WEKO3
アイテム
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Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved. \nRESULTS: Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. 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Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing
https://oist.repo.nii.ac.jp/records/2033
https://oist.repo.nii.ac.jp/records/20331b4a234d-b5bc-4f0e-82f2-c58a8f87d4d2
名前 / ファイル | ライセンス | アクション |
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Bliznina-2021-Telomere-to-telomere assembly of (1.5 MB)
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Creative Commons Attribution 4.0 International(https://creativecommons.org/licenses/by/4.0/)
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Item type | 学術雑誌論文 / Journal Article(1) | |||||
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公開日 | 2021-05-06 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing | |||||
言語 | ||||||
言語 | eng | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Oikopleura dioica | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Oxford Nanopore sequencing | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Hi-C | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Telomere-to-telomere | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Chromosome-scale assembly | |||||
キーワード | ||||||
言語 | en | |||||
主題Scheme | Other | |||||
主題 | Single individual | |||||
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) |
Bliznina, Aleksandra
× Bliznina, Aleksandra× Masunaga, Aki× Mansfield, Michael J.× Tan, Yongkai× Liu, Andrew W.× West, Charlotte× Rustagi, Tanmay× Chien, Hsiao-Chiao× Kumar, Saurabh× Pichon, Julien× Plessy, Charles× Luscombe, Nicholas M. |
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書誌情報 |
en : BMC Genomics 巻 22, 号 1, p. 222, 発行日 2021-03-29 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | BACKGROUND: The larvacean Oikopleura dioica is an abundant tunicate plankton with the smallest (65-70 Mbp) non-parasitic, non-extremophile animal genome identified to date. Currently, there are two genomes available for the Bergen (OdB3) and Osaka (OSKA2016) O. dioica laboratory strains. Both assemblies have full genome coverage and high sequence accuracy. However, a chromosome-scale assembly has not yet been achieved. RESULTS: Here, we present a chromosome-scale genome assembly (OKI2018_I69) of the Okinawan O. dioica produced using long-read Nanopore and short-read Illumina sequencing data from a single male, combined with Hi-C chromosomal conformation capture data for scaffolding. The OKI2018_I69 assembly has a total length of 64.3 Mbp distributed among 19 scaffolds. 99% of the assembly is contained within five megabase-scale scaffolds. We found telomeres on both ends of the two largest scaffolds, which represent assemblies of two fully contiguous autosomal chromosomes. Each of the other three large scaffolds have telomeres at one end only and we propose that they correspond to sex chromosomes split into a pseudo-autosomal region and X-specific or Y-specific regions. Indeed, these five scaffolds mostly correspond to equivalent linkage groups in OdB3, suggesting overall agreement in chromosomal organization between the two populations. At a more detailed level, the OKI2018_I69 assembly possesses similar genomic features in gene content and repetitive elements reported for OdB3. The Hi-C map suggests few reciprocal interactions between chromosome arms. At the sequence level, multiple genomic features such as GC content and repetitive elements are distributed differently along the short and long arms of the same chromosome. CONCLUSIONS: We show that a hybrid approach of integrating multiple sequencing technologies with chromosome conformation information results in an accurate de novo chromosome-scale assembly of O. dioica's highly polymorphic genome. This genome assembly opens up the possibility of cross-genome comparison between O. dioica populations, as well as of studies of chromosomal evolution in this lineage. |
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出版者 | ||||||
出版者 | BMC | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 1471-2164 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/33781200 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1186/s12864-021-07512-6 | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07512-6 | |||||
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 |