Info • Scenedesmus obliquus var. DOE0013 v1.0


[September 2020] The Scenedesmus obliquus var. DOE0013 v1.0 genome was sequenced with PacBio, assembled with MECAT, and annotated using the JGI Annotation Pipeline. The mitochondrial and chloroplast genomes were assembled separately and are available in the downloads section.

Summary statistics for the Scenedesmus obliquus var. DOE0013 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 102.77
Sequencing read coverage depth 517.02x
# of contigs 154
# of scaffolds 154
# of scaffolds >= 2Kbp 154
Scaffold N50 13
Scaffold L50 (Mbp) 2.89
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.11, 5.22, 4.91

Note: The Scenedesmus obliquus DOE0013 RNAseq data comes from other datasets combining Scenedesmus obliquus EN0004 and Scenedesmus obliquus UTEX3031 transcriptomic data. The assembled transcripts are from a PacBio IsoSeq assembly of the algae Scenedesmus obliquus EN0004, combined with an Illumina RNASeq assembly that was assembled using Oases provided by Dr. Juergen Polle, in addition to raw Illumina reads from UTEX3031 provided by Dr. Polle that were not part of the assembled transcriptome.

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 88775599 83462889 94.0%
Other JGI_RNA_contigs 314857 259392 82.4%

Gene Models FilteredModels1
length (bp) of: average median
gene 4341 3448
transcript 1996 1626
exon 288 159
intron 398 305
protein length (aa) 427 332
exons per gene 6.92 6
# of gene models 15938



The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.