Botrytis cinerea B05.10 Assembly and Gene Annotation
About the Botrytis cinerea genome
Botrytis cinerea is the causal agent of the grey mold disease. Similarly to Sclerotinia sclerotiorum, this Ascomycete can infect a wide range of plants in any stage of growth and is widespread in all continents. The most notable host is the wine grape where it not only causes detrimental bunch rot but, under favourable conditions, is able to cause a benevolent form of berry colonization called “noble rot”. Grapes infected with noble rot have been used for centuries in the production of sweet dessert wines. Botrytis cinerea can lead to important economic losses in many dozens of crops and harvested commodities, including vegetables (lettuce, tomato), fruit (berries, kiwifruit) and ornamentals (rose).
The first genomic assembly of B. cinerea strain B05.10 was generated by the Broad Institute at MIT and Harvard1,followed by an improved draft version2, The present assembly3, availabe in Ensembl Fungi since release 27, was generated by Wageningen University and Syngenta, was sequenced by a combination of Illumina and PacBio technology (at >50 x and ~40 x coverage, respectively), and assembled to 18 gapless contigs, representing separate chromosomes, of which two are very small (208 and 247 kb, respectively). Ten of the 18 chromosomes contain telomeric repeats at both ends. The assembly is fully supported by an optical map and a genetic linkage map. The total length of the assembly is 42.65 Mb; sequences lacking in the assembly are 0.27 Mb of telomeric repeats and 0.58 Mb of rDNA repeats.
Gene models were predicted by Wageningen University by several tools and integrated using EVM, resulting in 11,700 predicted protein-coding genes. RNASeq data of samples from >20 conditions were used for gene model validation. The gene models were then revised by an comprehensive manual review undertaken by a community of over 40 scientists and supported by Ensembl Genomes3, , and made availabe in release 34. Functional annotation and comparative analyses were conducted through the Ensembl Genomes pipeline.
Non coding RNA genes have been annotated using tRNAScan-SE (Lowe, T.M. and Eddy, S.R. 1997), RFAM (Griffiths-Jones et al 2005), and RNAmmer (Lagesen K.,et al 2007); additional analysis tools have also been applied.
- Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.
Amselem J, Cuomo CA, van Kan JA, Viaud M, ..., Rollins JA, Lebrun MH, Dickman M. 2011. PLoS Genet.. 7:e1002230.
- Genome update of Botrytis cinerea strains B05.10 and T4.
Staats M, van Kan JA. 2012. Eukaryotic Cell. 11:1413-1414.
- A gapless genome sequence of the fungus Botrytis cinerea.
Stassen JH, Mosbach A, Van Der Lee TA, Faino L, Farmer AD, Papasotiriou DG, Zhou S, Seidl MF, Cottam E, Edel D et al. 2017. Molecular Plant Pathology. 1:75-89.
Picture credit: Picture credit: Ninjatacoshell
General information about this species can be found in Wikipedia.
|Assembly||ASM83294v1 (Botrytis cinerea B05.10 assembly January 2015), INSDC Assembly GCA_000832945.1, Feb 2015|
|Golden Path Length||42,630,066|
|Genebuild method||Import from Wageningen University|
|Data source||Wageningen University|
|Non coding genes||299|
|Small non coding genes||297|
|Misc non coding genes||2|