Status
[April 2024] The genome and transcriptome sequences of Nereocystis luetkeana NB12FB3 were not determined by the Joint Genome Institute (JGI). The genome was sequenced with PacBio and assembled as part of the California Conservation Genomics Project (CCGP). RNAseq from the from the Alberto Lab at the University of Wisconsin-Milwaukee and was assembled with Trinity at the JGI. Subsequently, the JGI Annotation Pipeline was used to generate structural and functional annotations.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 449.79 |
| Sequencing read coverage depth | 30x |
| # of contigs | 2120 |
| # of scaffolds | 1561 |
| # of scaffolds >= 2Kbp | 1561 |
| Scaffold N50 | 17 |
| Scaffold L50 (Mbp) | 10.97 |
| # of gaps | 559 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 21.87, 21.15, 17.25 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 214129551 | 191602823 | 89.5% |
| Other | UWM_RNA_contigs | 671611 | 351748 | 52.4% |
- Please note: Using BLAST, unmapped RNA contigs were found to hit Homo sapiens and other mammals, suggesting that the RNA library was contaminated.
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 8312 | 5876 |
| transcript | 1569 | 1196 |
| exon | 266 | 150 |
| intron | 1382 | 949 |
| description: | ||
| protein length (aa) | 381 | 271 |
| exons per gene | 5.89 | 4 |
| # of gene models | 22952 |
Collaborators
- Cicero Alves-Lima at Center of Marine Sciences (CCMAR), University of Algarve, Portugal
- Filipe Alberto at University of Wisconsin Milwaukee, WI, USA
- Peter Raimondi at University of California Santa Cruz, CA, USA
- Sergey Nuzhdin at University of Southern California, CA, USA
- Merly Escalona at University of California Santa Cruz, CA, USA
Links
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Phaeophyta
- JGI EcoGroup Portals: Algae Seaweeds
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.
