Micrograph of Scenedesmus obliquus UTEX 3031 coenobium. Image credit: Juergen Polle.

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). The genome assembly of the previously published S. obliquus UTEX 3031 assembly (Starkenburg et al., 2017) was improved and scaffolded using a combination of PacBio HiFi, Oxford Nanopore, and Illumina Hi-C reads.

This portal contains the genomic data from haplotype 1 of Scenedesmus obliquus UTEX 3031.

All published models from this haplotype are available as ExternalModels. In order to ensure this genome is comparable to those sequenced and annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. A total of 3,744 external models were excluded based on one of the following classifications: 1) association with repetitive elements, 2) pseudogenes with internal stop codons, 3) alternative isoforms or overlapping transcript models, 4) alleles on secondary scaffolds, and 5) short models lacking functional annotation. Please note that this copy of the genome is not maintained by Starkenburg et al. 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 strain UTEX 3031 (=DOE0152Z)

S. obliquus belongs to the green algal class of the Chlorophyceae and to the order Sphaeropleales. Vegetative cells of S. obliquus are non-motile and often occur in coenobia (microcolonies) of four cells that are released from a mother cell. However, due to the multiple fission mode of reproduction sometimes even 8 or 16 cells may originate from one mother cell. In addition to the predominant asexual reproduction mode, S. obliquus has a sexual cell cycle that is rarely observed with gametogenesis resulting in biflagellate gametes.

The strain UTEX B 3031 is a subclone of the strain DOE0152, which had been isolated by the Polle lab at Brooklyn College of City University of New York (CUNY) in 2010 from a water sample originating from a turtle tank. Biomass productivity of strain UTEX B 3031 had been tested in small-scale race-way ponds and the strain was robust in indoor climate-controlled ponds as well as in outdoor pond cultivation trials. This strain is emerging as a new model and a platform for biofuels feedstock and bioproduct generation.

The diploid genome assembly and annotation from LANL are available at the Scenedemus obliquus UTEX 3031 diploid genome portal, along with the mitochondrial and plastid genomes from Starkenburg et al. (doi:10.1128/genomeA.00617-17).