Status
The genome sequence and gene models of Raphidocelis subcapitata NIES-35 were not determined by the JGI, but were downloaded from NCBI, on November 14, 2019. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 295 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by NCBI and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.
Genome Assembly | |
Genome Assembly size (Mbp) | 51.16 |
Sequencing read coverage depth | 80x |
# of contigs | 1480 |
# of scaffolds | 300 |
# of scaffolds >= 2Kbp | 300 |
Scaffold N50 | 46 |
Scaffold L50 (Mbp) | 0.34 |
# of gaps | 1180 |
% of scaffold length in gaps | 2.2% |
Three largest Scaffolds (Mbp) | 1.44, 1.07, 1.03 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 3019 | 2390 |
transcript | 1705 | 1356 |
exon | 251 | 141 |
intron | 229 | 205 |
description: | ||
protein length (aa) | 568 | 452 |
exons per gene | 6.78 | 5 |
# of gene models | 13088 |
Genome Reference(s)
Suzuki S, Yamaguchi H, Nakajima N, Kawachi M
Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales.
Sci Rep. 2018 May 23;8(1):8058. doi: 10.1038/s41598-018-26331-6
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Chlorophyceae Sphaeropleales