S. cerevisiae strain YJM339 genome sequence.

02/04/2015

This directory contains 6 files describing the genome of S. cerevisiae strain 
YJM339, a clinical isolate (Accession: JRIE00000000). 

genome fasta file: YJM339_Stanford_2014_JRIE00000000.fsa
nucleic acid coding sequence file: YJM339_JRIE00000000_cds.fsa
protein sequence file:  YJM339_JRIE00000000_pep.fsa
GFF file: YJM339_JRIE00000000.gff
snv variant call format file: YJM339.gatk.vcf.gz
indel variant call format file: YJM339.indel.gatk.vcf.gz

FASTA headers in each of the files include the following pieces of information:

genome fasta file: 
 GenBank GI number
 GenBank accession.version
 species name
 strain name
 scaffold number
 contig length

nucleic acid coding sequence file: 
 ORF name_strain name
 gene name
 feature type
 feature classification (Verified, Uncharacterized, or Dubious)
 feature description

protein sequence file: 
 ORF name_strain name
 gene name
 feature type
 feature classification (Verified, Uncharacterized, or Dubious)
 feature description

Feature definitions (for coding sequences and features in the gff file) were
assigned via homology-based annotation using LASTZ and AUGUSTUS vs. the R64-1
S288C reference sequence in conjuction with ab initio annotation using MAKER 
and BLASTX validation.

Assembly statistics
================================
Fold coverage:		102
Number of scaffolds:	994
Assembly size:		11683869
Longest scaffold:	216801
Scaffold N50:		47674
Number of ORFs:		5317

Reference for this S. cerevisiae YJM339 genome sequence, assembly and annotation:

Song G., et al., 2014. AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome 
Analysis of Saccharomyces cerevisiae.  PLoS ONE, in press.


For more information about YJM339:

Heck J, Argueso J, Gemici Z, Reeves R, Bernard A, et al. 2006. Negative epistasis 
between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes 
results in a defect in mismatch repair. Proc Natl Acad Sci U S A 103(9):3256-61.
PMID: 16492773


For more information about other yeast strains:

Engel SR, Cherry JM. 2013. The new modern era of yeast genomics: community 
sequencing and the resulting annotation of multiple Saccharomyces cerevisiae 
strains at the Saccharomyces Genome Database.
Database (Oxford). 2013 Mar 13;2013:bat012. doi: 10.1093/database/bat012.
PMID: 23487186

For more information about the S288C Reference Genome:

Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight 
SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato 
SR, Simison M, Cherry JM. 2014. The reference genome sequence of Saccharomyces 
cerevisiae: then and now. 
G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.
PMID: 24374639

To download the S288C Reference Genome sequence and annotation: 
http://www.yeastgenome.org/download-data/sequence