Status
The genome of Cryptococcus neoformans var neoformans JEC21 has not been sequenced by the JGI, but by TIGR. The genome sequence and gene predictions were obtained from NCBI GenBank (RefSeq: PRJNA10698). Note that the gene names of alternative splice forms on the same locus have been given suffixes in order to distinguish them (e.g. *.t01, *.t02, etc). JGI Eukaryotic tools were set up to assist with manual curation and comparative analysis of fungal genomes.
Summary statistics for the Cryptococcus neoformans JEC21
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 19.05 |
| Sequencing read coverage depth | 1 |
| # of contigs | 37 |
| # of scaffolds | 14 |
| # of scaffolds >= 2Kbp | 14 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 1.44 |
| # of gaps | 23 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.30, 2.11, 1.78 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | NCBI_ESTs * | 46826 | 46392 | 99.1% |
| Gene Models | ExternalModels | |
| length (bp) of: | average | median |
| gene | 2175 | 1943 |
| transcript | 1798 | 1599 |
| exon | 278 | 170 |
| intron | 71 | 58 |
| description: | ||
| protein length (aa) | 536 | 457 |
| exons per gene | 6.47 | 6 |
| # of gene models | 6475 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
Science. 2005 Feb 25;307(5713):1321-4. doi: 10.1126/science.1103773
Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
Science. 2005 Feb 25;307(5713):1321-4. doi: 10.1126/science.1103773
Links
- Source of these data on GenBank
- JGI portal of Cryptococcus neoformans var grubii H99 (serotype A)
Funding
This project was not sequenced at the JGI.
