Abstract:Please note, regarding the issue of orthology and shared function, we use the standard evolutionary definition of orthology: genes descended from a common ancestral gene sequence. This definition does not require that the genes are functionally equivalent after the speciation event, although it will often be the case.
We provide all pairwise ortholog mappings for the following genomes:
- C. albicans SC5314 Assembly 21 (haploid protein complement), from CGD
- C. glabrata CBS138, from CGD
- C. parapsilosis CDC317, from CGD
- S. cerevisiae, from the Saccharomyces Genome Database (SGD)
- S. pombe, from PomBase
- A. nidulans, from AspGD
- N. crassa , from the Broad Institute
The ortholog mappings among
Candida strains, and between
Candida strains and
S. cerevisiae, are derived from the curated syntenic groupings at the
Candida Gene Order Browser (CGOB). Please visit CGOB, or see
Fitzpatrick et al., 2010 for details.
The ortholog mappings between
Candida strains and
S. pombe,
A. nidulans, and
N. crassa are made by pairwise comparisons using the
InParanoid software, developed at the Karolinska Institutet.
C. elegans proteins are used as outgroup for the
S. pombe mappings, and
S. pombe proteins are used as the outgroup for the
A. nidulans and
N. crassa mappings. Stringent cutoffs are set: BLOSUM80 (instead of the default BLOSUM62), and an InParanoid score of 100% (parameters: -F \"m S\" -M BLOSUM80). Note that the InParanoid ortholog pairings are automatically generated, with no curator intervention. Thus, there will occasionally be pairings that may not occur using different methods or with a different scoring matrix.
Comparisons are updated approximately four times a year. Files used in and produced by each set of analyses are available for
download from CGD. Please note that orthologs are not computed or displayed for ORFs that were present in a previous version of the reference annotation, but which are designated as "deleted" in the current set.
For proteins that do not have an ortholog (in a given species) that meets the strict criteria we use to define orthology, we use BLASTP (with parameters -F \"m S\" -M BLOSUM80), with an expectation value (E) of 1e-5, to identify a best hit in the protein complement.