The Sclerotinia Sclerotiorum Whole Genome Sequencing Project

The genome sequence of the filamentous ascomycete Sclerotinia sclerotiorum has been sequenced by the Broad Institute through a project sponsored by the USDA Microbial Genomics Program. The Principal Investigators on this project are Drs. Christina Cuomo at MIT’s Broad Institute, Martin Dickman at the Texas A&M University, Linda Kohn at the University of Toronto, and Jeffrey Rollins at the University of Florida.

The first public release of the 8X genome sequence assembly was to the NCBI trace archives on 04/25/2005. The first draft assembly with annotation was released on October 01, 2005 on the Broad Web Server.

The release of this sequence data represented the first public release of an assembled genome from the Leotiales, and the first from a broad host range necrotrophic phytopathogenic fungus. Subsequent efforts sponsored by the European Community to sequence the genome of Botrytinia fuckelinia (Botrytis cinerea), provided an unprecedented opportunity for comparative genomics for evolutionary and functional biology inquiries. A joint community manual annotation project between the Botrytis and Sclerotinia communities resulted in the 2011 comparative genomics publication, Amselem, et al. 2011. Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet. 7:e1002230. doi:10.1371/journal.pgen.1002230.

The specific Objectives of this project, were to:

  1. Produce a high quality draft (HQD) sequence of the Sclerotinia sclerotiorum genome with an average depth of ~7X in Q20 bases and ~62X physical coverage in the assembly.
  2. Assemble the Sclerotinia genome sequence using the Arachne assembly program (Batzoglou et al. 2002).
  3. Sequence both ends of 12,000 cDNAs (6,000 from each of two different libraries). Align EST sequences to the genome and use this information as a training set to refine the gene prediction model and computational annotation of all genes to increase the accuracy of the S. sclerotiorum annotation.
  4. Make the assembly and annotation of Sclerotinia publicly available through the CGR web site at http://www.broad.mit.edu, which allowed users to:
    • Download the entire genome, protein set, or portions
    • Perform nucleotide or protein Blast searches
    • Interactively search for predicted genes based on name, location, homology information, protein domain, and multigene family
  • Graphically view the sequence annotated with genes, protein families, and regions of similarity to known sequences

This project:

  1. Sequenced the genome to a depth of 8.8x. This included 394,368 paired reads from a 4kb genomic library, 117,504 paired reads from a 10 kb genomic library, and 69,120 paired reads from a BAC library.
  2. Pair end Sanger sequenced and mapped 31,298 ESTs from three independent cDNA libraries. For the developing sclerotia library (SS_G781_seq.fasta), there are 17,533 sequences from 9,497 clones (8,036 clones have both ends sequenced). For the mycelia pH7 library (SS_G786_seq.fasta), there are 18,885 sequences from 10,566 clones (8,319 clones have both ends sequenced). For the developing apothecia library (SS_G787_seq.fasta), there are 21,333 sequences from 11,235 clones (10,098 clones have both ends sequenced). This sequence reads are available for download from NCBI under Accession PRJNA390952
  • Annotated the genome for structural and functional features and conducted comparative genomics with Botrytis cinerea. Published a community-driven joint genome paper in PLoS Genetics

Re-sequencing for a Complete Genome:

  1. In 2015, a community effort was undertaken to take advantage of next generation single molecule sequencing technology to produce a complete genome sequence of the previously sequenced ‘1980’ reference isolate.

The Re-sequencing project:

  1. Produced a gap-less genome (with the exception of the full rDNA repeat0: NCBI Accession PRJNA348385
  2. Assembled and mapped the genome to 16 chromosomes (14 of 16 chromosomes from telomere to telomere)
  3. Generated extensive RNA-seq data for accurate gene prediction and annotation of 11,130 gene models
  4. Predicted 70 effector candidates
  • Published the results in a 2017 publication, Derbyshire, M., M. Denton-Giles, D. Hegedus, S. Seifbarghy, J. Rollins, J. van Kan, M.F. Seidl, L. Faino, M. Mbengue, O. Navaud, S. Raffaele, K. Hammond-Kosack, S. Heard, and R. Oliver. 2017. The Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens. Genome Biol Evol. 9:593–618. doi:10.1093/gbe/evx030.

Updated 22 July 2017 by Jeffrey Rollins.