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 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.
The following text is modified from NCBI BioProject PRJNA936482:
Gracilaria gracilis Genome sequencing and assembly
The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also studied for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.
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
