Status
[June 2021] The genome was sequenced with PacBio and Illumina, assembled with MECAT, polished with ARROW, patched using the v5.0 assembly Chrzof1, and annotated with the JGI Annotation Pipeline. The transcriptome consisted of 3 parts: 1) sequenced with Illumina, downloaded from NCBI 05/21/20, and assembled with Trinity at JGI; 2) sequenced with PacBio and clustered into consensi with IsoSeq by JGI; 3) sequenced with Oxford Nanopore and assembled with rnaspades by JGI. The mitochondrial and plastid genomes are available in the Download tab.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 58.78 |
| Sequencing read coverage depth | 1131.29x |
| # of contigs | 82 |
| # of scaffolds | 69 |
| # of scaffolds >= 2Kbp | 69 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 3.32 |
| # of gaps | 13 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 4.79, 4.31, 4.14 |
| RNAs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | Illumina+PacBio+ONT RNA reads | 40233273 | 34186673 | 85.0% |
| Other | JGI_Illumina_RNA_contigs | 103005 | 98509 | 95.6% |
| Other | JGI_ONT_RNA_contigs | 60706 | 47575 | 78.4% |
| Other | JGI_PacBio_RNA_consensi | 193375 | 190056 | 98.3% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 3446 | 2917 |
| transcript | 2264 | 1915 |
| exon | 422 | 226 |
| intron | 273 | 260 |
| description: | ||
| protein length (aa) | 420 | 333 |
| exons per gene | 5.36 | 5 |
| # of gene models | 16265 |
Collaborators
- Kris Niyogi at UCB
- Melissa Roth at UCB
- Sabeeha Merchant at UCB
- Sean Gallaher at UCLA
- Crysten Blaby at BNL
Links
- JGI EcoGroup Portal: Algae
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Chlorophyceae Sphaeropleales
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.
