Info • Scenedesmus obliquus EN0004 v1.0


[November 2019] The Scenedesmus obliquus EN0004 genome was sequenced with PacBio, assembled using MECAT with polishing by ARROW, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assembled with Trinity. IsoSeq reads sequenced by Pacbio were also used in the annotation. RNASeq and IsoSeq reads were provided by our collaborators and not sequenced by JGI. Mitochondrial and chloroplast genomes were assembled separately and are available in the downloads section.

Summary statistics for the Scenedesmus obliquus EN0004 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 100.08
Sequencing read coverage depth 236.48x
# of contigs 99
# of scaffolds 99
# of scaffolds >= 2Kbp 99
Scaffold N50 13
Scaffold L50 (Mbp) 2.49
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 10.97, 5.63, 4.30

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 159169885 95185614 59.8%
Other IsoSeq_reads 182475 163006 89.3%
Other JGI_RNA_contigs 56668 20666 36.5%
  • Please note: Using BLAST, unmapped RNA reads and contigs were found to hit Homo sapiens, as well as Proteobacteria (Burkholderia contaminans) and Actinobacteria (Cutibacterium acnes), suggesting that the RNA library was contaminated.

Gene Models FilteredModels1
length (bp) of: average median
gene 4071 2946
transcript 1855 1470
exon 275 148
intron 388 299
protein length (aa) 446 308
exons per gene 6.74 5
# of gene models 15053



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.