Status
[November 2022] The Proteomonas sulcata CCMP 1175 v1.1 genome assembly was sequenced with PacBio, assembled with HiFiAsm, and annotated with the JGI Annotation Pipeline. This annotation release includes JGI transcriptomics data, both Iso-Seq CCS and Illumina RNAseq libraries assembled by Trinity.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 270.34 |
| Sequencing read coverage depth | 123.08x |
| # of contigs | 113 |
| # of scaffolds | 113 |
| # of scaffolds >= 2Kbp | 113 |
| Scaffold N50 | 41 |
| Scaffold L50 (Mbp) | 2.86 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 4.47, 4.47, 4.19 |
Please Note: The cultures that were used for RNA extractions are
non-axenic P. sulcata cultures grown in a batch culture.
50-60% alignment to reference is anticipated. Unmapped RNA contigs
have BLAST hits to bacteria (E. coli and
Pseudomonas genus).
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 194690608 | 116131439 | 59.6% |
| Other | Polished_IsoSeq | 57464 | 33339 | 58.0% |
| Other | RNAseq_contigs | 278228 | 160770 | 57.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 3858 | 2606 |
| transcript | 1857 | 1484 |
| exon | 194 | 85 |
| intron | 236 | 131 |
| description: | ||
| protein length (aa) | 476 | 352 |
| exons per gene | 9.55 | 7 |
| # of gene models | 34130 |
Collaborators
- Jeffry Dudycha - University of South Carolina, USA
- Matthew Greenwold - University of Texas at Tyler, USA
- Tammi Richardson - University of South Carolina, USA
- John Archibald - Dalhousie University, Nova Scotia, Canada
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.
