Status
Assembly v1 (19 May 2010) is a draft assembly of Sanger gDNA
reads. 302 scaffolds and 94.7 Mbp were assembled using Arachne.
| Nuclear Genome Assembly: | v1.0 |
| Scaffold count: | 302 |
| All Contig count: | 3736 |
| Scaffold sequence bases total: | 94.7 Mbp |
| Scaffolded (Large) Contig sequence bases total: | 91.4 Mbp |
| Estimated % sequence bases in gaps: | 3.5% |
| Scaffold N50 / L50: | 36 / 820.0 kbp |
| Contig N50 / L50: | 423 / 59.5 kbp |
| Number of scaffolds > 50.0 Kb: | 143 |
| % in scaffolds > 50.0 Kb: | 98.9% |
| Percent GC: | 45% |
| % ESTs that align with assembly: | 86.1% |
Annotation v1 (19 May 2010) of the v1.0 assembly was
produced by the JGI Annotation Pipeline, using a variety of
cDNA-based, protein-based, and ab initio gene predictors.
After filtering for EST and protein homology support, a total of
21708 genes were structurally and functionally annotated.
| Nuclear Genome Annotation: | v1.0 |
| # gene models: | 21708 |
| Gene density: | 229 genes per Mbp scaffold |
| Avg.gene length: | 2834 nt |
| Avg. protein length: | 443 aa |
| Avg. exon frequency: | 8.9 exons per gene |
| % genes with intron: | 86 % |
| % complete gene models (with start and stop codons): | 92% |
| % genes with NR support: | 71% |
| % genes with Pfam domains: | 47% |
| % genes with transmembrane domain: | 21% |
| % genes in multigene family: | 57% |
| % genes with EST support: | 36% |
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.
