Info • Scenedesmus obliquus UTEX 393 v2.0


[August 2020] The Scenedesmus obliquus strain UTEX 393 genome assembly was constructed by merging multiple assemblies that originated from three independent Illumina assemblies (NCBI GCA_900108755.1; an unpublished dataset provided by D.R. Nelson from New York University Abu Dhabi; JGI CSP Proposal Id: 503423) and one PacBio assembly (Reads from JGI CSP Proposal Id: 503423). Merging of the assemblies was performed by Dr. Zaid McKie-Krisberg at Brooklyn College of the City University of New York. The gene models were predicted and annotated by the Joint Genome Institute (JGI) Annotation Pipeline. Note that scaffold_72 and scaffold_154 are predicted to be the chloroplast and mitochondrial genomes, respectively.

Summary statistics for the Scenedesmus obliquus UTEX 393 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 107.86
Sequencing read coverage depth 190x
# of contigs 390
# of scaffolds 329
# of scaffolds >= 2Kbp 329
Scaffold N50 14
Scaffold L50 (Mbp) 2.62
# of gaps 61
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 6.09, 5.91, 5.21

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 268942607 260372079 96.8%
Other IsoSeq_reads 182475 124825 68.4%
Other JGI_RNA_contigs 141583 88975 62.8%

Gene Models FilteredModels6
length (bp) of: average median
gene 4237 3435
transcript 2158 1812
exon 333 172
intron 381 303
protein length (aa) 458 360
exons per gene 6.49 5
# of gene models 19017



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.