Status
The Auxenochlorella protothecoides UTEX 25 genome sequence and gene models have not been determined by the JGI, but were downloaded from the Los Alamos National Laboratory (LANL) Greenhouse portal on October 31, 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 353 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 LANL 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) | 21.22 |
Sequencing read coverage depth | 38.0x |
# of contigs | 1892 |
# of scaffolds | 217 |
# of scaffolds >= 2Kbp | 93 |
Scaffold N50 | 12 |
Scaffold L50 (Mbp) | 0.64 |
# of gaps | 1675 |
% of scaffold length in gaps | 0.8% |
Three largest Scaffolds (Mbp) | 2.06, 1.24, 0.98 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2752 | 1960 |
transcript | 1441 | 1107 |
exon | 211 | 150 |
intron | 227 | 186 |
description: | ||
protein length (aa) | 479 | 367 |
exons per gene | 6.83 | 5 |
# of gene models | 5688 |
Genome Reference(s)
Vogler Brian W., Starkenburg Shawn R., Sudasinghe Nilusha, Schambach Jenna Y., Rollin Joseph A., Pattathil Sivakumar, Barry Amanda N.
Characterization of plant carbon substrate utilization by Auxenochlorella protothecoides
Algal Research. 2018;34:37-48. doi: 10.1016/j.algal.2018.07.001
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Archaeplastida Viridiplantae Chlorophyta Trebouxiophyceae