Status
[March 2017] Nannochloropsis oceanica was sequenced by the laboratory of Christoph Benning at Michigan State University. The genome and gene models of Nannochloropsis oceanica were downloaded from Nannochloropsis oceanica CCMP1779 at Michigan State University on January 15, 2017. JGI tools were used to add functional annotations to the gene models. Please note that this copy of the genome is not maintained by MSU and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into JGI.
Summary statistics for the Nannochloropsis oceanica
CCMP1779 v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 28.74 |
| Sequencing read coverage depth | |
| # of contigs | 3731 |
| # of scaffolds | 3731 |
| # of scaffolds >= 2Kbp | 2120 |
| Scaffold N50 | 269 |
| Scaffold L50 (Mbp) | 0.02 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.30, 0.19, 0.18 |
| Gene Models | ExternalModels | |
| length (bp) of: | average | median |
| gene | 1546 | 1287 |
| transcript | 1143 | 882 |
| exon | 417 | 184 |
| intron | 234 | 175 |
| description: | ||
| protein length (aa) | 346 | 259 |
| exons per gene | 2.74 | 2 |
| # of gene models | 12012 |
Collaborators
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.
PLoS Genet. 2012;8(11):e1003064. doi: 10.1371/journal.pgen.1003064
Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.
PLoS Genet. 2012;8(11):e1003064. doi: 10.1371/journal.pgen.1003064
Funding
This project was not sequenced at the JGI.
