Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Genome Biol Evol
2023 Jun 01;156:. doi: 10.1093/gbe/evad083.
Show Gene links
Show Anatomy links
The First Genome of the Cold-Water Octocoral, the Pink Sea Fan, Eunicella verrucosa.
Macleod KL
,
Paris JR
,
Jenkins TL
,
Stevens JR
.
Abstract
Cold-water corals form an important part of temperate benthic ecosystems by increasing three-dimensionality and providing an important ecological substrate for other benthic fauna. However, the fragile three-dimensional structure and life-history characteristics of cold-water corals can leave populations vulnerable to anthropogenic disturbance. Meanwhile, the ability of temperate octocorals, particularly shallow-water species, to respond to adjustments in their environment linked to climate change has not been studied. This study reports the first genome assembly of the pink sea fan (Eunicella verrucosa), a temperate shallow-water octocoral species. We produced an assembly of 467 Mb, comprising 4,277 contigs and an N50 of 250,417 bp. In total, 213 Mb (45.96% of the genome) comprised repetitive sequences. Annotation of the genome using RNA-seq data derived from polyp tissue and gorgonin skeleton resulted in 36,099 protein-coding genes after 90% similarity clustering, capturing 92.2% of the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) ortholog benchmark genes. Functional annotation of the proteome using orthology inference identified 25,419 annotated genes. This genome adds to the very few genomic resources currently available in the octocoral community and represents a key step in allowing scientists to investigate the genomic and transcriptomic responses of octocorals to climate change.
Altschul,
Basic local alignment search tool.
1990, Pubmed
Altschul,
Basic local alignment search tool.
1990,
Pubmed
Brůna,
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.
2021,
Pubmed
Cantalapiedra,
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.
2021,
Pubmed
Crisci,
Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species.
2017,
Pubmed
Dobin,
STAR: ultrafast universal RNA-seq aligner.
2013,
Pubmed
Donelson,
Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change.
2019,
Pubmed
Ferrier-Pagès,
Physiological response of the symbiotic gorgonian Eunicella singularis to a long-term temperature increase.
2009,
Pubmed
Flynn,
RepeatModeler2 for automated genomic discovery of transposable element families.
2020,
Pubmed
Fu,
CD-HIT: accelerated for clustering the next-generation sequencing data.
2012,
Pubmed
Guan,
Identifying and removing haplotypic duplication in primary genome assemblies.
2020,
Pubmed
Hall-Spencer,
Diseases affect cold-water corals too: Eunicella verrucosa (Cnidaria: Gorgonacea) necrosis in SW England.
2007,
Pubmed
Holland,
Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals.
2017,
Pubmed
Jenkins,
Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.
2019,
Pubmed
Jenkins,
Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic.
2022,
Pubmed
,
Echinobase
Jeon,
The Draft Genome of an Octocoral, Dendronephthya gigantea.
2019,
Pubmed
Jones,
InterProScan 5: genome-scale protein function classification.
2014,
Pubmed
Kolmogorov,
Assembly of long, error-prone reads using repeat graphs.
2019,
Pubmed
Quinlan,
BEDTools: a flexible suite of utilities for comparing genomic features.
2010,
Pubmed
Simão,
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
2015,
Pubmed
Stanke,
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
2006,
Pubmed
Storer,
The Dfam community resource of transposable element families, sequence models, and genome annotations.
2021,
Pubmed
Tarailo-Graovac,
Using RepeatMasker to identify repetitive elements in genomic sequences.
2009,
Pubmed
Voolstra,
Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals.
2017,
Pubmed
Zhou,
The First Draft Genome of a Cold-Water Coral Trachythela sp. (Alcyonacea: Stolonifera: Clavulariidae).
2021,
Pubmed
