Status
The Undaria pinnatifida M23 genome sequence and gene models have not been determined by the JGI, but were downloaded from Shan et al. 2020 on July 14, 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 1801 models and the generation of the FilteredModels1 (GeneCatalog) gene track. All published models are available in the ExternalModels track. Please note that this copy f 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) | 511.28 |
Sequencing read coverage depth | |
# of contigs | 618 |
# of scaffolds | 114 |
# of scaffolds >= 2Kbp | 84 |
Scaffold N50 | 12 |
Scaffold L50 (Mbp) | 16.51 |
# of gaps | 504 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 32.30, 29.17, 27.54 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 14757 | 11200 |
transcript | 2161 | 1725 |
exon | 243 | 144 |
intron | 1600 | 965 |
description: | ||
protein length (aa) | 628 | 467 |
exons per gene | 8.88 | 7 |
# of gene models | 12499 |
Genome Reference(s)
Shan T, Yuan J, Su L, Li J, Leng X, Zhang Y, Gao H, Pang S
First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies.
Front Genet. 2020;11():140. doi: 10.3389/fgene.2020.00140
Links
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Phaeophyta
- JGI EcoGroup Portals: Algae Seaweeds