Status
[June 2019] The Monoraphidium minutum 26B-AM genome was sequenced using Pacbio. The transcriptome was sequenced with Illumina and assembled with Trinity. Substantial contamination by several bacterial species was detected, and the genome assemblies of Mesorhizobium, a couple Pseudomonas species, and a Microbacteriaceae were assembled with Flye. Reads that did not match any contaminant bacterium were assembled with Flye to generate the main assembly. The low percentage of RNA contigs mapped to the genome is likely due to bacterial contamination. The mitochondrial and chloroplast genomes were assembled separately and are available on the Download page.
Summary statistics for the Monoraphidium minutum 26B-AM
v1.0 release are below.
Genome Assembly | |
Genome Assembly size (Mbp) | 68.17 |
Sequencing read coverage depth | 73.2x |
# of contigs | 512 |
# of scaffolds | 511 |
# of scaffolds >= 2Kbp | 498 |
Scaffold N50 | 82 |
Scaffold L50 (Mbp) | 0.26 |
# of gaps | 1 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 0.78, 0.75, 0.74 |
ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
Ests | est.fasta | 91404149 | 82349393 | 90.1% |
Other | JGI_RNA_contigs | 153162 | 80327 | 52.4% |
Gene Models | FilteredModels2 | |
length (bp) of: | average | median |
gene | 3394 | 2660 |
transcript | 1875 | 1489 |
exon | 260 | 141 |
intron | 246 | 211 |
description: | ||
protein length (aa) | 485 | 353 |
exons per gene | 7.22 | 6 |
# of gene models | 15337 |
Collaborators
- Shawn Starkenburg at LANL
- Michael Huesemann at PNNL
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Calhoun Sara, Kamel Bishoy, Bell Tisza A.S., Kruse Colin P.S., Riley Robert, Singan Vasanth, Kunde Yuliya, Gleasner Cheryl D., Chovatia Mansi, Sandor Laura, Daum Christopher, Treen Daniel, Bowen Benjamin P., Louie Katherine B., Northen Trent R., Starkenburg Shawn R., Grigoriev Igor V.
Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress
Algal Research. 2022;66:102794. doi: 10.1016/j.algal.2022.102794
Calhoun Sara, Kamel Bishoy, Bell Tisza A.S., Kruse Colin P.S., Riley Robert, Singan Vasanth, Kunde Yuliya, Gleasner Cheryl D., Chovatia Mansi, Sandor Laura, Daum Christopher, Treen Daniel, Bowen Benjamin P., Louie Katherine B., Northen Trent R., Starkenburg Shawn R., Grigoriev Igor V.
Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress
Algal Research. 2022;66:102794. doi: 10.1016/j.algal.2022.102794
Links
Metagenome-assembled genomes
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.