Status
[September 2019] The Phaeocystis antarctica CCMP1374 v2.0 genome was assembled using MECAT using PacBio reads and the resulting sequence was polished using ARROW. This v2.2 annotation was originally produced by the JGI Plant Program and has been imported to PhycoCosm for use in algal comparative genomic analyses. The mitochondrial and chloroplast genomes were assembled separately and are available in the downloads section.
Summary statistics for the Phaeocystis antarctica v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 198.94 |
| Sequencing read coverage depth | 42.03x |
| # of contigs | 375 |
| # of scaffolds | 375 |
| # of scaffolds >= 2Kbp | 375 |
| Scaffold N50 | 42 |
| Scaffold L50 (Mbp) | 1.56 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 5.54, 4.72, 4.13 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| RNAseq reads | RNAseq | 527293110 | 204786542 | 38.8% |
| pertran | PASA alignments | 126953 | 104656 | 82.4% |
| PASA assemblies | 104656 | 104656 | 100% |
| Gene Models | PhytozomeGeneModels | |
| length (bp) of: | average | median |
| gene | 1904 | 1493 |
| transcript | 1308 | 1133 |
| exon | 318 | 150 |
| intron | 194 | 146 |
| description: | ||
| protein length (aa) | 331 | 263 |
| exons per gene | 4.11 | 2 |
| # of gene models | 41088 |
Collaborators
- Kevin Arrigo, Stanford University
- Andrew Allen, J. Craig Venter Institute
Links
- JGI PhyloGroup Portals: Phycocosm Haptophyta
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.
