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. 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 the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.
Summary statistics for the Seminavis robusta D6 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 125.57 |
| Sequencing read coverage depth | |
| # 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 | ExternalModels | |
| length (bp) of: | average | median |
| gene | 1782 | 1405 |
| transcript | 1677 | 1333 |
| exon | 860 | 605 |
| intron | 112 | 95 |
| description: | ||
| protein length (aa) | 479 | 378 |
| exons per gene | 1.95 | 1 |
| # of gene models | 37455 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
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
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
Funding
This project was not sequenced at the JGI.
