Status
The Gracilaria domingensis SP 400837 genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were downloaded from NCBI on March 2, 2023. 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 1,580 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) | 77.74 |
Sequencing read coverage depth | 180.0x |
# of contigs | 1087 |
# of scaffolds | 684 |
# of scaffolds >= 2Kbp | 684 |
Scaffold N50 | 117 |
Scaffold L50 (Mbp) | 0.19 |
# of gaps | 403 |
% of scaffold length in gaps | 1.1% |
Three largest Scaffolds (Mbp) | 1.01, 0.81, 0.79 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1311 | 1074 |
transcript | 1271 | 1038 |
exon | 873 | 663 |
intron | 89 | 58 |
description: | ||
protein length (aa) | 424 | 346 |
exons per gene | 1.46 | 1 |
# of gene models | 9746 |
Genome Reference(s)
Nakamura-Gouvea N, Alves-Lima C, Benites LF, Iha C, Maracaja-Coutinho V, Aliaga-Tobar V, Araujo Amaral Carneiro M, Yokoya NS, Marinho-Soriano E, Graminha MAS, Collén J, Oliveira MC, Setubal JC, Colepicolo P
Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales).
J Phycol. 2022 Jun;58(3):406-423. doi: 10.1111/jpy.13238
Links
- JGI EcoGroup Portals: Algae Seaweeds
- JGI PhyloGroup Portals: Archaeplastida Rhodophyta Florideophyceae