Status
The Cyclotella cryptica CCMP332 genome sequence and gene models have not been determined by the JGI, but were downloaded from CoGe on October 24, 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 16980 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 the genes.
Genome Assembly | |
Genome Assembly size (Mbp) | 171.14 |
Sequencing read coverage depth | |
# of contigs | 756 |
# of scaffolds | 662 |
# of scaffolds >= 2Kbp | 660 |
Scaffold N50 | 101 |
Scaffold L50 (Mbp) | 0.49 |
# of gaps | 94 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 2.50, 2.10, 2.02 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2506 | 1983 |
transcript | 2266 | 1818 |
exon | 798 | 546 |
intron | 132 | 91 |
description: | ||
protein length (aa) | 519 | 421 |
exons per gene | 2.84 | 2 |
# of gene models | 14429 |
Genome Reference(s)
Traller JC, Cokus SJ, Lopez DA, Gaidarenko O, Smith SR, McCrow JP, Gallaher SD, Podell S, Thompson M, Cook O, Morselli M, Jaroszewicz A, Allen EE, Allen AE, Merchant SS, Pellegrini M, Hildebrand M
Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype.
Biotechnol Biofuels. 2016;9():258. doi: 10.1186/s13068-016-0670-3
Roberts WR, Downey KM, Ruck EC, Traller JC, Alverson AJ
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta).
G3 (Bethesda). 2020 Sep 2;10(9):2965-2974. doi: 10.1534/g3.120.401408
Links
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Bacillariophyta Coscinodiscophyceae
- JGI EcoGroup Portals: Algae Oceanic phytoplankton