gene genealogies reveal cryptic species Beauveria rudraprayagi sp. nov. from India. Mycosphere 5(5):719–736CrossRefGoogle Scholar
  2. Bischoff JF, Rehner SA, Humber RA (2009) A multilocus phylogeny of the Metarhizium anisopliae lineage. Mycologia 101(4):512–530.  https://doi.org/10.3852/07-202 CrossRefPubMedGoogle Scholar
  3. Craven KD, Hsiau PTW, Leuchtmann A, Hollin W, Schardl CL (2001) Multigene phylogeny of Epichloë species, fungal symbionts of grasses. Ann Missouri Bot Gard 88(1):14–34CrossRefGoogle Scholar
  4. Druzhinina IS, Kopchinskiy AG, Komoń M, Bissett J, Szakacs G, Kubicek CP (2005) An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genet Biol 42(10):813–828.  https://doi.org/10.1016/j.fgb.2005.06.007 CrossRefPubMedGoogle Scholar
  5. Geiser DM et al (2004) FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium. Eur J Plant Pathol 110(5–6):473–479.  https://doi.org/10.1023/B:EJPP.0000032386.75915.a0 CrossRefGoogle Scholar
  6. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, Van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Opinion: re-evaluating prokaryotic species. Nat Rev Microbiol 9:733–739.  https://doi.org/10.1038/nrmicro1236 CrossRefGoogle Scholar
  7. Grünwald NJ et al (2011) Phytophthora-ID.org: a sequence-based Phytophthora identification tool. Plant Dis 95(3):337–342.  https://doi.org/10.1094/PDIS-08-10-0609 CrossRefGoogle Scholar
  8. Humber RA (2016) Seeking stability for research and applied uses of entomopathogenic fungi as biological control agents. J Asia-Pacif Entomol 19(4):1019–1025.  https://doi.org/10.1016/j.aspen.2016.09.006 CrossRefGoogle Scholar
  9. Jolley KA, Maiden MCJ (2010) BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinform 11:595.  https://doi.org/10.1186/1471-2105-11-595 CrossRefGoogle Scholar
  10. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol.  https://doi.org/10.1093/molbev/msw054 Google Scholar
  11. Labeda DP et al (2017) Phylogenetic relationships in the family Streptomycetaceae using multi-locus sequence analysis. Antonie Van Leeuwenhoek 110(4):563–583.  https://doi.org/10.1007/s10482-016-0824-0 CrossRefPubMedGoogle Scholar
  12. Lutzoni F et al (2004) Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits. Am J Bot 91(10):1446–1480.  https://doi.org/10.3732/ajb.91.10.1446 CrossRefPubMedGoogle Scholar
  13. O’Donnell K et al (2012) Phylogenetic diversity of insecticolous fusaria inferred from multilocus DNA sequence data and their molecular identification via FUSARIUM-ID and Fusarium MLST. Mycologia 104(2):427–445.  https://doi.org/10.3852/11-179 CrossRefPubMedGoogle Scholar
  14. O’Leary NA et al (2016) Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 44(D1):D733–D745.  https://doi.org/10.1093/nar/gkv1189 CrossRefPubMedGoogle Scholar
  15. Ratnasingham S, Hebert PDN (2007) BOLD: the barcode of life data system: barcoding. Mol Ecol Notes 7(3):355–364.  https://doi.org/10.1111/j.1471-8286.2007.01678.x CrossRefPubMedPubMedCentralGoogle Scholar
  16. Rehner SA, Minnis AM, Sung GH, Luangsa-ard JJ, Devotto L, Humber RA (2011) Phylogeny and systematics of the anamorphic, entomopathogenic genus Beauveria. Mycologia 103(5):1055–1073.  https://doi.org/10.3852/10-302 CrossRefPubMedGoogle Scholar
  17. Schoch CL et al (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109(16):6241–6246.  https://doi.org/10.1073/pnas.1117018109 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Seifert KA (2009) Progress towards DNA barcoding of fungi. Mol Ecol Resour 9(Suppl 1):83–89.  https://doi.org/10.1111/j.1755-0998.2009.02635.x CrossRefPubMedGoogle Scholar
  19. Simmons DR, Kepler RM, Rehner SA, Groden E (2015) Phylogeny of Hirsutella species (Ophiocordycipitaceae) from the USA: remedying the paucity of Hirsutella sequence data. IMA Fungus 6(2):345–356.  https://doi.org/10.5598/imafungus.2015.06.02.06 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Sung G-H, Hywel-Jones NL, Sung J-M, Luangsa-ard JJ, Shrestha B, Spatafora JW (2007) Phylogenetic classification of Cordyceps and the clavicipitaceous fungi. Stud Mycol 57:5–59.  https://doi.org/10.3114/sim.2007.57.01 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature (outside the USA)  2017

Authors and Affiliations

  • Christopher A. Dunlap
    • 1
  • José Luis Ramirez
    • 1
  • Gabriel Moura Mascarin
    • 2
  • David P. Labeda
    • 3
  1. 1.Crop Bioprotection Research Unit, National Center for Agricultural Utilization Research, Agricultural Research ServiceUnited States Department of AgriculturePeoriaUSA
  2. 2.Embrapa Meio AmbienteJaguariúnaBrazil
  3. 3.Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research ServiceUnited States Department of AgriculturePeoriaUSA

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