title: A gapless genome sequence of the fungus Botrytis cinerea.
abstract: Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, a gapless, near-finished genome sequence for B. cinerea strain B05.10 is reported. The assembly comprised 18 chromosomes and was confirmed by an optical map and a genetic map based on approximately 75 000 single nucleotide polymorphism (SNP) markers. All chromosomes contained fully assembled centromeric regions, and 10 chromosomes had telomeres on both ends. The genetic map consisted of 4153 cM and a comparison of the genetic distances with the physical distances identified 40 recombination hotspots. The linkage map also identified two mutations, located in the previously described genes Bos1 and BcsdhB, that conferred resistance to the fungicides boscalid and iprodione. The genome was predicted to encode 11 701 proteins. RNAseq data from >20 different samples were used to validate and improve gene models. Manual curation of chromosome 1 revealed interesting features, such as the occurrence of a dicistronic transcript and fully overlapping genes in opposite orientations, as well as many spliced antisense transcripts. Manual curation also revealed that the untranslated regions (UTRs) of genes can be complex and long, with many UTRs exceeding lengths of 1 kb and possessing multiple introns. Community annotation is in progress.
authors.affiliation: Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Jan A L
authors.initials: JA
authors.lastname: Van Kan
authors.affiliation: Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Joost H M
authors.initials: JH
authors.lastname: Stassen
authors.affiliation: Syngenta Crop Protection Münchwilen AG, Crop Protection Research, CH-4332, Stein, Switzerland.
authors.forename: Andreas
authors.initials: A
authors.lastname: Mosbach
authors.affiliation: Wageningen UR Plant Research International, 6708 PB, Wageningen, the Netherlands.
authors.forename: Theo A J
authors.initials: TA
authors.lastname: Van Der Lee
authors.affiliation: Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Luigi
authors.initials: L
authors.lastname: Faino
authors.affiliation: National Center for Genome Resources, Santa Fe, NM, 87505, USA.|Syngenta Biotechnology Inc., Research Triangle Park, NC, 27709, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.affiliation: Syngenta Jealotts Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
authors.forename: Dimitrios G
authors.initials: DG
authors.lastname: Papasotiriou
authors.affiliation: Department of Chemistry, Laboratory of Genetics and Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.affiliation: Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands.
authors.forename: Michael F
authors.initials: MF
authors.lastname: Seidl
authors.affiliation: General Bioinformatics, Jealotts Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
authors.forename: Eleanor
authors.initials: E
authors.lastname: Cottam
authors.affiliation: Syngenta Crop Protection Münchwilen AG, Crop Protection Research, CH-4332, Stein, Switzerland.
authors.forename: Dominique
authors.initials: D
authors.lastname: Edel
authors.affiliation: Faculty of Biology, Technical University Kaiserslautern, 67653 Kaiserslautern, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Hahn
authors.affiliation: Department of Chemistry, Laboratory of Genetics and Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin, Madison, WI, 53706, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.affiliation: Syngenta Biotechnology Inc., Research Triangle Park, NC, 27709, USA.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Dietrich
authors.affiliation: General Bioinformatics, Jealotts Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Widdison
authors.affiliation: Syngenta Crop Protection Münchwilen AG, Crop Protection Research, CH-4332, Stein, Switzerland.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Scalliet
mesh_terms: D020029:Base Pairing / Q000235:genetics; D001483:Base Sequence; D020171:Botrytis / Q000166:cytology / Q000187:drug effects / Q000235:genetics*; D002874:Chromosome Mapping; D015825:Chromosomes, Fungal / Q000235:genetics; D025141:Drug Resistance, Fungal / Q000187:drug effects / Q000235:genetics; D019143:Evolution, Molecular; D005659:Fungicides, Industrial / Q000494:pharmacology; D005800:Genes, Fungal; D008040:Genetic Linkage; D056426:Genetic Loci; D016681:Genome, Fungal; D008540:Meiosis / Q000187:drug effects; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D062308:Optogenetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D020543:Proteome / Q000378:metabolism; D040901:Proteomics; D011995:Recombination, Genetic / Q000187:drug effects / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D005659:Fungicides, Industrial; D020543:Proteome
keywords: SMRT sequencing; genetic map; grey mould; optical map