Status
The Seminavis robusta D6 genome sequence and gene models have not been determined by the JGI, but were downloaded from the Online Resource for Community Annotation of Eukaryotes (ORCAE) web portal on August 5, 2020. 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 4,312 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 ORCAE and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome. The mitochondrial and chloroplast assemblies were separated from the nuclear assembly FASTA and are available in the downloads section.
Genome Assembly | |
Genome Assembly size (Mbp) | 125.57 |
# of contigs | 4756 |
# of scaffolds | 4752 |
# of scaffolds >= 2Kbp | 4351 |
Scaffold N50 | 736 |
Scaffold L50 (Mbp) | 0.05 |
# of gaps | 4 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 0.32, 0.29, 0.28 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1878 | 1493 |
transcript | 1766 | 1416 |
exon | 873 | 623 |
intron | 112 | 95 |
description: | ||
protein length (aa) | 502 | 398 |
exons per gene | 2.02 | 1 |
# of gene models | 33143 |
Genome Reference(s)
Osuna-Cruz CM, Bilcke G, Vancaester E, De Decker S, Bones AM, Winge P, Poulsen N, Bulankova P, Verhelst B, Audoor S, Belisova D, Pargana A, Russo M, Stock F, Cirri E, Brembu T, Pohnert G, Piganeau G, Ferrante MI, Mock T, Sterck L, Sabbe K, De Veylder L, Vyverman W, Vandepoele K
The Seminavis robusta genome provides insights into the evolutionary adaptations of benthic diatoms.
Nat Commun. 2020 Jul 3;11(1):3320. doi: 10.1038/s41467-020-17191-8
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Bacillariophyta Bacillariophyceae