Gapless genome sequence of Botrytis cinerea strain B05.10

J.A.L. van Kan, G. Scalliet

Research output: Chapter in Book/Report/Conference proceedingAbstract

Abstract

Through a combination of sequencing technologies (Illumina, PacBio), we have assembled a gapless genome sequence of Botrytis cinerea strain B05.10, which is corroborated by an optical map. The assembly comprises 18 chromosomes, of which 10 are full-length from one telomere to the other. Two chromosomes are very small (208 and 247 kbp). RNAseq information from a wide range of developmental stages and culture conditions was included in gene prediction pipelines, which permitted to improve gene models significantly and (partly) annotate splice variants. RNASeq analysis revealed non-coding transcripts in intergenic regions. The previously unresolved structure of some secondary metabolite gene clusters was determined (e.g. the botcinic acid cluster, which is important in virulence). Several transcripts appear to have an operon structure, with a single mRNA encoding two proteins. Large scale proteomics was performed to experimentally assess the quality of current gene models and compare it with former versions of the B. cinerea genome. Genetic characterization was performed of a progeny of ~70 individuals from a cross between B05.10 and a field isolate, using Illumina resequencing. A high density linkage map was obtained on which multiple fungicide resistance factors could be mapped. One translocation was observed between the two strains used in the cross. Comparison of genetic with physical distances enabled to identify regions with low recombination rates as well as potential recombination hotspots. This novel, near-finished genome sequence is a major step forward for the community and provides a valuable resource for future research on B.cinerea. A community annotation effort will be organized with support from EBI in the framework of the Ensembl Fungi platform. Community members are invited to participate in the process by adopting chromosomes for curation and annotation.
Original languageEnglish
Title of host publicationBook of Abstracts 28th Fungal Genetics Conference
Pages129-130
Publication statusPublished - 2015
Event28th Fungal Genetics Conference, Pacific Grove, CA, USA -
Duration: 17 Mar 201522 Mar 2015

Conference

Conference28th Fungal Genetics Conference, Pacific Grove, CA, USA
Period17/03/1522/03/15

Fingerprint

Botrytis
Genome
Genetic Recombination
Chromosomes
Genes
Chromosomes, Human, Pair 10
Intergenic DNA
R Factors
Telomere
Operon
Multigene Family
Proteomics
Virulence
Fungi
Technology
Messenger RNA
Proteins

Cite this

van Kan, J. A. L., & Scalliet, G. (2015). Gapless genome sequence of Botrytis cinerea strain B05.10. In Book of Abstracts 28th Fungal Genetics Conference (pp. 129-130)
van Kan, J.A.L. ; Scalliet, G. / Gapless genome sequence of Botrytis cinerea strain B05.10. Book of Abstracts 28th Fungal Genetics Conference. 2015. pp. 129-130
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van Kan, JAL & Scalliet, G 2015, Gapless genome sequence of Botrytis cinerea strain B05.10. in Book of Abstracts 28th Fungal Genetics Conference. pp. 129-130, 28th Fungal Genetics Conference, Pacific Grove, CA, USA, 17/03/15.

Gapless genome sequence of Botrytis cinerea strain B05.10. / van Kan, J.A.L.; Scalliet, G.

Book of Abstracts 28th Fungal Genetics Conference. 2015. p. 129-130.

Research output: Chapter in Book/Report/Conference proceedingAbstract

TY - CHAP

T1 - Gapless genome sequence of Botrytis cinerea strain B05.10

AU - van Kan, J.A.L.

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N2 - Through a combination of sequencing technologies (Illumina, PacBio), we have assembled a gapless genome sequence of Botrytis cinerea strain B05.10, which is corroborated by an optical map. The assembly comprises 18 chromosomes, of which 10 are full-length from one telomere to the other. Two chromosomes are very small (208 and 247 kbp). RNAseq information from a wide range of developmental stages and culture conditions was included in gene prediction pipelines, which permitted to improve gene models significantly and (partly) annotate splice variants. RNASeq analysis revealed non-coding transcripts in intergenic regions. The previously unresolved structure of some secondary metabolite gene clusters was determined (e.g. the botcinic acid cluster, which is important in virulence). Several transcripts appear to have an operon structure, with a single mRNA encoding two proteins. Large scale proteomics was performed to experimentally assess the quality of current gene models and compare it with former versions of the B. cinerea genome. Genetic characterization was performed of a progeny of ~70 individuals from a cross between B05.10 and a field isolate, using Illumina resequencing. A high density linkage map was obtained on which multiple fungicide resistance factors could be mapped. One translocation was observed between the two strains used in the cross. Comparison of genetic with physical distances enabled to identify regions with low recombination rates as well as potential recombination hotspots. This novel, near-finished genome sequence is a major step forward for the community and provides a valuable resource for future research on B.cinerea. A community annotation effort will be organized with support from EBI in the framework of the Ensembl Fungi platform. Community members are invited to participate in the process by adopting chromosomes for curation and annotation.

AB - Through a combination of sequencing technologies (Illumina, PacBio), we have assembled a gapless genome sequence of Botrytis cinerea strain B05.10, which is corroborated by an optical map. The assembly comprises 18 chromosomes, of which 10 are full-length from one telomere to the other. Two chromosomes are very small (208 and 247 kbp). RNAseq information from a wide range of developmental stages and culture conditions was included in gene prediction pipelines, which permitted to improve gene models significantly and (partly) annotate splice variants. RNASeq analysis revealed non-coding transcripts in intergenic regions. The previously unresolved structure of some secondary metabolite gene clusters was determined (e.g. the botcinic acid cluster, which is important in virulence). Several transcripts appear to have an operon structure, with a single mRNA encoding two proteins. Large scale proteomics was performed to experimentally assess the quality of current gene models and compare it with former versions of the B. cinerea genome. Genetic characterization was performed of a progeny of ~70 individuals from a cross between B05.10 and a field isolate, using Illumina resequencing. A high density linkage map was obtained on which multiple fungicide resistance factors could be mapped. One translocation was observed between the two strains used in the cross. Comparison of genetic with physical distances enabled to identify regions with low recombination rates as well as potential recombination hotspots. This novel, near-finished genome sequence is a major step forward for the community and provides a valuable resource for future research on B.cinerea. A community annotation effort will be organized with support from EBI in the framework of the Ensembl Fungi platform. Community members are invited to participate in the process by adopting chromosomes for curation and annotation.

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van Kan JAL, Scalliet G. Gapless genome sequence of Botrytis cinerea strain B05.10. In Book of Abstracts 28th Fungal Genetics Conference. 2015. p. 129-130