Status
The Pedinophyceae sp. YPF-701 genome assembly and gene models have not been determined by the JGI, but were downloaded from the NCBI 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 NCBI 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 181 models from Pedinophyceae sp. YPF-701 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) | 27.90 |
# of contigs | 32 |
# of scaffolds | 32 |
# of scaffolds >= 2Kbp | 32 |
Scaffold N50 | 8 |
Scaffold L50 (Mbp) | 1.23 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 2.74, 2.20, 2.05 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2295 | 1867 |
transcript | 1702 | 1296 |
exon | 417 | 223 |
intron | 194 | 151 |
description: | ||
protein length (aa) | 567 | 432 |
exons per gene | 4.08 | 4 |
# of gene models | 7759 |
Genome Reference(s)
Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H
Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae.
New Phytol. 2022 Mar;233(5):2144-2154. doi: 10.1111/nph.17926
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Pedinophyceae