Info • Monoraphidium minutum 26B-AM v1.0

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

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

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.