Status
The Cyanophora paradoxa CCMP329 genome assembly and gene models have not been determined by the JGI, but were downloaded from the publication supplemental datashare (cyanophora.rutgers.edu) on September 25, 2019. All published models are available as ExternalModels. In order to ensure this genome is comparable to those sequenced and annotated by the JGI, we applied standard filters to ExternalModels to produce the initial GeneCatalog. A total of 3,983 external models were excluded based on one of the following classifications: 1) association with repetitive elements, 2) pseudogenes with internal stop codons, 3) alternative isoforms or overlapping transcript models, 4) alleles on secondary scaffolds, and 5) short models lacking functional annotation. Please note that this copy of the genome is not maintained by Rutgers University 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 the genes.
Genome Assembly | |
Genome Assembly size (Mbp) | 98.35 |
Sequencing read coverage depth | 315x |
# of contigs | 704 |
# of scaffolds | 704 |
# of scaffolds >= 2Kbp | 704 |
Scaffold N50 | 132 |
Scaffold L50 (Mbp) | 0.21 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 1.23, 0.90, 0.88 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 2456 | 1859 |
transcript | 1606 | 1182 |
exon | 147 | 93 |
intron | 87 | 68 |
description: | ||
protein length (aa) | 535 | 394 |
exons per gene | 10.96 | 8 |
# of gene models | 21535 |
Genome Reference(s)
Price DC, Goodenough UW, Roth R, Lee JH, Kariyawasam T, Mutwil M, Ferrari C, Facchinelli F, Ball SG, Cenci U, Chan CX, Wagner NE, Yoon HS, Weber APM, Bhattacharya D
Analysis of an improved Cyanophora paradoxa genome assembly.
DNA Res. 2019 Aug 1;26(4):287-299. doi: 10.1093/dnares/dsz009
Links
- JGI Algae EcoGroup Portal
- JGI PhyloGroup Portals: Archaeplastida Glaucophyta