A gapless genome sequence of the fungus Botrytis cinerea

Jan A.L. Van Kan*, Joost H.M. Stassen, Andreas Mosbach, Theo A.J. Van Der Lee, Luigi Faino, Andrew D. Farmer, Dimitrios G. Papasotiriou, Shiguo Zhou, Michael F. Seidl, Eleanor Cottam, Dominique Edel, Matthias Hahn, David C. Schwartz, Robert A. Dietrich, Stephanie Widdison, Gabriel Scalliet

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

63 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)75-89
JournalMolecular Plant Pathology
Volume18
Issue number1
DOIs
Publication statusPublished - 2017

Fingerprint

Botrytis
Botrytis cinerea
Untranslated Regions
chromosome
Fungi
iprodione
genome
fungus
Genome
chromosomes
fungi
gene
Overlapping Genes
Genes
Chromosomes, Human, Pair 18
Chromosomes, Human, Pair 10
genes
Chromosomes, Human, Pair 1
Telomere
boscalid

Keywords

  • Genetic map
  • Grey mould
  • Optical map
  • SMRT sequencing

Cite this

Van Kan, J. A. L., Stassen, J. H. M., Mosbach, A., Van Der Lee, T. A. J., Faino, L., Farmer, A. D., ... Scalliet, G. (2017). A gapless genome sequence of the fungus Botrytis cinerea. Molecular Plant Pathology, 18(1), 75-89. https://doi.org/10.1111/mpp.12384
Van Kan, Jan A.L. ; Stassen, Joost H.M. ; Mosbach, Andreas ; Van Der Lee, Theo A.J. ; Faino, Luigi ; Farmer, Andrew D. ; Papasotiriou, Dimitrios G. ; Zhou, Shiguo ; Seidl, Michael F. ; Cottam, Eleanor ; Edel, Dominique ; Hahn, Matthias ; Schwartz, David C. ; Dietrich, Robert A. ; Widdison, Stephanie ; Scalliet, Gabriel. / A gapless genome sequence of the fungus Botrytis cinerea. In: Molecular Plant Pathology. 2017 ; Vol. 18, No. 1. pp. 75-89.
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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.",
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author = "{Van Kan}, {Jan A.L.} and Stassen, {Joost H.M.} and Andreas Mosbach and {Van Der Lee}, {Theo A.J.} and Luigi Faino and Farmer, {Andrew D.} and Papasotiriou, {Dimitrios G.} and Shiguo Zhou and Seidl, {Michael F.} and Eleanor Cottam and Dominique Edel and Matthias Hahn and Schwartz, {David C.} and Dietrich, {Robert A.} and Stephanie Widdison and Gabriel Scalliet",
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Van Kan, JAL, Stassen, JHM, Mosbach, A, Van Der Lee, TAJ, Faino, L, Farmer, AD, Papasotiriou, DG, Zhou, S, Seidl, MF, Cottam, E, Edel, D, Hahn, M, Schwartz, DC, Dietrich, RA, Widdison, S & Scalliet, G 2017, 'A gapless genome sequence of the fungus Botrytis cinerea', Molecular Plant Pathology, vol. 18, no. 1, pp. 75-89. https://doi.org/10.1111/mpp.12384

A gapless genome sequence of the fungus Botrytis cinerea. / Van Kan, Jan A.L.; Stassen, Joost H.M.; Mosbach, Andreas; Van Der Lee, Theo A.J.; Faino, Luigi; Farmer, Andrew D.; Papasotiriou, Dimitrios G.; Zhou, Shiguo; Seidl, Michael F.; Cottam, Eleanor; Edel, Dominique; Hahn, Matthias; Schwartz, David C.; Dietrich, Robert A.; Widdison, Stephanie; Scalliet, Gabriel.

In: Molecular Plant Pathology, Vol. 18, No. 1, 2017, p. 75-89.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A gapless genome sequence of the fungus Botrytis cinerea

AU - Van Kan, Jan A.L.

AU - Stassen, Joost H.M.

AU - Mosbach, Andreas

AU - Van Der Lee, Theo A.J.

AU - Faino, Luigi

AU - Farmer, Andrew D.

AU - Papasotiriou, Dimitrios G.

AU - Zhou, Shiguo

AU - Seidl, Michael F.

AU - Cottam, Eleanor

AU - Edel, Dominique

AU - Hahn, Matthias

AU - Schwartz, David C.

AU - Dietrich, Robert A.

AU - Widdison, Stephanie

AU - Scalliet, Gabriel

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - Genetic map

KW - Grey mould

KW - Optical map

KW - SMRT sequencing

U2 - 10.1111/mpp.12384

DO - 10.1111/mpp.12384

M3 - Article

VL - 18

SP - 75

EP - 89

JO - Molecular Plant Pathology

JF - Molecular Plant Pathology

SN - 1464-6722

IS - 1

ER -