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).

Assembly

The first genomic assembly of B. cinerea strain B05.10 was generated by the Broad Institute at MIT and Harvard^1,^ followed by an improved draft version^2,^ The present assembly^3^, 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.

Annotation

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 ~25 scientists and supported by Ensembl Genomes3, and made availabe in release 34. Functional annotation and comparative analyses were conducted through the Ensembl Genomes pipeline.

The following members of the Botrytis community participated in the structural curation of gene models: Matthias Hahn, Sylvia Thoms, Juliane Schurig, Nathalie Knüppel (University of Kaiserslautern, Germany); Ernesto Benito (University of Salamanca, Spain); Daniela Santander, Vinicio Armijos (Universidad de Las Américas, Quito, Ecuador); Celedonio Gonzalez, Nelida Brito, Mario Gonzalez (University of La Laguna, Spain); Rita Milvia DeMiccolis Angelini, Caterina Rotolo (University of Bari, Italy); Nathalie Poussereau, Cecile Ribot, Amelie Devallee, Christine Rascle, MarieJoseph Gagey, Mathias Choquer, Christophe Bruel (University Claude Bernard Lyon 1, France); Adeline Simon, Muriel Viaud, Jaafar Kilani (Versailles-Grignon Research Centre, INRA, France); Andreas Mosbach, Gabriel Scalliet (Syngenta, Switzerland); Paulo Canessa (Universidad Andres Bello, Santiago, Chile); Jan van Kan (Wageningen University, the Netherlands). Their tireless efforts to improve the annotations to the best of their capacity are gratefully acknowledged.

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.

References

1. 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.
2. Genome update of Botrytis cinerea strains B05.10 and T4.
   Staats M, van Kan JA. 2012. Eukaryotic Cell. 11:1413-1414.
3. 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

More information

General information about this species can be found in Wikipedia.