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A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster
https://oist.repo.nii.ac.jp/records/2843
https://oist.repo.nii.ac.jp/records/2843f5347109-71ff-4852-88cd-a2b33be244c7
名前 / ファイル | ライセンス | アクション |
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Takeuchi-2022-A high-quality, haplotype-phased_VoR (2.4 MB)
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CC BY 4.0
Creative Commons Attribution 4.0 International (https://creativecommons.org/licenses/by/4.0/) |
Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2022-11-14 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | Mollusca | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | pearl oyster | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | haplotype-phased genome assembly | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | immunity | |||||
キーワード | ||||||
主題Scheme | Other | |||||
主題 | aquaculture | |||||
資源タイプ | ||||||
資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
資源タイプ | journal article | |||||
著者(英) |
Takeuchi, Takeshi
× Takeuchi, Takeshi× Suzuki, Yoshihiko× Watabe, Shugo× Nagai, Kiyohito× Masaoka, Tetsuji× Fujie, Manabu× Kawamitsu, Mayumi× Satoh, Noriyuki× Myers, Eugene W |
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書誌情報 |
en : DNA Research 巻 29, 号 6, p. dsac035, 発行日 2022-11-10 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (>38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997%. Moreover, the haplotypes contain 95.2% and 95.9%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals. | |||||
出版者 | ||||||
出版者 | Oxford University Press | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1340-2838 | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1756-1663 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/36351462 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1093/dnares/dsac035 | |||||
権利 | ||||||
権利情報 | © The Author(s) 2022. | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://academic.oup.com/dnaresearch/article/29/6/dsac035/6815630 | |||||
著者版フラグ | ||||||
出版タイプ | VoR | |||||
出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 |