Status
v1.0 (November 2008): This Fragilariopsis cylindrus CCMP 1102 genome sequence assembly v1.0 was built with Arachne assembler from whole genome shotgun and paired end sequencing reads. Nuclear genome sequence annotation from this draft assembly is from the JGI Genome Annotation Pipeline and custom analyses .
Summary statistics for the Fragilariopsis_cylindrus CCMP 1102 v1.0 release:
| Nuclear Genome Assembly | v1.0 |
| Nuclear genome size(Mbp) | 80,5 |
| Sequencing read coverage depth | 7.25x |
| # of contigs | 4602 |
| # of scaffolds | 271 |
| # of nuclear scaffolds >50 Kbp | 118 |
| Nuclear scaffold N/L50 | 16/1.3 MB |
| Configs N/L50 | 164/78.2 KB |
| % genome in scaffolds >50 Kbp | 98.4 % |
| % genome in gaps | 5.4 % |
| % genome in repeats | 4.3 % |
| Gene Models | v1.01 |
| length (bp) of: | average |
| gene | 1572.35 |
| transcript | 1292.94 |
| exon | 615.29 |
| intron | 255.7 |
| description: | |
| protein length(aa) | 408.64 |
| exons per gene | 2.1 |
| # of gene models | 27137 |
| % gene models with : | |
| nr homology support EST support PFAM domains |
67% 30% 42% |
1 FilteredModels2 gene model set
| ESTs | Data set | # sequences | # mapped to genome | % mapped to genome | Notes |
| EST clusters | Fracy1_EstClusters.fasta | 9,122 | 7,955 | 87% | Consensus sequences, one per cluster, for Fracy1_Ests |
| ESTs | Fracy1_Ests.fasta | 21,526 | 19,924 | 93% | Pooled ESTs for T. terrestris, sequenced at JGI plus ~3,000 ESTs downloaded from GenBank |
Collaborators:
- Thomas Mock, Univ. of Washington
- Micaela Parker, Univ. of Washington
- E. Virginia Armbrust, Univ. of Washington
- Klaus Valentin, Alfred-Wegener Inst. for Polar and Marine Research
- Chris Bowler, Ecole Normale Superieure
Links:
Funding
This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.
