Status
The Gracilariopsis chorda isolate SKKU-2015 genome sequence and gene models have not been determined by the JGI, but were downloaded from NCBI on October 11, 2019. 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 1951 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 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) | 92.18 |
Sequencing read coverage depth | |
# of contigs | 1211 |
# of scaffolds | 1211 |
# of scaffolds >= 2Kbp | 1203 |
Scaffold N50 | 124 |
Scaffold L50 (Mbp) | 0.22 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 1.36, 1.13, 0.84 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1316 | 1069 |
transcript | 1280 | 1041 |
exon | 1019 | 807 |
intron | 142 | 100 |
description: | ||
protein length (aa) | 427 | 347 |
exons per gene | 1.26 | 1 |
# of gene models | 8855 |
Genome Reference(s)
Lee J, Yang EC, Graf L, Yang JH, Qiu H, Zelzion U, Chan CX, Stephens TG, Weber APM, Boo GH, Boo SM, Kim KM, Shin Y, Jung M, Lee SJ, Yim HS, Lee JH, Bhattacharya D, Yoon HS
Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta.
Mol Biol Evol. 2018 Aug 1;35(8):1869-1886. doi: 10.1093/molbev/msy081
Links
- JGI PhyloGroup Portals: Archaeplastida Rhodophyta Florideophyceae
- JGI EcoGroup Portals: Algae Seaweeds