Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna
The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality...
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ftpubmed:oai:pubmedcentral.nih.gov:10716251 2024-01-14T10:02:27+01:00 Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna Jo, Euna Choi, Soyun Lee, Seung Jae Kim, Jinmu Choi, Eun Kyung Cho, Minjoo Kim, Jangyeon Chung, Sangdeok Lee, Jaebong Kim, Jeong-Hoon Park, Hyun 2023-12-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716251/ http://www.ncbi.nlm.nih.gov/pubmed/38086886 https://doi.org/10.1038/s41597-023-02811-x en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716251/ http://www.ncbi.nlm.nih.gov/pubmed/38086886 http://dx.doi.org/10.1038/s41597-023-02811-x © 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . Sci Data Data Descriptor Text 2023 ftpubmed https://doi.org/10.1038/s41597-023-02811-x 2023-12-17T01:59:10Z The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality genome assembly and annotation employing long-read sequencing have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for P. albipinna, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The resulting genome assembly spans approximately 1.07 Gb, with a longest scaffold measuring 59.39 Mb and an N50 length of 41.76 Mb. Of the 1,111 Hi-C scaffolds, 23 exceeded 10 Mb and were thus classified as chromosome-level. BUSCO completeness was assessed at 95.6%. The assembled genome comprises 50.68% repeat sequences, and a total of 31,128 protein-coding genes were predicted. This study will enhance our understanding of the genomic characteristics of cryonotothenioids and facilitate comparative analyses of their adaptation and evolution in extreme environments. Text Antarc* Antarctic Antarctica PubMed Central (PMC) Antarctic The Antarctic Scientific Data 10 1 |
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Data Descriptor Jo, Euna Choi, Soyun Lee, Seung Jae Kim, Jinmu Choi, Eun Kyung Cho, Minjoo Kim, Jangyeon Chung, Sangdeok Lee, Jaebong Kim, Jeong-Hoon Park, Hyun Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
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Data Descriptor |
description |
The Antarctic whitefin plunderfish Pogonophryne albipinna belongs to the family Artedidraconidae, a key component of Antarctic benthic ecosystems within the order Perciformes and the suborder Notothenioidei. While genome research on P. albipinna using short-read sequencing is available, high-quality genome assembly and annotation employing long-read sequencing have yet to be performed. This study presents a chromosome-scale genome assembly and annotation for P. albipinna, utilizing a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. The resulting genome assembly spans approximately 1.07 Gb, with a longest scaffold measuring 59.39 Mb and an N50 length of 41.76 Mb. Of the 1,111 Hi-C scaffolds, 23 exceeded 10 Mb and were thus classified as chromosome-level. BUSCO completeness was assessed at 95.6%. The assembled genome comprises 50.68% repeat sequences, and a total of 31,128 protein-coding genes were predicted. This study will enhance our understanding of the genomic characteristics of cryonotothenioids and facilitate comparative analyses of their adaptation and evolution in extreme environments. |
format |
Text |
author |
Jo, Euna Choi, Soyun Lee, Seung Jae Kim, Jinmu Choi, Eun Kyung Cho, Minjoo Kim, Jangyeon Chung, Sangdeok Lee, Jaebong Kim, Jeong-Hoon Park, Hyun |
author_facet |
Jo, Euna Choi, Soyun Lee, Seung Jae Kim, Jinmu Choi, Eun Kyung Cho, Minjoo Kim, Jangyeon Chung, Sangdeok Lee, Jaebong Kim, Jeong-Hoon Park, Hyun |
author_sort |
Jo, Euna |
title |
Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
title_short |
Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
title_full |
Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
title_fullStr |
Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
title_full_unstemmed |
Chromosome-level genome assembly and annotation of the Antarctica whitefin plunderfish Pogonophryne albipinna |
title_sort |
chromosome-level genome assembly and annotation of the antarctica whitefin plunderfish pogonophryne albipinna |
publisher |
Nature Publishing Group UK |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716251/ http://www.ncbi.nlm.nih.gov/pubmed/38086886 https://doi.org/10.1038/s41597-023-02811-x |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
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Antarc* Antarctic Antarctica |
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Antarc* Antarctic Antarctica |
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Sci Data |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10716251/ http://www.ncbi.nlm.nih.gov/pubmed/38086886 http://dx.doi.org/10.1038/s41597-023-02811-x |
op_rights |
© 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
op_doi |
https://doi.org/10.1038/s41597-023-02811-x |
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Scientific Data |
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