ToxGen: an improved reference database for the identification of type B-trichothecene genotypes in<i>Fusarium</i>

PeerJ - Tập 5 - Trang e2992
Tomasz Kulik1, Kessy Abarenkov2, Maciej Buśko3, Katarzyna Bilska1, Anne D. van Diepeningen4,5, Anna Ostrowska-Kołodziejczak3, Katarzyna Krawczyk1, Balázs Brankovics4,5, Sebastián A. Stenglein6,7, Jakub Sawicki8,1, J. Perkowski3
1Department of Botany and Nature Protection, University of Warmia and Mazury, Olsztyn, Poland
2Natural History Museum, University of Tartu, Tartu, Estonia
3Department of Chemistry, Poznań University of Life Sciences, Poznań, Poland
4CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands
5Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
6Cátedra de Microbiología-Facultad de Agronomía de Azul-UNCPBA, Azul, Buenos Aires, Argentina
7Laboratorio de Biología Funcional y Biotecnología (BIOLAB)-CICBA-INBIOTEC, CONICET, Azul, Buenos Aires, Argentina
8Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic

Tóm tắt

Type B trichothecenes, which pose a serious hazard to consumer health, occur worldwide in grains. These mycotoxins are produced mainly by three different trichothecene genotypes/chemotypes: 3ADON (3-acetyldeoxynivalenol), 15ADON (15-acetyldeoxynivalenol) and NIV (nivalenol), named after these three major mycotoxin compounds. Correct identification of these genotypes is elementary for all studies relating to population surveys, fungal ecology and mycotoxicology. Trichothecene producers exhibit enormous strain-dependent chemical diversity, which may result in variation in levels of the genotype’s determining toxin and in the production of low to high amounts of atypical compounds. New high-throughput DNA-sequencing technologies promise to boost the diagnostics of mycotoxin genotypes. However, this requires a reference database containing a satisfactory taxonomic sampling of sequences showing high correlation to actually produced chemotypes. We believe that one of the most pressing current challenges of such a database is the linking of molecular identification with chemical diversity of the strains, as well as other metadata. In this study, we use the Tri12 gene involved in mycotoxin biosynthesis for identification of Tri genotypes through sequence comparison. Tri12 sequences from a range of geographically diverse fungal strains comprising 22Fusariumspecies were stored in the ToxGen database, which covers descriptive and up-to-date annotations such as indication on Tri genotype and chemotype of the strains, chemical diversity, information on trichothecene-inducing host, substrate or media, geographical locality, and most recent taxonomic affiliations. The present initiative bridges the gap between the demands of comprehensive studies on trichothecene producers and the existing nucleotide sequence databases, which lack toxicological and other auxiliary data. We invite researchers working in the fields of fungal taxonomy, epidemiology and mycotoxicology to join the freely available annotation effort.

Từ khóa


Tài liệu tham khảo

Abarenkov, 2010, PlutoF-a web based workbench for ecological and taxonomic research, with an online implementation for fungal ITS sequences, Evolutionary Bioinformatics, 6, 189, 10.4137/EBO.S6271

Aoki, 2012, Systematics, phylogeny, and trichothecene mycotoxin potential of Fusarium head blight cereal pathogen, Mycotoxins, 62, 91, 10.2520/myco.62.91

Audenaert, 2013, Deoxynivalenol: a major player in the multifaceted response of Fusarium to its environment, Toxins, 6, 1, 10.3390/toxins6010001

Begerow, 2010, Current state and perspectives of fungal DNA barcoding and rapid identification procedures, Applied Microbiology and Biotechnology, 87, 99, 10.1007/s00253-010-2585-4

Buśko, 2014, Quantitative volatile compound profiles in fungal cultures of three different Fusarium graminearum chemotypes, FEMS Microbiology Letters, 359, 85, 10.1111/1574-6968.12569

Castañares, 2014, Trichothecene genotypes and production profiles of Fusarium graminearum isolates obtained from barley cultivated in Argentina, International Journal of Food Microbiology, 179, 57, 10.1016/j.ijfoodmicro.2014.03.024

Desjardins, 2006, Fusarium mycotoxins chemistry, genetics and biology

Desjardins, 2008, Gibberella ear rot of maize (Zea mays) in Nepal: distribution of the mycotoxins nivalenol and deoxynivalenol in naturally and experimentally infected maize, Journal of Agricultural and Food Chemistry, 56, 5428, 10.1021/jf8003702

Felsenstein, 1985, Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 39, 783, 10.2307/2408678

Frisvad, 2012, Media growth conditions for induction of secondary metabolite production, Fungal secondary metabolism: methods and protocols, methods in molecular biology, 47, 10.1007/978-1-62703-122-6_3

Gale, 2007, Population subdivision of Fusarium graminearum sensu stricto in the Upper Midwestern United States, Phytopathology, 97, 1434, 10.1094/PHYTO-97-11-1434

Geiser, 2013, One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use, Phytopathology, 103, 400, 10.1094/PHYTO-07-12-0150-LE

Geiser, 2004, FUSARIUM-ID v. 1.0: a DNA sequence database for identifying Fusarium, European Journal of Plant Pathology, 110, 473, 10.1023/B:EJPP.0000032386.75915.a0

Grigoriev, 2014, MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Research, 42, 699, 10.1093/nar/gkt1183

Guldener, 2006, FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum, Nucleic Acids Research, 34, 456, 10.1093/nar/gkj026

Hou, 2013, Mycotoxin-containing diet causes oxidative stress in the mouse, PLOS ONE, 8, e60374, 10.1371/journal.pone.0060374

Jestoi, 2008, In vitro and in vivo mycotoxin production of Fusarium species isolated from Finnish grains, Archives of Phytopathology and Plant Protection, 41, 545, 10.1080/03235400600881547

Kimura, 1980, A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, 16, 111, 10.1007/BF01731581

Kimura, 2003, The trichothecene biosynthesis gene cluster of Fusarium graminearum F15 contains a limited number of essential pathway genes and expressed non-essential genes, FEBS Letters, 539, 105, 10.1016/S0014-5793(03)00208-4

Kosiak, 2005, Morphological, chemical and molecular differentiation of Fusarium equiseti isolated from Norwegian cereals, International Journal of Food Microbiology, 99, 195, 10.1016/j.ijfoodmicro.2004.08.015

Kress, 2007, A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region, PLOS ONE, 2, e508, 10.1371/journal.pone.0000508

Kulik, 2011, Development of TaqMan assays for 3ADON, 15-ADON and NIV Fusarium genotypes based on Tri12 gene, Cereal Research Communications, 39, 200, 10.1556/CRC.39.2011.2.4

Kulik, 2016, Depicting the discrepancy between tri genotype and chemotype on the basis of strain CBS 139514 from a field population of F. graminearum sensu stricto from Argentina, Toxins, 8, 10.3390/toxins8110330

Lee, 2001, Identification of deoxynivalenol- and nivalenol-producing chemotypes of Gibberella zeae by using PCR, Applied and Environmental Microbiology, 67, 2966, 10.1128/AEM.67.7.2966-2972.2001

Lindahl, 2013, Fungal community analysis by high-throughput sequencing of amplified markers—a user’s guide, New Phytologist, 199, 288, 10.1111/nph.12243

Marin, 2013, Mycotoxins: occurrence, toxicology, and exposure assessment, Food and Chemical Toxicology, 60, 218, 10.1016/j.fct.2013.07.047

McCormick, 2011, Trichothecenes: from simple to complex mycotoxins, Toxins, 3, 802, 10.3390/toxins3070802

Meier, 2006, DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success, Systematic Biology, 55, 715, 10.1080/10635150600969864

Mugrabi de Kuppler, 2011, Genotyping and phenotyping of Fusarium graminearum isolates from Germany related to their mycotoxin biosynthesis, International Journal of Food Microbiology, 151, 78, 10.1016/j.ijfoodmicro.2011.08.006

Nielsen, 2012, TRI12 based quantitative real-time PCR assays reveal the distribution of trichothecene genotypes of F. graminearum and F. culmorum isolates in Danish small grain cereals, International Journal of Food Microbiology, 157, 384, 10.1016/j.ijfoodmicro.2012.06.010

Nilsson, 2006, Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective, PLOS ONE, 1, e59, 10.1371/journal.pone.0000059

O’Donnell, 2008, Multilocus genotyping and molecular phylogenetics resolve a novel head blight pathogen within the Fusarium graminearum species complex from Ethiopia, Fungal Genetics and Biology, 45, 1514, 10.1016/j.fgb.2008.09.002

Pasquali, 2016, A European database of Fusarium graminearum and F. culmorum trichothecene genotypes, Frontiers in Microbiology, 7, 10.3389/fmicb.2016.00406

Pasquali, 2016, The effect of agmatine on trichothecene type B and zearalenone production in Fusarium graminearum, F. culmorum and F. poae, PeerJ, 4, e1672, 10.7717/peerj.1672

Pasquali, 2010, Genetic Fusarium chemotyping as a useful tool for predicting nivalenol contamination in winter wheat, International Journal of Food Microbiology, 137, 246, 10.1016/j.ijfoodmicro.2009.11.009

Pasquali, 2014, Genetic approaches to chemotype determination in type B- trichothecene producing Fusaria, International Journal of Food Microbiology, 17, 164, 10.1016/j.ijfoodmicro.2014.08.011

Pestka, 1985, Deoxynivalenol and 15-monoacetyl deoxynivalenol production by Fusarium graminearum R6576 in liquid media, Mycopathologia, 91, 23, 10.1007/BF00437282

Sarver, 2011, Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multilocus genealogical concordance, Fungal Genetics and Biology, 48, 1096, 10.1016/j.fgb.2011.09.002

Scherm, 2013, Fusarium culmorum: causal agent of foot and root rot and head blight on wheat, Molecular Plant Pathology, 14, 323, 10.1111/mpp.12011

Shokralla, 2014, Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens, Molecular Ecology Resources, 14, 892, 10.1111/1755-0998.12236

Tamura, 2013, MEGA6: molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, 30, 2725, 10.1093/molbev/mst197

Van der Lee, 2015, Biogeography of Fusarium graminearum species complex and chemotypes: a review, Food Additives & Contaminants: Part A, 8, 1, 10.1080/19440049.2014.984244

Varga, 2015, New tricks of an old enemy: isolates of Fusarium graminearum produce a type a trichothecene mycotoxin, Environmental Microbiology, 17, 2588, 10.1111/1462-2920.12718

Wang, 2008, Development of a generic PCR detection of 3-acetyldeoxy-nivalenol-, 15-acetyldeoxynivalenol- and nivalenol-chemotypes of Fusarium graminearum Clade, International Journal of Molecular Sciences, 9, 2495, 10.3390/ijms9122495

Ward, 2002, Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium, Proceedings of the National Academy of Sciences of the United States of America, 99, 9278, 10.1073/pnas.142307199

Ward, 2008, An adaptive evolutionary shift in Fusarium head blight pathogen populations is driving the rapid spread of more toxigenic Fusarium graminearum in North America, Fungal Genetics and Biology, 45, 473, 10.1016/j.fgb.2007.10.003

Zhang, 2010, Population genetic analyses of Fusarium asiaticum populations from barley suggest a recent shift favoring 3-ADON producers in Southern China, Phytopathology, 100, 328, 10.1094/PHYTO-100-4-0328

Zhao, 2009, FPPI: Fusarium graminearum protein-protein interaction Database, Journal of Proteome Research, 8, 4714, 10.1021/pr900415b

Thông tin
Thông tin xuất bản

PeerJ

Tập 5

e2992

Thông tin tác giả