S. cerevisiae strain JK9-3d genome sequence.

11/23/2015

This directory contains 4 files describing the genome of S. cerevisiae strain
JK9-3d, a commonly used laboratory strain (Accession: JRIZ00000000; ATCC 
Number: MYA-555).

genome fasta file: JK9-3d_SGD_2015_JRIZ00000000.fsa
nucleic acid coding sequence file: JK9-3d_JRIZ00000000_SGD_cds.fsa
protein sequence file: JK9-3d_JRIZ00000000_SGD_pep.fsa
GFF file: JK9-3d_JRIZ00000000_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:          154
Number of scaffolds:    197
Assembly size:          11669230
Longest scaffold:       320854
Scaffold N50:           103867
Number of ORFs:         5358

Reference for this S. cerevisiae JK9-3d 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 JK9-3d:

Heitman J, Movva NR, Hall MN. 1991. Targets for cell cycle arrest by the 
immunosuppressant rapamycin in yeast. Science 253(5022):905-9.
PMID: 1715094


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