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. Please note that this copy of the genome is not maintained by Shan et al. 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.
Summary statistics for the Undaria pinnatifida M23 release
are below.
Genome Assembly | |
Genome Assembly size (Mbp) | 511.28 |
Sequencing read coverage depth | ~120X |
# 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 | ExternalModels | |
length (bp) of: | average | median |
gene | 14496 | 10534 |
transcript | 2089 | 1652 |
exon | 248 | 145 |
intron | 1673 | 958 |
description: | ||
protein length (aa) | 605 | 451 |
exons per gene | 8.43 | 7 |
# of gene models | 14300 |
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
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
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 Algae EcoGroup Portal
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Phaeophyta
Funding
This project was not sequenced at the JGI.