Status
The genome and gene models of Candida albicans SC5314 were downloaded from NCBI on Oct 21, 2016. JGI tools were used to add functional annotations to the gene models. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into Mycocosm.
Assembly Method :: Bowtie v. 1.0
Sequencing Technology :: Illumina GAIIx
Summary statistics for the Candida albicans SC5314 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 14.28 |
| Sequencing read coverage depth | 700x |
| # of contigs | 38 |
| # of scaffolds | 8 |
| # of scaffolds >= 2Kbp | 8 |
| Scaffold N50 | 3 |
| Scaffold L50 (Mbp) | 2.23 |
| # of gaps | 30 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 3.19, 2.29, 2.23 |
| Gene Models | ExternalModels | |
| length (bp) of: | average | median |
| gene | 1496 | 1242 |
| transcript | 1485 | 1239 |
| exon | 1392 | 1161 |
| intron | 167 | 87 |
| description: | ||
| protein length (aa) | 495 | 413 |
| exons per gene | 1.07 | 1 |
| # of gene models | 6040 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S
The diploid genome sequence of Candida albicans.
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34. doi: 10.1073/pnas.0401648101
van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT
Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.
Genome Biol. 2007;8(4):R52. doi: 10.1186/gb-2007-8-4-r52
Muzzey D, Schwartz K, Weissman JS, Sherlock G
Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure.
Genome Biol. 2013;14(9):R97. doi: 10.1186/gb-2013-14-9-r97
Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S
The diploid genome sequence of Candida albicans.
Proc Natl Acad Sci U S A. 2004 May 11;101(19):7329-34. doi: 10.1073/pnas.0401648101
van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT
Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes.
Genome Biol. 2007;8(4):R52. doi: 10.1186/gb-2007-8-4-r52
Muzzey D, Schwartz K, Weissman JS, Sherlock G
Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure.
Genome Biol. 2013;14(9):R97. doi: 10.1186/gb-2013-14-9-r97
Funding
This project was not sequenced at the JGI.
