The first high-quality genome assembly and annotation of Patiria pectinifera

The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We asse...

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Autores principales: Jung, Jaehoon, Jhang, So Yun, Kim, Bongsang, Koh, Bomin, Ban, Chaeyoung, Seo, Hyojung, Park, Taeseo, Chi, Won-Jae, Kim, Soonok, Kim, Heebal, Yu, Jaewoong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
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Data Descriptor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10511450/
https://www.ncbi.nlm.nih.gov/pubmed/37730712
http://dx.doi.org/10.1038/s41597-023-02508-1
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author Jung, Jaehoon
Jhang, So Yun
Kim, Bongsang
Koh, Bomin
Ban, Chaeyoung
Seo, Hyojung
Park, Taeseo
Chi, Won-Jae
Kim, Soonok
Kim, Heebal
Yu, Jaewoong
author_facet Jung, Jaehoon
Jhang, So Yun
Kim, Bongsang
Koh, Bomin
Ban, Chaeyoung
Seo, Hyojung
Park, Taeseo
Chi, Won-Jae
Kim, Soonok
Kim, Heebal
Yu, Jaewoong
author_sort Jung, Jaehoon
collection PubMed
description The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We assembled the genome using Nanopore and Illumina sequences, yielding a total length of 615 Mb and a scaffold N50 of 24,204,423 bp. Hi-C analysis allowed us to anchor the scaffold sequences onto 22 pseudochromosomes. K-mer based analysis revealed 5.16% heterozygosity rate of the genome, higher than any previously reported echinoderm species. Our transposable element analysis exposed a substantial number of genome-wide retrotransposons and DNA transposons. These results offer valuable resources for understanding the evolutionary mechanisms behind P. pectinifera’s successful adaptation in fluctuating environments.
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spelling pubmed-105114502023-09-22 The first high-quality genome assembly and annotation of Patiria pectinifera Jung, Jaehoon Jhang, So Yun Kim, Bongsang Koh, Bomin Ban, Chaeyoung Seo, Hyojung Park, Taeseo Chi, Won-Jae Kim, Soonok Kim, Heebal Yu, Jaewoong Sci Data Data Descriptor The blue bat star, a highly adaptive species in the East Sea of Korea, has displayed remarkable success in adapting to recent climate change. The genetic mechanisms behind this success were not well-understood, prompting our report on the first chromosome-level assembly of the Patiria genus. We assembled the genome using Nanopore and Illumina sequences, yielding a total length of 615 Mb and a scaffold N50 of 24,204,423 bp. Hi-C analysis allowed us to anchor the scaffold sequences onto 22 pseudochromosomes. K-mer based analysis revealed 5.16% heterozygosity rate of the genome, higher than any previously reported echinoderm species. Our transposable element analysis exposed a substantial number of genome-wide retrotransposons and DNA transposons. These results offer valuable resources for understanding the evolutionary mechanisms behind P. pectinifera’s successful adaptation in fluctuating environments. Nature Publishing Group UK 2023-09-20 /pmc/articles/PMC10511450/ /pubmed/37730712 http://dx.doi.org/10.1038/s41597-023-02508-1 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 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/) .
spellingShingle Data Descriptor
Jung, Jaehoon
Jhang, So Yun
Kim, Bongsang
Koh, Bomin
Ban, Chaeyoung
Seo, Hyojung
Park, Taeseo
Chi, Won-Jae
Kim, Soonok
Kim, Heebal
Yu, Jaewoong
The first high-quality genome assembly and annotation of Patiria pectinifera
title The first high-quality genome assembly and annotation of Patiria pectinifera
title_full The first high-quality genome assembly and annotation of Patiria pectinifera
title_fullStr The first high-quality genome assembly and annotation of Patiria pectinifera
title_full_unstemmed The first high-quality genome assembly and annotation of Patiria pectinifera
title_short The first high-quality genome assembly and annotation of Patiria pectinifera
title_sort first high-quality genome assembly and annotation of patiria pectinifera
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10511450/
https://www.ncbi.nlm.nih.gov/pubmed/37730712
http://dx.doi.org/10.1038/s41597-023-02508-1
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