Cargando…

Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus

Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmen...

Descripción completa

Detalles Bibliográficos
Autores principales: Sun, Lina, Jiang, Chunxi, Su, Fang, Cui, Wei, Yang, Hongsheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10344927/
https://www.ncbi.nlm.nih.gov/pubmed/37443361
http://dx.doi.org/10.1038/s41597-023-02368-9
_version_ 1785072970386898944
author Sun, Lina
Jiang, Chunxi
Su, Fang
Cui, Wei
Yang, Hongsheng
author_facet Sun, Lina
Jiang, Chunxi
Su, Fang
Cui, Wei
Yang, Hongsheng
author_sort Sun, Lina
collection PubMed
description Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation.
format Online
Article
Text
id pubmed-10344927
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-103449272023-07-15 Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus Sun, Lina Jiang, Chunxi Su, Fang Cui, Wei Yang, Hongsheng Sci Data Data Descriptor Sea cucumber is a morphologically diverse and ecologically important clade of echinoderms. The sea cucumber Apostichopus japonicus is the most economically valuable species of sea cucumber. The initial assembly of the A. japonicus genome was released in 2017. However, this genome assembly is fragmented and lacks relative position information of genes on chromosomes. In this study, we produced a high-quality chromosome-level genome of A. japonicus using Pacbio HiFi long-reads and Hi-C sequencing data. The assembled A. japonicus genome spanned 671.60 Mb with a contig N50 size of 17.20 Mb and scaffold N50 size of 29.65 Mb. A total of 99.9% of the assembly was anchored to 23 chromosomes. In total, 19,828 genes were annotated, and 97.2% of BUSCO genes were fully represented. This high-quality genome of A. japonicus will not only aid in the development of sustainable aquaculture practices, but also lay a foundation for a deeper understanding of their genetic makeup, evolutionary history, and ecological adaptation. Nature Publishing Group UK 2023-07-13 /pmc/articles/PMC10344927/ /pubmed/37443361 http://dx.doi.org/10.1038/s41597-023-02368-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Sun, Lina
Jiang, Chunxi
Su, Fang
Cui, Wei
Yang, Hongsheng
Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title_full Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title_fullStr Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title_full_unstemmed Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title_short Chromosome-level genome assembly of the sea cucumber Apostichopus japonicus
title_sort chromosome-level genome assembly of the sea cucumber apostichopus japonicus
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10344927/
https://www.ncbi.nlm.nih.gov/pubmed/37443361
http://dx.doi.org/10.1038/s41597-023-02368-9
work_keys_str_mv AT sunlina chromosomelevelgenomeassemblyoftheseacucumberapostichopusjaponicus
AT jiangchunxi chromosomelevelgenomeassemblyoftheseacucumberapostichopusjaponicus
AT sufang chromosomelevelgenomeassemblyoftheseacucumberapostichopusjaponicus
AT cuiwei chromosomelevelgenomeassemblyoftheseacucumberapostichopusjaponicus
AT yanghongsheng chromosomelevelgenomeassemblyoftheseacucumberapostichopusjaponicus