S. cerevisiae strain YPH499 genome sequence.

02/04/2015

This directory contains 6 files describing the genome of S. cerevisiae strain 
YPH499, a laboratory strain congenic with Reference Strain S288C (Accession: 
JRIO00000000; ATCC Number 204679). 

genome fasta file: YPH499_Stanford_2014_JRIO00000000.fsa
nucleic acid coding sequence file: YPH499_JRIO00000000_cds.fsa
protein sequence file:  YPH499_JRIO00000000_pep.fsa
GFF file: YPH499_JRIO00000000.gff
snv variant call format file: YPH499.gatk.vcf.gz
indel variant call format file: YPH499.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:		69
Number of scaffolds:	749
Assembly size:		11721435
Longest scaffold:	462932
Scaffold N50:		125709
Number of ORFs:		5421

Reference for this S. cerevisiae YPH499 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.


Regarding the provenance of YPH499:

Sikorski RS, Hieter P. 1989. A system of shuttle vectors and yeast host strains 
designed for efficient manipulation of DNA in Saccharomyces cerevisiae. 
Genetics 122(1):19-27
PMID: 2659436

For more information about YPH499:

Kumar C, Sharma R, Bachhawat A. 2003. Investigations into the polymorphisms 
at the ECM38 locus of two widely used Saccharomyces cerevisiae S288C strains, 
YPH499 and BY4742. Yeast 20(10):857-63.
PMID: 12868055


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