WEKO3
アイテム
{"_buckets": {"deposit": "c7befb26-cc6f-4dab-9eed-abf01fafa61d"}, "_deposit": {"created_by": 30, "id": "1683", "owners": [30], "pid": {"revision_id": 0, "type": "depid", "value": "1683"}, "status": "published"}, "_oai": {"id": "oai:oist.repo.nii.ac.jp:00001683", "sets": ["27"]}, "author_link": ["10129", "10130", "10131", "10132", "10133"], "item_10001_biblio_info_7": {"attribute_name": "Bibliographic Information", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2020-01-09", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "1", "bibliographicPageStart": "78", "bibliographicVolumeNumber": "10", "bibliographic_titles": [{}, {"bibliographic_title": "Scientific Reports", "bibliographic_titleLang": "en"}]}]}, "item_10001_creator_3": {"attribute_name": "Author", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "de Kerdrel, Guillemette A."}], "nameIdentifiers": [{"nameIdentifier": "10129", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Andersen, Jeremy C."}], "nameIdentifiers": [{"nameIdentifier": "10130", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Kennedy, Susan R."}], "nameIdentifiers": [{"nameIdentifier": "10131", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Gillespie, Rosemary"}], "nameIdentifiers": [{"nameIdentifier": "10132", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Krehenwinkel, Henrik"}], "nameIdentifiers": [{"nameIdentifier": "10133", "nameIdentifierScheme": "WEKO"}]}]}, "item_10001_description_5": {"attribute_name": "Abstract", "attribute_value_mlt": [{"subitem_description": "In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.", "subitem_description_type": "Other"}]}, "item_10001_publisher_8": {"attribute_name": "Publisher", "attribute_value_mlt": [{"subitem_publisher": "Nature Research "}]}, "item_10001_relation_13": {"attribute_name": "PubMedNo.", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:pmid/31919378", "subitem_relation_type_select": "PMID"}}]}, "item_10001_relation_14": {"attribute_name": "DOI", "attribute_value_mlt": [{"subitem_relation_type": "isIdenticalTo", "subitem_relation_type_id": {"subitem_relation_type_id_text": "info:doi/10.1038/s41598-019-54927-z", "subitem_relation_type_select": "DOI"}}]}, "item_10001_relation_17": {"attribute_name": "Related site", "attribute_value_mlt": [{"subitem_relation_type_id": {"subitem_relation_type_id_text": "https://www.nature.com/articles/s41598-019-54927-z#article-info", "subitem_relation_type_select": "URI"}}]}, "item_10001_rights_15": {"attribute_name": "Rights", "attribute_value_mlt": [{"subitem_rights": "© 2020 The Author(s)"}]}, "item_10001_source_id_9": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "2045-2322", "subitem_source_identifier_type": "ISSN"}]}, "item_10001_version_type_20": {"attribute_name": "Author\u0027s flag", "attribute_value_mlt": [{"subitem_version_resource": "http://purl.org/coar/version/c_970fb48d4fbd8a85", "subitem_version_type": "VoR"}]}, "item_files": {"attribute_name": "ファイル情報", "attribute_type": "file", "attribute_value_mlt": [{"accessrole": "open_date", "date": [{"dateType": "Available", "dateValue": "2020-08-19"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "de Kerdrel-2020-Rapid and cost-effective gener.pdf", "filesize": [{"value": "3.5 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensefree": "Creative Commons Attribution 4.0 International(https://creativecommons.org/licenses/by/4.0/)", "licensetype": "license_free", "mimetype": "application/pdf", "size": 3500000.0, "url": {"label": "de Kerdrel-2020-Rapid and cost-effective gener", "url": "https://oist.repo.nii.ac.jp/record/1683/files/de Kerdrel-2020-Rapid and cost-effective gener.pdf"}, "version_id": "7e40fd2a-d314-4e6d-8185-f838b62fc66e"}]}, "item_language": {"attribute_name": "言語", "attribute_value_mlt": [{"subitem_language": "eng"}]}, "item_resource_type": {"attribute_name": "資源タイプ", "attribute_value_mlt": [{"resourcetype": "journal article", "resourceuri": "http://purl.org/coar/resource_type/c_6501"}]}, "item_title": "Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing", "subitem_title_language": "en"}]}, "item_type_id": "10001", "owner": "30", "path": ["27"], "permalink_uri": "https://oist.repo.nii.ac.jp/records/1683", "pubdate": {"attribute_name": "公開日", "attribute_value": "2020-08-19"}, "publish_date": "2020-08-19", "publish_status": "0", "recid": "1683", "relation": {}, "relation_version_is_last": true, "title": ["Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing"], "weko_shared_id": 30}
Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing
https://oist.repo.nii.ac.jp/records/1683
https://oist.repo.nii.ac.jp/records/1683e8318377-f3e4-4006-bb84-ca99d89b51e8
名前 / ファイル | ライセンス | アクション |
---|---|---|
de Kerdrel-2020-Rapid and cost-effective gener (3.5 MB)
|
Creative Commons Attribution 4.0 International(https://creativecommons.org/licenses/by/4.0/)
|
Item type | 学術雑誌論文 / Journal Article(1) | |||||
---|---|---|---|---|---|---|
公開日 | 2020-08-19 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing | |||||
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) |
de Kerdrel, Guillemette A.
× de Kerdrel, Guillemette A.× Andersen, Jeremy C.× Kennedy, Susan R.× Gillespie, Rosemary× Krehenwinkel, Henrik |
|||||
書誌情報 |
en : Scientific Reports 巻 10, 号 1, p. 78, 発行日 2020-01-09 |
|||||
抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems. | |||||
出版者 | ||||||
出版者 | Nature Research | |||||
ISSN | ||||||
収録物識別子タイプ | ISSN | |||||
収録物識別子 | 2045-2322 | |||||
PubMed番号 | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | PMID | |||||
関連識別子 | info:pmid/31919378 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1038/s41598-019-54927-z | |||||
権利 | ||||||
権利情報 | © 2020 The Author(s) | |||||
関連サイト | ||||||
識別子タイプ | URI | |||||
関連識別子 | https://www.nature.com/articles/s41598-019-54927-z#article-info | |||||
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 |