Status
[December 2022] The Chloromonas remiasii CCCryo 005-99 v1.0 genome was sequenced with PacBio, assembled with MECAT, and annotated with the JGI Annotation Pipeline.
Alternative haplotypes were identified in the main genome and removed from this assembly. Subsequently, another 5% of allelic variation in segmental duplication was detected during annotation. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 493.13 |
| Sequencing read coverage depth | 139.89x |
| # of contigs | 2434 |
| # of scaffolds | 2434 |
| # of scaffolds >= 2Kbp | 2434 |
| Scaffold N50 | 328 |
| Scaffold L50 (Mbp) | 0.42 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 2.08, 2.05, 2.02 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 215463 | 185096 | 85.9% |
| Ests | est.fasta | 621794683 | 591450147 | 95.1% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 5033 | 3438 |
| transcript | 1641 | 1395 |
| exon | 284 | 153 |
| intron | 713 | 643 |
| description: | ||
| protein length (aa) | 418 | 321 |
| exons per gene | 5.77 | 4 |
| # of gene models | 38828 |
Collaborators
- Sabeeha Merchant, University of California - Berkeley
- Matteo Pellegrini, University of California - Los Angeles
- Ian Blaby, DOE Joint Genome Institute
- Thomas Leya, CCCryo - Culture Collection of Cryophilic Algae, Fraunhofer IZI-BB, Potsdam, Germany
