A Human-Curated Annotation of the Candida albicans Genome

Abstract

Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.

Transcript Profiles of Candida albicans Cortical Actin Patch Mutants Reflect Their Cellular Defects: Contribution of the Hog1p and Mkc1p Signaling Pathways

“…Transcript profiles of the myo5⌬ vs. wild type (Wt), mkc1⌬ vs. Wt, and myo5 mkc1⌬ vs. myo5⌬ mutants, described in the latter part of this report, were produced with Cy3-and Cy5-labeled cDNA probes prepared from 40 g of total RNA and hybridized to a new generation of long oligonucleotide microarrays. These were spotted with 6,263 70-mer oligonucleotides that are specific for genes recently identified as part of a reannotation of the C. albicans genome (10). More details about these microarrays are available on our web page at http://www.bri.nrc.gc.ca/services/microarray/scanning_e .html.…”

Fungal Genomic Annotation

“…For the larger filamentous fungus, P. chrysosporium (Martinez et al 2004) no analysis of pseudogenes has been provided because of ambiguity in their discovery. This is also the case for N. crassa, Magnaporthe grisea (Dean et al 2005),and C. albicans (Braun et al 2005, Jones et al 2004) likely because of the ambiguity of stop codons in draft genomes.…”

“…Of the genomes from Table 1, 40 have been through the gene-modeling process, and several have at least preliminary functional annotations. While many biologists feel that manual annotation is best, and will volunteer to examine the staggering numbers of gene models that are predicted for their organism of interest, (e.g., the manual annotation of C. albicans) (Braun et al 2005) and the continued annotation by the Munich Information Center for Protein Sequences (MIPS) ), there appears to be a need for a reliable automated functional annotation. The N. crassa genome alone contains 4,140 (40%) completely unknown genes.…”

“…Even for yeasts the package was used as a first-pass tool combined with the use of GeneMark in the intragenic regions. A similar combination of tools was used in the annotation of C. albicans (Braun et al 2005) MIPS ) provides both structural and functional annotation for many of the genomes listed in Table 1. For all genomes housed at MIPS the automated functional annotation system Pedant ) is used.…”

“…Other fungal genomes have employed the community annotation model, such as the Aspergillus (www.cadre.man.ac.uk) and C. albicans (Braun et al 2005) communities.. The Aspergillus site uses the Ensembl (Hubbard et al 2005) system, while the C. albicans annotation project used the Artemis system (Berriman and Rutherford 2003).…”