Status
[November 2023] The Scenedesmus obliquus SAG 2326 v1.0 genome was sequenced with PacBio, assembled with HiFiAsm, polished using RACON, and annotated with the JGI Annotation Pipelines. The transcriptome consisted of 2 parts: 1) reads sequenced with Illumina and assembled with Trinity; 2) reads sequenced with PacBio and clustered into consensi with IsoSeq.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 104.25 |
| Sequencing read coverage depth | 149.05x |
| # of contigs | 19 |
| # of scaffolds | 19 |
| # of scaffolds >= 2Kbp | 19 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 6.09 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 11.41, 8.41, 8.06 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 491552234 | 488004641 | 99.3% |
| Other | JGI_IsoSeq_consensus | 40552 | 38993 | 96.2% |
| Other | JGI_RNA_contigs | 135796 | 117836 | 86.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 4215 | 3417 |
| transcript | 2046 | 1738 |
| exon | 314 | 169 |
| intron | 395 | 310 |
| description: | ||
| protein length (aa) | 440 | 350 |
| exons per gene | 6.52 | 5 |
| # of gene models | 17007 |
Collaborators
- James Umen at Danforth Center
- Juergen Polle at Brooklyn College of CUNY
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Chlorophyceae Sphaeropleales Scenedesmaceae
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.
