Status
[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.
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 |
description: | ||
protein length (aa) | 407 | 296 |
exons per gene | 6.06 | 5 |
# of gene models | 17399 |
Collaborators
- Shawn Starkenburg at LANL
- Michael Guarnieri at NREL
Genome Reference(s)
Calhoun S, Bell TAS, Dahlin LR, Kunde Y, LaButti K, Louie KB, Kuftin A, Treen D, Dilworth D, Mihaltcheva S, Daum C, Bowen BP, Northen TR, Guarnieri MT, Starkenburg SR, Grigoriev IV
A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology.
Commun Biol. 2021 Mar 12;4(1):333. doi: 10.1038/s42003-021-01859-y