S. cerevisiae strain Sigma1278b-10560-6B genome sequence.

11/23/2015

This directory contains 4 files describing the genome of S. cerevisiae strain
Sigma1278b-10560-6B, a commonly used Sigma1278b-derivative laboratory strain 
(Accession: JRIQ00000000). 

genome fasta file: Sigma1278b-10560-6B_SGD_2015_JRIQ00000000.fsa
nucleic acid coding sequence file: Sigma1278b-10560-6B_JRIQ00000000_SGD_cds.fsa
protein sequence file: Sigma1278b-10560-6B_JRIQ00000000_SGD_pep.fsa
GFF file: Sigma1278b-10560-6B_JRIQ00000000_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:          191
Number of scaffolds:    206
Assembly size:          11642710
Longest scaffold:       458709
Scaffold N50:           109268
Number of ORFs:         5343

Reference for this S. cerevisiae Sigma1278b-10560-6B 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

Regarding the provenance of Sigma1278b-10560-6B:

Meyrial V, Laize V, Gobin R, Ripoche P, Hohmann S, et al. 2001. Existence of a 
tightly regulated water channel in Saccharomyces cerevisiae. 
Eur J Biochem 268(2):334-43.
PMID: 11168368

For more information about Sigma1278b and 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