Status
The Prasinoderma coloniale CCMP1413 genome assembly and gene models have not been determined by the JGI, but were downloaded from the CNGB Nucleotide Sequence Archive (accession no. CNP0000924) on July 20, 2020. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 212 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All published models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by CNGB and is therefore not automatically updated. In order to allow comparative analyses with other algal genomes sequenced by the JGI, a copy of this genome is incorporated into PhycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.
Genome Assembly | |
Genome Assembly size (Mbp) | 25.32 |
# of contigs | 22 |
# of scaffolds | 22 |
# of scaffolds >= 2Kbp | 22 |
Scaffold N50 | 7 |
Scaffold L50 (Mbp) | 1.23 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 3.60, 2.45, 2.23 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1921 | 1572 |
transcript | 1637 | 1311 |
exon | 725 | 398 |
intron | 227 | 164 |
description: | ||
protein length (aa) | 500 | 398 |
exons per gene | 2.26 | 2 |
# of gene models | 6927 |
Genome Reference(s)
Li L, Wang S, Wang H, Sahu SK, Marin B, Li H, Xu Y, Liang H, Li Z, Cheng S, Reder T, Çebi Z, Wittek S, Petersen M, Melkonian B, Du H, Yang H, Wang J, Wong GK, Xu X, Liu X, Van de Peer Y, Melkonian M, Liu H
The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.
Nat Ecol Evol. 2020 Sep;4(9):1220-1231. doi: 10.1038/s41559-020-1221-7
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Archaeplastida Viridiplantae Prasinodermophyta Prasinodermophyceae