Info • Scenedesmus obliquus var. UTEX2630 v1.0


[September 2020] The Scenedesmus obliquus var. UTEX2630 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. UTEX 2630 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 106.02
Sequencing read coverage depth 489.95x
# of contigs 157
# of scaffolds 157
# of scaffolds >= 2Kbp 157
Scaffold N50 14
Scaffold L50 (Mbp) 2.37
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 5.61, 5.59, 5.57

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 446920490 426655578 95.5%
Other JGI_RNA_contigs 314857 264208 83.9%

Note: The Scenedesmus obliquus UTEX2630 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.

Gene Models FilteredModels1
length (bp) of: average median
gene 4426 3442
transcript 2009 1636
exon 286 157
intron 403 304
protein length (aa) 426 329
exons per gene 7.02 6
# of gene models 16604



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.