Status
[December 2023] The Scenedesmus dimorphus UTEX 1237 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 cluster into consensi with IsoSeq.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 102.57 |
| Sequencing read coverage depth | 286.05x |
| # of contigs | 30 |
| # of scaffolds | 30 |
| # of scaffolds >= 2Kbp | 30 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 5.95 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 8.19, 7.49, 6.84 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 263923972 | 262148441 | 99.3% |
| Other | JGI_IsoSeq_consensus | 82697 | 80455 | 97.3% |
| Other | JGI_RNA_contigs | 127671 | 113349 | 88.8% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 4252 | 3448 |
| transcript | 2060 | 1761 |
| exon | 316 | 169 |
| intron | 399 | 313 |
| description: | ||
| protein length (aa) | 445 | 355 |
| exons per gene | 6.53 | 5 |
| # of gene models | 17373 |
Collaborators
- Juergen Polle at Brooklyn College of CUNY
- James Umen at Danforth Center
- Shawn Starkenburg at LANL
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Chlorophyceae Sphaeropleales Scenedesmaceae Scenedesmus
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.
