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SGD Help: Synteny Viewer

This resource allows users to see the degree of synteny shared among chromosomes in closely related Saccharomyces species. Displayed are S. cerevisiae ORFs, tRNAs, and transpoons aligned with those predicted for Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces bayanus sequences, published in Kellis, M. et. al. (2003) Nature 423(6937):241-54.

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, they are not displayed on this page, but are instead available via the Fungal Alignment link on the SGD locus pages, the Fungal Sequence Alignment search page, or the BLAST server at the Washington University Genome Sequencing Center.

Contents

  1. Analysis
    1. ORFs
    2. Transposons
    3. tRNAs
  2. Results
  3. Display Help
    1. Colors and Symbols
    2. Contig and ORF Display
    3. Navigation
    4. Hyperlinked Display Features

 

Analysis

For a full description of the methods and analysis, please see Kellis, M. et. al. (2003) Nature 423(6937):241-54.

ORFs

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:

ORF categories:

Orthologs In this case a one-to-one relationship could be established between the query ORF and a S. cerevisiae gene.
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).
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.
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

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

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.

Results

A complete description of the results appears in Kellis, M. et. al. (2003) Nature 423(6937):241-54.

As an indication of the global conservation rates between species, the following figures display the degree of amino acid identity between S. cerevisiae ORFs and predicted ORFs for S. paradoxus, S. mikatae, and S. bayanus.

 

Display Help

The display is a graphical view of conserved genes between Saccharomyces cerevisiae, Saccharomyces paradoxus, Saccharomyces mikatae, and Saccharomyces bayanus.

Colors and Symbols

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.

Contig and ORF Display

Contigs are displayed to show aligned genes of sequence similarity. If a single contig contains genes that could be aligned with different chromosomes, that contig is displayed in all possible chromosomal alignments. However, only the ORFs that align in the selected chromosomal coordinates are displayed.

Navigation

To see sequences to the left or to the right of the current chromosome view, you may click on the left or right of the dark green chromosome at the top of the page. Alternatively, there are buttons below the display that will accomplish the same thing. They are labeled "Retrieve map left" and "Retrieve map right".

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.

Hyperlinked Display Features

Each chromosomal feature on the map display is linked to more information.

S. cerevisiae ORFs linked to the correcsponding SGD locus pages
Orthologous ORFs from other species linked to a "Fungal Alignment" page for those ORFs. The "Fungal Alignment" page displays a Clustal W multiple sequence alignment of the protein sequences from all four species (when available), and lists the protein sequences for all ORFs included in the alignment. This page also provides links to a Clustal W multiple alignments of the ORF DNA sequence and of the ORF DNA + flanking intergenic sequence
Parologous ORFs (grey or tan) fromĀ  other species linked to a "Fungal Group Information" page which lists details about the paralogous ORFs including percent amino acid identity and similarity with corresponding S. cerevisiae ORF, etc. The "Fungal Group Information" page also provides links to the sequences for these ORFs
Transposon elements (purple) linked to corresponding sequences
tRNAs (green) linked to corresponding sequences
ORFs with no similarity in S. cerevisiae (black) linked to corresponding sequences
Contigs linked to the corresponding contig sequences

 

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