Status
[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by merging multiple assemblies that originated from three independent Illumina assemblies (NCBI GCA_900108755.1; an unpublished dataset provided by D.R. Nelson from New York University Abu Dhabi; JGI CSP Proposal Id: 503423) and one PacBio assembly (Reads from JGI CSP Proposal Id: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 |
description: | ||
protein length (aa) | 458 | 360 |
exons per gene | 6.49 | 5 |
# of gene models | 19017 |
Collaborators
- Dr. James Umen at Danforth Center
- Dr. Shawn Starkenburg at LANL
- Dr. Juergen Polle at Brooklyn College of CUNY
- Dr. Zaid McKie-Krisberg at Brooklyn College of CUNY
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Archaeplastida Viridiplantae Chlorophyta Chlorophyceae Sphaeropleales Scenedesmaceae
Funding
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.