Draft genome sequences of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E-polonica and Penicillium freii DAOMC 242723

The genomes of Armillaria fuscipes, Ceratocystiopsis minuta, Ceratocystis adiposa, Endoconidiophora laricicola, E. polonica, and Penicillium freii DAOMC 242723 are presented in this genome announcement. These six genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 21 Mb in the case of Ceratocystiopsis minuta to 58 Mb for the basidiomycete Armillaria fuscipes. These genomes include the first reports of genomes for the genus Endoconidiophora. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these pathogens cause disease.

[1]  G. S. de Hoog,et al.  Draft Genome Sequence of the Dimorphic Fungus Sporothrix pallida, a Nonpathogenic Species Belonging to Sporothrix, a Genus Containing Agents of Human and Feline Sporotrichosis , 2016, Genome Announcements.

[2]  M. Wingfield,et al.  Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose , 2015, BMC Evolutionary Biology.

[3]  A. McTaggart,et al.  Saprophytic and pathogenic fungi in the Ceratocystidaceae differ in their ability to metabolize plant-derived sucrose , 2015, BMC Evolutionary Biology.

[4]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[5]  M. Wingfield,et al.  Unisexual reproduction in Huntiella moniliformis. , 2015, Fungal genetics and biology : FG & B.

[6]  C. Fields,et al.  Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata , 2015 .

[7]  D. Hibbett,et al.  Evolution of novel wood decay mechanisms in Agaricales revealed by the genome sequences of Fistulina hepatica and Cylindrobasidium torrendii. , 2015, Fungal genetics and biology : FG & B.

[8]  Paul R. Sesink Clee,et al.  Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot , 2015, BMC Evolutionary Biology.

[9]  M. Wingfield,et al.  Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana , and Sclerotinia echinophila , 2014 .

[10]  Rangel C. Souza,et al.  Comparative genomics of the major fungal agents of human and animal Sporotrichosis: Sporothrix schenckii and Sporothrix brasiliensis , 2014, BMC Genomics.

[11]  M. Wingfield,et al.  Redefining Ceratocystis and allied genera , 2014, Studies in mycology.

[12]  Enrico Rubagotti,et al.  Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis , 2014 .

[13]  Enrico Rubagotti,et al.  IMA Genome-F 2: Ceratocystis manginecans, Ceratocystis moniliformis, Diplodia sapinea , 2014, IMA fungus.

[14]  J. Varga,et al.  Identification and nomenclature of the genus Penicillium , 2014, Studies in mycology.

[15]  Q. Zeng,et al.  Genome Sequence of the Pathogenic Fungus Sporothrix schenckii (ATCC 58251) , 2014, Genome Announcements.

[16]  Seonwook Lee,et al.  Whole Genome and Global Gene Expression Analyses of the Model Mushroom Flammulina velutipes Reveal a High Capacity for Lignocellulose Degradation , 2014, PloS one.

[17]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[18]  M. Wingfield,et al.  DNA Loss at the Ceratocystis fimbriata Mating Locus Results in Self-Sterility , 2014, PloS one.

[19]  M. Wingfield,et al.  IMA Genome-F 1: Ceratocystis fimbriata , 2013, IMA fungus.

[20]  B. Richardson,et al.  Transcriptome of an Armillaria root disease pathogen reveals candidate genes involved in host substrate utilization at the host–pathogen interface , 2013 .

[21]  Inna Dubchak,et al.  MycoCosm portal: gearing up for 1000 fungal genomes , 2013, Nucleic Acids Res..

[22]  Shaun D. Jackman,et al.  The genome and transcriptome of the pine saprophyte Ophiostoma piceae, and a comparison with the bark beetle-associated pine pathogen Grosmannia clavigera , 2013, BMC Genomics.

[23]  Z. D. de Beer,et al.  Characterization of the mating-type genes in Leptographium procerum and Leptographium profanum. , 2013, Fungal biology.

[24]  Katharina J. Hoff,et al.  WebAUGUSTUS—a web service for training AUGUSTUS and predicting genes in eukaryotes , 2013, Nucleic Acids Res..

[25]  Thomas M. Keane,et al.  Genomic and Proteomic Dissection of the Ubiquitous Plant Pathogen, Armillaria mellea: Toward a New Infection Model System , 2013, Journal of proteome research.

[26]  Paul Medvedev,et al.  Informed and automated k-mer size selection for genome assembly , 2013, Bioinform..

[27]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[28]  K. Dewar,et al.  Sequencing of the Dutch elm disease fungus genome using the Roche/454 GS-FLX Titanium System in a comparison of multiple genomics core facilities. , 2013, Journal of biomolecular techniques : JBT.

[29]  Alan M. Moses,et al.  Sequencing and annotation of the Ophiostoma ulmi genome , 2013, BMC Genomics.

[30]  Sergey I. Nikolenko,et al.  BayesHammer: Bayesian clustering for error correction in single-cell sequencing , 2012, BMC Genomics.

[31]  Joaquín Dopazo,et al.  Qualimap: evaluating next-generation sequencing alignment data , 2012, Bioinform..

[32]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[33]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[34]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[35]  M. Wingfield,et al.  Paleogene Radiation of a Plant Pathogenic Mushroom , 2011, PloS one.

[36]  J. Houbraken,et al.  Phylogeny of Penicillium and the segregation of Trichocomaceae into three families , 2011, Studies in mycology.

[37]  M. Coetzee,et al.  Secrets of the subterranean pathosystem of Armillaria. , 2011, Molecular plant pathology.

[38]  Martin Kollmar,et al.  A novel hybrid gene prediction method employing protein multiple sequence alignments , 2011, Bioinform..

[39]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[40]  Steven J. M. Jones,et al.  Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen , 2011, Proceedings of the National Academy of Sciences.

[41]  C. Breuil,et al.  Resolving taxonomic and phylogenetic incongruence within species Ceratocystiopsis minuta , 2009, Mycologia.

[42]  E. Christiansen,et al.  Combined Ips/Ceratocystis attack on Norway spruce, and defensive mechanisms of the trees1 , 2009 .

[43]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[44]  Sergey Koren,et al.  Aggressive assembly of pyrosequencing reads with mates , 2008, Bioinform..

[45]  Sofia M. C. Robb,et al.  MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.

[46]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[47]  B. Morgenstern,et al.  AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome , 2006, Genome Biology.

[48]  Burkhard Morgenstern,et al.  AUGUSTUS: ab initio prediction of alternative transcripts , 2006, Nucleic Acids Res..

[49]  Mauricio Marín Montoya,et al.  REVISIÓN DE Ceratocystis sensu stricto CON ESPECIAL REFERENCIA A LOS COMPLEJOS DE LAS ESPECIES C. coerulescens Y C. fimbriata , 2006 .

[50]  M. Wingfield,et al.  Phylogenetic analyses of DNA sequences reveal species partitions amongst isolates of Armillaria from Africa. , 2005, Mycological research.

[51]  C. Breuil,et al.  Ophiostomatoid and basidiomycetous fungi associated with green, red, and grey lodgepole pines after mountain pine beetle (Dendroctonus ponderosae) infestation , 2005 .

[52]  M. Wingfield,et al.  Ceratocystis species infecting stem wounds on Eucalyptus grandis in South Africa , 2004 .

[53]  Burkhard Morgenstern,et al.  AUGUSTUS: a web server for gene finding in eukaryotes , 2004, Nucleic Acids Res..

[54]  M. Wingfield,et al.  Characterisation of Ophiostoma species associated with pine bark beetles from Mexico, including O. pulvinisporum sp. nov. , 2004, Mycological research.

[55]  M. Wingfield,et al.  Identification of the Armillaria root rot pathogen in Ethiopian plantations , 2004 .

[56]  A. Pérez-Sierra,et al.  Characterization of Armillaria heimii from Africa , 2004 .

[57]  Nansheng Chen,et al.  Using RepeatMasker to Identify Repetitive Elements in Genomic Sequences , 2009, Current protocols in bioinformatics.

[58]  J. Elkinton,et al.  Pathogenicity and virulence. , 2004, Journal of invertebrate pathology.

[59]  M. Wingfield,et al.  Molecular characterisation of Armillaria species from Zimbabwe. , 2003, Mycological research.

[60]  T. Harrington,et al.  Phylogenetic and taxonomic evaluation of Chalara, Chalaropsis, and Thielaviopsis anamorphs associated with Ceratocystis , 2002 .

[61]  M. Wingfield,et al.  Identification of the causal agent of Armillaria root rot of Pinus species in South Africa , 2000 .

[62]  J. Ride,et al.  Purification and characterization of an endo-polygalacturonase (PG1) from a Zimbabwean species ofArmillaria , 1999 .

[63]  M. Wingfield,et al.  Ophiostomatoid fungi associated withIps cembrae in Japan and their pathogenicity of Japanese larch , 1998 .

[64]  S. Aljanabi,et al.  Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. , 1997, Nucleic acids research.

[65]  J. Ride,et al.  The use of pectic enzymes in the characterization of Armillaria isolates from Africa , 1997 .

[66]  M. Wingfield,et al.  Two species in the Ceratocystis coerulescens complex from conifers in western North America , 1997 .

[67]  C. Mohammed,et al.  Species delimitation in the African Armillaria complex by analysis of the ribosomal DNA spacers. , 1997, The Journal of general and applied microbiology.

[68]  J. Ride,et al.  Morphological and biochemical characterization of Armillaria isolates from Zimbabwe , 1996 .

[69]  C. Mohammed,et al.  Discrimination of some African Armillaria species by isozyme electrophoretic analysis. , 1994, The New phytologist.

[70]  M. Wingfield,et al.  Ceratocystis and Ophiostoma: Taxonomy, Ecology, and Pathogenicity , 1993 .

[71]  D. Minter,et al.  Dieback and death of larch caused by Ceratocystis laricicola sp. nov. following attack by Ips cembrae , 1987 .

[72]  B. Lowy.  A monograph of ceratocystis and ceratocystiopsis , 1982, Economic Botany.

[73]  P. Talbot.  New and Interesting Records of South African Fungi. Part II. , 1956 .

[74]  P. Talbot.  New and Interesting Records of South African Fungi. , 1951 .

[75]  R. W. Davidson.  Some additional species of Ceratostomella in the United States. , 1942 .

[76]  M. Sayari,et al.  Draft genome sequences of Ceratocystis eucalypticola , Chrysoporthe cubensis , C . deuterocubensis , Davidsoniella virescens , Fusarium temperatum , Graphilbum fragrans , Penicillium nordicum , and Thielaviopsis musarum , 2015 .

[77]  Guohui Yao,et al.  Graph accordance of next-generation sequence assemblies , 2012, Bioinform..

[78]  D. Six,et al.  The role of phytopathogenicity in bark beetle-fungus symbioses: a challenge to the classic paradigm. , 2011, Annual review of entomology.

[79]  M. Wingfield,et al.  A review of ceratocystis sensu stricto with special reference to the species complexes c. coerulescens and c. fimbriata. , 2006 .

[80]  J. Frisvad,et al.  Mycotoxins, drugs and other extrolites produced by species in Penicillium subgenus Penicillium , 2004 .

[81]  B. Wingfield,et al.  Ophiostoma and Ceratocystiopsis spp . associated with two pine-infesting bark beetles in Chile , 2004 .

[82]  Jens Christian Frisvad,et al.  Penicillium subgenus Penicillium - A guide to identification of food and air-borne terverticillate Penicillia and their mycotoxins , 2004 .

[83]  T. Harrington,et al.  Phylogenetic and taxonomic evaluation of Chalara, Chalaropsis, and Thielaviopsis anamorphs associated with Ceratocystis. , 2002, Mycologia.

[84]  M. Wingfield,et al.  Ophiostomatoid fungi associated with three pine-infesting bark beetles in South Africa. , 2001 .

[85]  T. Paine,et al.  Interactions among Scolytid bark beetles, their associated fungi, and live host conifers. , 1997, Annual review of entomology.

[86]  H. Upadhyay.  Monograph of Ceratocystis and Ceratocystiopsis , 1981 .

[87]  Aino Mathiesen-Kaarik.  Studies on the ecology, taxonomy and physiology of Swedish insect-associated blue stain fungi, especially the genus Ceratocystis. , 1960 .

[88]  W. Siemaszko.  Fungi associated with bark beetles in Poland. , 1939 .