Status
The Pedinomonas minor SAG 1965-3 genome assembly and gene models have not been determined by the JGI, but were downloaded from the CNGB Nucleotide Sequence Archive (accession no. CNP0002569) on September 16, 2022. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. Please note that this copy of the genome is not maintained by CNGB and is therefore not automatically updated.
We applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, and 4) unsupported short models. This resulted in removal of 709 models from P. minor and generation of the FilteredModels1 gene track. All published models are available in the ExternalModels track. The JGI Annotation Pipeline was used to add functional annotation to this genome.
Genome Assembly | |
Genome Assembly size (Mbp) | 54.97 |
Sequencing read coverage depth | |
# of contigs | 101 |
# of scaffolds | 85 |
# of scaffolds >= 2Kbp | 85 |
Scaffold N50 | 9 |
Scaffold L50 (Mbp) | 2.41 |
# of gaps | 16 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 3.82, 3.66, 3.55 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2992 | 2271 |
transcript | 1576 | 1200 |
exon | 185 | 139 |
intron | 190 | 146 |
description: | ||
protein length (aa) | 525 | 400 |
exons per gene | 8.54 | 7 |
# of gene models | 10504 |
Genome Reference(s)
Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GK, Melkonian B, Melkonian M, Liu H, Wang S
Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment.
New Phytol. 2022 Aug;235(4):1409-1425. doi: 10.1111/nph.18220
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Pedinophyceae