Status
The Volvox reticuliferus NIES-3785 genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were downloaded from NCBI on March 6, 2023. 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 8,982 out of 22,160 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/smaller scaffolds, and 5) short models lacking functional annotation. Please note that this copy of the genome is not maintained by NCBI 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) | 133.07 |
Sequencing read coverage depth | 369.0x |
# of contigs | 200 |
# of scaffolds | 200 |
# of scaffolds >= 2Kbp | 200 |
Scaffold N50 | 24 |
Scaffold L50 (Mbp) | 1.91 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 4.94, 4.89, 4.77 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 4363 | 3356 |
transcript | 1836 | 1386 |
exon | 242 | 145 |
intron | 386 | 325 |
description: | ||
protein length (aa) | 612 | 462 |
exons per gene | 7.59 | 6 |
# of gene models | 13178 |
Collaborators
- Hisayoshi Nozako, University of Tokyo, Japan
Genome Reference(s)
Yamamoto K, Hamaji T, Kawai-Toyooka H, Matsuzaki R, Takahashi F, Nishimura Y, Kawachi M, Noguchi H, Minakuchi Y, Umen JG, Toyoda A, Nozaki H
Three genomes in the algal genus Volvox reveal the fate of a haploid sex-determining region after a transition to homothallism.
Proc Natl Acad Sci U S A. 2021 May 25;118(21):. doi: 10.1073/pnas.2100712118
Links
- JGI EcoGroup Portals: Algae
- JGI PhyloGroup Portals: Viridiplantae Chlorophyta Chlorophyceae Chlamydomonadales