The Scenedesmus obliquus UTEX 3031 (DOE0152z) genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were provided by collaborators at Los Alamos National Laboratory (LANL). 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 19,542 models from S. obliquus and the generation of the FilteredModels2 (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 this genome.

Scenedesmus obliquus UTEX 3031 is likely a diploid genome, and this is reflected in an assembly and annotation with significant separation of alleles. Many of the smaller scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

The diploid genome assembly and annotation from LANL are available in the Downloads tab, along with the mitochondrial and plastid genomes from Starkenburg et al. (doi:10.1128/genomeA.00617-17).