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SGD Help: Synteny Viewer |
Contents
NOTE: Cliften et al have independently sequenced and analyzed the genomes of S. mikatae, S. kudriavzevii, S. bayanus, S. castellii, and S. kluyveri at Washington University in St. Louis. Because some of these species are more distant from cerevisiae (see the phylogenetic tree), they are not displayed on this page, but are instead available via the Fungal Alignment link on the SGD locus pages, the search page, or the BLAST server at the Washington University Genome Sequencing Center.
ORFs were predicted for the entire genomes of S. paradoxus, S. mikatae and S. bayanus. These query ORFs were then BLASTed against the entire set of annotated S. cerevisiae ORFs. Based on amino acid identity and conserved synteny, relationships between S. cerevisiae ORFs and the predicted ORFs were divided into four different categories:
1. Orthologs: In this case a one-to-one relationship could be established between the query ORF and a S. cerevisiae gene.
2. Paralogs: In this case, more than one predicted ORF from the query species is homologous to a S. cerevisiae gene. Of these homologous query ORFs, only one is in the same relative position on the chromosome as the S. cerevisiae gene and is thus designated as the ortholog (see above) based on synteny. All the other homologous query ORFs (those that are NOT in the same relative chromosomal position) are paralogs. Note that Kellis et. al. designated genes as paralogs only in cases when an ortholog could be distinguished. If, based on synteny, an ortholog could not be distinguished amongst a group of homologous genes, then all the genes are designated as "Unresolved" (see below).
3. Unresolved: In this case, more than one predicted ORF from the query species is homologous to one or more S. cerevisiae genes. None (or more than one, in the case of tandem duplications) of these homologous query ORFs are in the same relative position on the chromosome as the S. cerevisiae gene. It is unclear which query ORF is the single, genuine ortholog of the S. cerevisiae gene. Note that if an ORF is split between two contigs (located at the end of one contig and the beginning of the other), it will be classified as a paralog - computationally, it appears to be two distict ORFs both of which are syntenous and homologous to a single S. cerevisiae gene.
4. No Similarity: Some query ORFs had no significant sequence similarity with any S. cerevisiae ORFs (and vice versa). This may have occurred if the sequence was unique to a Saccharomyces species (truly had no homolog) or if the sequence was excluded from the analysis for technical reasons. Note that this analysis considered only predicted orfs that were at least 50 amino acids long and that did not contain an intron within the first 150 nucleotides of genomic DNA. To see a list of S. cerevisiae genes that were excluded from the analysis for this reason are available, click here.
Transposons were predicted for the entire genomes of S. paradoxus, S. mikatae
and S. bayanus by BLASTing the entire set of
S. cerevisiae annotated Ty elements against the other
genomes. These positions were simply labeled on the chromosomes. There
was no attempt to determine orthology. There is
currently no distinction made between full length transposons,
transposon ORFs, or LTRs; all are labeled as Transposon elements.
tRNAs were predicted for the entire genomes of S. paradoxus, S. mikatae
and S. bayanus. These positions were simply labeled on the
chromosomes. There was no attempt to determine orthology.
| Figure 1: ORF conservation in Saccharomyces species | ||
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The dark green bar at the top of the display corresponds to the
Saccharomyces cerevisiae chromosome. The chromosome number is shown in
blue on the right arm of the chromosome. The red box on this bar is a
reference point; it shows you what part of the chromosome is displayed
on a larger scale below. The numbers above the bar are chromosomal
coordinates.
Below the dark green chromosome is a zoomed in view of a portion of
the chromosome. The highlited text just above this, >> zoom in << and << zoom out >>, are buttons that allow you to see
more or fewer details, respectively, for the region.
The first gray section displays Saccharomyces
cerevisiae chromosomal features. The genes are represented with arrows; the end with the
arrow head is the 3' end of the gene. The different colors of the
arrows represent different types of genes (ORFs, tRNAs, and
transposons, see the key below).
The subsequent sections display the predicted genes of
Saccharomyces paradoxus, Saccharomyces mikatae, and
Saccharomyces bayanus. For orthologs,
the color of the arrows indicate the extent of conservation between
this gene and the corresponding S. cerevisiae gene. Below the
orthologs for each species are solid bars that correspond to the
contig that contains the genes (eg. c134) or the scaffold on which
multiple contigs are assembled (eg. s5). Paralogs (tan), ORFs of unresolved orthology (grey) and ORFs with no similarity in S. cerevisiae(black) are
displayed underneath the contig. Paralogous ORFs of unresolved
orthology (grey) are only displayed when aligned with the
S. cerevisiae gene of closest sequence similarity.
Colors and Symbols
| Figure 2: Key to budding yeasts map |
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You can also jump to any region of any other chromosome by entering a gene name in the Enter a locus/ORF name search. This will center the view around the gene that you enter.
Each chromosomal feature on the map display is linked to more information.
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