S. cerevisiae strain Y55 genome sequence.

11/23/2015

This directory contains 4 files describing the genome of S. cerevisiae strain 
Y55, a commonly-used laboratory strain (Accession: JRIF00000000; ATCC Number: 52530).

genome fasta file: Y55_SGD_2015_JRIF00000000.fsa
nucleic acid coding sequence file: Y55_JRIF00000000_SGD_cds.fsa
protein sequence file:  Y55_JRIF00000000_SGD_pep.fsa
GFF file: Y55_JRIF00000000_SGD.gff

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
initially assigned via the AGAPE pipeline, which generated 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. The genomes were further
curated manually by SGD biocurators.

Assembly statistics
================================
Fold coverage:          112
Number of scaffolds:    198
Assembly size:          11700636
Longest scaffold:       406493
Scaffold N50:           107844
Number of ORFs:         5332

Reference for this S. cerevisiae Y55 genome sequence, assembly and annotation:

Song G., et al., 2015. AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome 
Analysis of Saccharomyces cerevisiae.  PLoS ONE, 10(3):e0120671.
PMID: 25781462

For more information about Y55:

Borts RH, et al. 1984. Physical monitoring of meiotic recombination in 
Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol 49:67-76 
PMID: 6397320


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