Status
Assembly v1 (October 2010) is a draft assembly of mainly Sanger gDNA reads supplemented by 454 gDNA reads. A total of 670 scaffolds and 87.2 Mbp were assembled using Arachne.
Summary statistics for the Guillardia theta v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 87.16 |
| Sequencing read coverage depth | 23.66x |
| # of contigs | 9586 |
| # of scaffolds | 670 |
| # of scaffolds >= 2Kbp | 638 |
| Scaffold N50 | 52 |
| Scaffold L50 (Mbp) | 0.55 |
| # of gaps | 4458 |
| % of scaffold length in gaps | 4.2% |
| Three largest Scaffolds (Mbp) | 1.42, 1.30, 1.29 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | JGI ESTs | 45645 | 40729 | 89.2% |
| Ests | NCBI ESTs | 15173 | 11287 | 74.4% |
| Other | EST cluster consensi | 14142 | 11932 | 84.4% |
| Gene Models | FilteredModels4 | |
| length (bp) of: | average | median |
| gene | 1868 | 1353 |
| transcript | 1283 | 927 |
| exon | 199 | 85 |
| intron | 110 | 55 |
| description: | ||
| protein length (aa) | 410 | 293 |
| exons per gene | 6.43 | 4 |
| # of gene models | 24840 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Kořený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681
Curtis BA, Tanifuji G, Burki F, Gruber A, Irimia M, Maruyama S, Arias MC, Ball SG, Gile GH, Hirakawa Y, Hopkins JF, Kuo A, Rensing SA, Schmutz J, Symeonidi A, Elias M, Eveleigh RJ, Herman EK, Klute MJ, Nakayama T, Oborník M, Reyes-Prieto A, Armbrust EV, Aves SJ, Beiko RG, Coutinho P, Dacks JB, Durnford DG, Fast NM, Green BR, Grisdale CJ, Hempel F, Henrissat B, Höppner MP, Ishida K, Kim E, Kořený L, Kroth PG, Liu Y, Malik SB, Maier UG, McRose D, Mock T, Neilson JA, Onodera NT, Poole AM, Pritham EJ, Richards TA, Rocap G, Roy SW, Sarai C, Schaack S, Shirato S, Slamovits CH, Spencer DF, Suzuki S, Worden AZ, Zauner S, Barry K, Bell C, Bharti AK, Crow JA, Grimwood J, Kramer R, Lindquist E, Lucas S, Salamov A, McFadden GI, Lane CE, Keeling PJ, Gray MW, Grigoriev IV, Archibald JM
Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.
Nature. 2012 Dec 6;492(7427):59-65. doi: 10.1038/nature11681
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
