Status
[June 2022] The Scenedesmus sp. WC-1 v1.0 genome was sequenced with PacBio, assembled with HiFiAsm, polished using RACON, and annotated with the JGI Annotation Pipeline. 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) | 102.32 |
| Sequencing read coverage depth | 214.99x |
| # of contigs | 26 |
| # of scaffolds | 26 |
| # of scaffolds >= 2Kbp | 26 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 5.63 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 11.04, 8.00, 7.95 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 1185490 | 1116944 | 94.2% |
| Other | JGI_IsoSeq_consensus | 104519 | 99977 | 95.7% |
| Other | JGI_RNA_contigs | 129841 | 107986 | 83.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 4231 | 3445 |
| transcript | 2103 | 1812 |
| exon | 328 | 168 |
| intron | 396 | 311 |
| description: | ||
| protein length (aa) | 431 | 338 |
| exons per gene | 6.40 | 5 |
| # of gene models | 17012 |
Collaborators
- Robin Gerlach at Montana State University, MT, USA
- Huyen Bui at Montana State University, MT, USA
- Brent Peyton at Montana State University, MT, USA
- Matthew Fields at Montana State University, MT, USA
- Sridhar Viamajala at University of Toledo, OH, USA
Links
- JGI Algae EcoGroup Portal
- 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.
