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Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance
https://oist.repo.nii.ac.jp/records/1477
https://oist.repo.nii.ac.jp/records/1477ed15a073-a263-43c6-befc-7ee5484d274f
名前 / ファイル | ライセンス | アクション |
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Choo-2020-Novel genomic resources for shelled (907.9 kB)
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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 | 2020-05-12 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance | |||||
言語 | ||||||
言語 | eng | |||||
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) |
Choo, Le Qin
× Choo, Le Qin× Bal, Thijs M. P.× Choquet, Marvin× Smolina, Irina× Ramos-Silva, Paula× Marlétaz, Ferdinand× Kopp, Martina× Hoarau, Galice× Peijnenburg, Katja T. C. A. |
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書誌情報 |
en : BMC Genomics 巻 21, 号 1, p. 11, 発行日 2020-01-03 |
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抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | BACKGROUND: Pteropods are planktonic gastropods that are considered as bio-indicators to monitor impacts of ocean acidification on marine ecosystems. In order to gain insight into their adaptive potential to future environmental changes, it is critical to use adequate molecular tools to delimit species and population boundaries and to assess their genetic connectivity. We developed a set of target capture probes to investigate genetic variation across their large-sized genome using a population genomics approach. Target capture is less limited by DNA amount and quality than other genome-reduced representation protocols, and has the potential for application on closely related species based on probes designed from one species. RESULTS: We generated the first draft genome of a pteropod, Limacina bulimoides, resulting in a fragmented assembly of 2.9 Gbp. Using this assembly and a transcriptome as a reference, we designed a set of 2899 genome-wide target capture probes for L. bulimoides. The set of probes includes 2812 single copy nuclear targets, the 28S rDNA sequence, ten mitochondrial genes, 35 candidate biomineralisation genes, and 41 non-coding regions. The capture reaction performed with these probes was highly efficient with 97% of the targets recovered on the focal species. A total of 137,938 single nucleotide polymorphism markers were obtained from the captured sequences across a test panel of nine individuals. The probes set was also tested on four related species: L. trochiformis, L. lesueurii, L. helicina, and Heliconoides inflatus, showing an exponential decrease in capture efficiency with increased genetic distance from the focal species. Sixty-two targets were sufficiently conserved to be recovered consistently across all five species. CONCLUSION: The target capture protocol used in this study was effective in capturing genome-wide variation in the focal species L. bulimoides, suitable for population genomic analyses, while providing insights into conserved genomic regions in related species. The present study provides new genomic resources for pteropods and supports the use of target capture-based protocols to efficiently characterise genomic variation in small non-model organisms with large genomes. |
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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/31900119 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1186/s12864-019-6372-z | |||||
権利 | ||||||
権利情報 | © 2020 The Author(s) | |||||
情報源 | ||||||
関連名称 | https://creativecommons.org/licenses/by/4.0/ | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6372-z | |||||
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 |