Status
The Nannochloropsis gaditana CCMP1894 genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were downloaded from Figshare on Oct 26, 2022. 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 647 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 Figshare 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) | 30.87 |
Sequencing read coverage depth | 288.0x |
# of contigs | 88 |
# of scaffolds | 85 |
# of scaffolds >= 2Kbp | 85 |
Scaffold N50 | 12 |
Scaffold L50 (Mbp) | 1.14 |
# of gaps | 3 |
% of scaffold length in gaps | 0.1% |
Three largest Scaffolds (Mbp) | 1.57, 1.54, 1.51 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2379 | 1792 |
transcript | 1726 | 1362 |
exon | 410 | 142 |
intron | 206 | 182 |
description: | ||
protein length (aa) | 575 | 454 |
exons per gene | 4.21 | 3 |
# of gene models | 8928 |
Genome Reference(s)
Schwartz AS, Brown R, Ajjawi I, McCarren J, Atilla S, Bauman N, Richardson TH
Complete Genome Sequence of the Model Oleaginous Alga Nannochloropsis gaditana CCMP1894.
Genome Announc. 2018 Feb 15;6(7):. doi: 10.1128/genomeA.01448-17
Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW
Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae.
Genome Biol Evol. 2021 Nov 5;13(11):. doi: 10.1093/gbe/evab233
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Eustigmatophyta