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 % |
| 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 |
| 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% |
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
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803
Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803
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.
