Yeast Gene Order Browser

YGOB Versions & Associated Papers
Version 7 (Aug2012) Latest DATA
Added in August 2012 and including three new genomes (Saccharomyces mikatae, S. kudriavzevii and S. bayanus var. uvarum) from Scannell et al. G3 (2011) and the finalised versions of the three draft genomes in Version 6. We've updated the S. cerevisiae data in YGOB to the latest release (R64) from SGD. As a visual aid we have also added bars to the top of gene boxes to inidicate the relative length of homologs.

We expect this to be a 'benchmark' version of the browser, suitable for many types of analyses and likely to remain as the current YGOB version for the next few years. Researchers may find the associated datasets listed at the right of use to them.
  1. Homology
  2. Gene Order & Annotation
  3. Genome Sequences
  4. Protein & Nucleotide Sequences
  5. Genus Specific
  6. Species Phylogeny
  7. GenBank Annotations
  8. S. cerevisiae Ohnologs
New Server & Domain Name
With this version we have also migrated YGOB to a new faster and more powerful server, which renders all aspects of YGOB much quicker than before and facilitates heavy traffic and large numbers of simultaneous users. The browser can now be found at http://ygob.ucd.ie
Version 6 (Dec2011) DATA
Added in December 2011 and including six new genomes sequenced by our laboratory: Tetrapisispora phaffii, Tetrapisispora blattae*, Naumovozyma dairenensis, Kazachstania africana*, Kazachstania naganishii*, and Torulaspora delbrueckii. We also added our complete sequence of Naumovozyma castellii (which was previously draft sequenced by Cliften et al. and called S. castellii), and the genome Eremothecium cymbalariae (Wendland and Walther G3 2011). There are now 18 genomes in YGOB as well as the ancestral gene order. This version has some further small changes to the visual interface to improve clarity with so many genomes. To save vertical space, some genomes are not displayed by default and must be turned on using the menus at the bottom of the screen.

* These 3 genomes are draft annotations. The temporary annotations are labelled with the letter X instead of the correct species initial (XAFR, XNAG, XBLA).
  1. Homology
  2. Gene Order & Annotation
  3. Genome Sequences
  4. Protein & Nucleotide Sequences
  5. GenBank Annotations
Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents
 Gordon JL, Armisén D, Proux-Wéra E, ÓhÉigeartaigh SS, Byrne KP and Wolfe KH
PNAS. 2011 Dec 13;108(50):20024-9.
Supplemental: Supplemental Information Information
Version 5 (Jan2011) DATA
Added in January 2011 this version features hundreds of newly annotated genes (discovered using software described in the paper below) in a near-exhaustive search for previously unannotated features.
  1. Homology
  2. Gene Order & Annotation
  3. Genome Sequences
  4. Protein & Nucleotide Sequences
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments
 ÓhÉigeartaigh SS, Armisén D, Byrne KP and Wolfe KH
BMC Genomics. 2011 July;12(1):377.
Supplemental: Supplemental File 1 File 1
Version 4 (May2010) DATA
Added in May 2010 this version for the first time includes centromeres (represented on screen as black boxes), RNA features (white boxes) and Ty proteins (dark grey boxes). We have also implemented a more streamlined look to the visual interface.
  1. Homology
  2. Gene Order & Annotation
  3. Genome Sequences
  4. Protein & Nucleotide Sequences
Mechanisms of chromosome number evolution in yeast
 Gordon JL, Byrne KP and Wolfe KH
PLoS Genetics. 2011 July;7(7):e1002190.
Supplemental: Supplemental Information Dataset 1 Supplemental Information Figure 1 Supplemental Information Figure 2 Supplemental Information Figure 3 Supplemental Information Table 1
Supplemental Information Table 2 Supplemental Information Table 3 Supplemental Information Table 4 Supplemental Information Table 5 Supplemental Information Table 6
Version 3 (Apr2009) DATA
Added in April 2009 and featuring the published ancestral yeast gene order, two new genomes (Z. rouxii & K. thermotolerans), improved annotations of two others (S. kluyveri & S. bayanus) and updates to all other genomes. This version for the first time is completely nucleotide and co-ordinate based, offering access to intergenic sequences.
  1. Homology
  2. Gene Order & Annotation
  3. Genome Sequences
  4. Protein & Nucleotide Sequences
Additions, losses and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome
 Gordon JL, Byrne KP and Wolfe KH
PLoS Genetics. 2009 May;5(5):e1000483.
Supplemental: Supplemental Figure 1 Figure 1 Supplemental Table 1 Table 1 Supplemental Table 2 Table 2
Version 2 (Jun2007) DATA
Added in June 2007 and including three new genomes: Kluyveromyces polysporus, Saccharomyces bayanus, and a draft ancestral yeast gene order.
  1. Homology
  2. Gene Order
  3. Protein Sequences
  4. Kluyveromyces polysporus GenBank Annotation
  5. GenBank flatfile
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
 Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M and Wolfe KH
PNAS. 2007 May 15;104(20):8397-402.
Supplemental: Supplemental Information Information
Version 1 (Sep2005) DATA
The original version of YGOB used in our 2005 Genome Research paper and 2006 Nature paper is also available. It contains seven genomes.
  1. Homology
  2. Gene Order
  3. Protein Sequences
  4. Synteny Scores
  5. S. castellii Re-annotation
  6. Locus Classes
Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts
 Scannell DR*, Byrne KP*, Gordon JL, Wong S and Wolfe KH
Nature. 2006 Mar 16;440(7082):341-5.
Supplemental: Supplemental Table 1 Table 1 Supplemental Note 2 Note 2 Supplemental Note 3 Note 3 Supplemental Note 4 Note 4 Supplemental Note 5 Note 5
© Dr Kevin Byrne - Wolfe Laboratory

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