Status
[December 2023] The Pavlova sp. CC15 RCC6257 v1.0 genome assembly was sequenced with PacBio, assembled with HiFiAsm, and annotated with the JGI Annotation Pipeline. The mitochondrial and chloroplast assemblies were assembled separately and are available in the downloads section. This annotation release includes JGI transcriptomics data, both Iso-Seq CCS and Illumina RNA-seq libraries assembled by Trinity.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 77.86 |
| Sequencing read coverage depth | 61.22x |
| # of contigs | 41 |
| # of scaffolds | 41 |
| # of scaffolds >= 2Kbp | 41 |
| Scaffold N50 | 12 |
| Scaffold L50 (Mbp) | 2.54 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 5.08, 4.72, 3.91 |
Note: low Trinity mapping is attributed to 9.24% rRNA content and
bacterial contamination in the RNA-seq libraries.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 283253193 | 275351760 | 97.2% |
| Other | IsoSeq_hq_reads | 624197 | 601295 | 96.3% |
| Other | RNAseq_contigs | 116578 | 64335 | 55.2% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1844 | 1462 |
| transcript | 1542 | 1297 |
| exon | 821 | 635 |
| intron | 346 | 202 |
| description: | ||
| protein length (aa) | 415 | 329 |
| exons per gene | 1.88 | 1 |
| # of gene models | 24303 |
Collaborators
- Betsy Read, California State University, San Marcos
- Richard Dorrell, Institut de Biologie, Sorbonne Université (siège), Paris, France
Links
- JGI EcoGroup Portals: Algae Phytoplankton
- JGI PhyloGroup Portals: Haptophyta Pavlovales Pavlovaceae
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.
