Status
The Gracilaria gracilis GNS1m genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were downloaded from Rhodoexplorer on July 18, 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 981 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 its authors and is therefore not automatically updated. In order to allow comparative analyses with other 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) | 76.01 |
Sequencing read coverage depth | 364.0x |
# of contigs | 279 |
# of scaffolds | 279 |
# of scaffolds >= 2Kbp | 279 |
Scaffold N50 | 38 |
Scaffold L50 (Mbp) | 0.58 |
# of gaps | 0 |
% of scaffold length in gaps | 0.0% |
Three largest Scaffolds (Mbp) | 2.31, 1.75, 1.55 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1643 | 1191 |
transcript | 1371 | 1119 |
exon | 895 | 690 |
intron | 514 | 110 |
description: | ||
protein length (aa) | 457 | 373 |
exons per gene | 1.53 | 1 |
# of gene models | 8693 |
Genome Reference(s)
Lipinska AP, Krueger-Hadfield SA, Godfroy O, Dittami SM, Ayres-Ostrock L, Bonthond G, Brillet-Guéguen L, Coelho S, Corre E, Cossard G, Destombe C, Epperlein P, Faugeron S, Ficko-Blean E, Beltrán J, Lavaut E, Le Bars A, Marchi F, Mauger S, Michel G, Potin P, Scornet D, Sotka EE, Weinberger F, Cabral de Oliveira M, Guillemin ML, Plastino EM, Valero M
The Rhodoexplorer Platform for Red Algal Genomics and Whole-Genome Assemblies for Several Gracilaria Species.
Genome Biol Evol. 2023 Jul 3;15(7):. doi: 10.1093/gbe/evad124
Links
- JGI PhyloGroup Portals: Archaeplastida Rhodophyta Florideophyceae
- JGI EcoGroup Portals: Algae Seaweeds