Genome assembly of the deep-sea coral Lophelia pertusa
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep...
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2023
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ftdoajarticles:oai:doaj.org/article:d76e43a744da464c9e7aa7741c4c6c76 2023-05-15T17:08:36+02:00 Genome assembly of the deep-sea coral Lophelia pertusa Santiago Herrera Erik E. Cordes 2023-03-01T00:00:00Z https://doi.org/10.46471/gigabyte.78 https://doaj.org/article/d76e43a744da464c9e7aa7741c4c6c76 EN eng GigaScience Press https://gigabytejournal.com/articles/78 https://doaj.org/toc/2709-4715 doi:10.46471/gigabyte.78 2709-4715 https://doaj.org/article/d76e43a744da464c9e7aa7741c4c6c76 GigaByte (2023) Electronic computers. Computer science QA75.5-76.95 article 2023 ftdoajarticles https://doi.org/10.46471/gigabyte.78 2023-03-19T01:30:33Z Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals. Article in Journal/Newspaper Lophelia pertusa Directory of Open Access Journals: DOAJ Articles Gigabyte 2023 1 12 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Electronic computers. Computer science QA75.5-76.95 |
spellingShingle |
Electronic computers. Computer science QA75.5-76.95 Santiago Herrera Erik E. Cordes Genome assembly of the deep-sea coral Lophelia pertusa |
topic_facet |
Electronic computers. Computer science QA75.5-76.95 |
description |
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals. |
format |
Article in Journal/Newspaper |
author |
Santiago Herrera Erik E. Cordes |
author_facet |
Santiago Herrera Erik E. Cordes |
author_sort |
Santiago Herrera |
title |
Genome assembly of the deep-sea coral Lophelia pertusa |
title_short |
Genome assembly of the deep-sea coral Lophelia pertusa |
title_full |
Genome assembly of the deep-sea coral Lophelia pertusa |
title_fullStr |
Genome assembly of the deep-sea coral Lophelia pertusa |
title_full_unstemmed |
Genome assembly of the deep-sea coral Lophelia pertusa |
title_sort |
genome assembly of the deep-sea coral lophelia pertusa |
publisher |
GigaScience Press |
publishDate |
2023 |
url |
https://doi.org/10.46471/gigabyte.78 https://doaj.org/article/d76e43a744da464c9e7aa7741c4c6c76 |
genre |
Lophelia pertusa |
genre_facet |
Lophelia pertusa |
op_source |
GigaByte (2023) |
op_relation |
https://gigabytejournal.com/articles/78 https://doaj.org/toc/2709-4715 doi:10.46471/gigabyte.78 2709-4715 https://doaj.org/article/d76e43a744da464c9e7aa7741c4c6c76 |
op_doi |
https://doi.org/10.46471/gigabyte.78 |
container_title |
Gigabyte |
container_volume |
2023 |
container_start_page |
1 |
op_container_end_page |
12 |
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1766064404727595008 |