Info • Scenedesmus sp. NREL 46B-D3 v1.0


[February 2018] The Scenedesmus sp. NREL 46B-D3 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. Mitochondrial and chloroplast genomes were assembled separately and are available in the downloads section.

Scenedesmus sp. NREL 46B-D3 is likely diploid, and this is reflected in an assembly and annotation with significant separation of alleles. 1,606 of the 2,661 scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertoire of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Scenedesmus sp. NREL 46B-D3 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 151.90
Sequencing read coverage depth 81.46x
# of contigs 2661
# of scaffolds 2661
# of scaffolds >= 2Kbp 2604
Scaffold N50 181
Scaffold L50 (Mbp) 0.20
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.67, 1.61, 1.19

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 283853507 272376592 96.0%
Other JGI_RNA_contigs 37917 33107 87.3%

Gene Models FilteredModels2
length (bp) of: average median
gene 3664 2752
transcript 1710 1363
exon 282 163
intron 388 309
protein length (aa) 407 296
exons per gene 6.06 5
# of gene models 17399


Genome Reference(s)


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.