WEKO3
アイテム
{"_buckets": {"deposit": "2c42e1bc-2b3c-4b17-9c44-4c802a6e2627"}, "_deposit": {"created_by": 28, "id": "1036", "owners": [28], "pid": {"revision_id": 0, "type": "depid", "value": "1036"}, "status": "published"}, "_oai": {"id": "oai:oist.repo.nii.ac.jp:00001036", "sets": ["44"]}, "author_link": ["5727", "5731", "5729", "5735", "5728", "5732", "5730", "5734", "5733", "5736"], "item_10001_biblio_info_7": {"attribute_name": "Bibliographic Information", "attribute_value_mlt": [{"bibliographicIssueDates": {"bibliographicIssueDate": "2019-04-08", "bibliographicIssueDateType": "Issued"}, "bibliographicIssueNumber": "1", "bibliographicPageStart": "275", "bibliographicVolumeNumber": "20", "bibliographic_titles": [{}, {"bibliographic_title": "BMC Genomics", "bibliographic_titleLang": "en"}]}]}, "item_10001_creator_3": {"attribute_name": "Author", "attribute_type": "creator", "attribute_value_mlt": [{"creatorNames": [{"creatorName": "Wallberg, Andreas"}], "nameIdentifiers": [{"nameIdentifier": "5727", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Bunikis, Ignas"}], "nameIdentifiers": [{"nameIdentifier": "5728", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Pettersson, Olga Vinnere"}], "nameIdentifiers": [{"nameIdentifier": "5729", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Mosbech, Mai-Britt"}], "nameIdentifiers": [{"nameIdentifier": "5730", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Childers, Anna K."}], "nameIdentifiers": [{"nameIdentifier": "5731", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Evans, Jay D."}], "nameIdentifiers": [{"nameIdentifier": "5732", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Mikheyev, Alexander S."}], "nameIdentifiers": [{"nameIdentifier": "5733", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Robertson, Hugh M."}], "nameIdentifiers": [{"nameIdentifier": "5734", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Robinson, Gene E."}], "nameIdentifiers": [{"nameIdentifier": "5735", "nameIdentifierScheme": "WEKO"}]}, {"creatorNames": [{"creatorName": "Webster, Matthew T."}], "nameIdentifiers": [{"nameIdentifier": "5736", "nameIdentifierScheme": "WEKO"}]}]}, "item_10001_description_5": {"attribute_name": "Abstract", "attribute_value_mlt": [{"subitem_description": "Background: The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.\n\nResults: Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor \u003e98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.\n\nConclusions: The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.", "subitem_description_type": "Other"}]}, "item_10001_publisher_8": {"attribute_name": "Publisher", "attribute_value_mlt": [{"subitem_publisher": "BioMed Central Ltd"}]}, "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/30961563", "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/10.1186/s12864-019-5642-0", "subitem_relation_type_select": "DOI"}}]}, "item_10001_relation_16": {"attribute_name": "情報源", "attribute_value_mlt": [{"subitem_relation_name": [{"subitem_relation_name_text": "https://creativecommons.org/licenses/by/4.0/"}]}]}, "item_10001_relation_17": {"attribute_name": "Related site", "attribute_value_mlt": [{"subitem_relation_type_id": {"subitem_relation_type_id_text": "https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5642-0", "subitem_relation_type_select": "URI"}}]}, "item_10001_rights_15": {"attribute_name": "Rights", "attribute_value_mlt": [{"subitem_rights": "© 2019 The Author(s)."}]}, "item_10001_source_id_9": {"attribute_name": "ISSN", "attribute_value_mlt": [{"subitem_source_identifier": "1471-2164", "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": "2019-07-26"}], "displaytype": "detail", "download_preview_message": "", "file_order": 0, "filename": "Wallberg-2019-A hybrid de novo genome assembly.pdf", "filesize": [{"value": "2.2 MB"}], "format": "application/pdf", "future_date_message": "", "is_thumbnail": false, "licensefree": "Creative Commons\nAttribution 4.0 International\n(https://creativecommons.org/licenses/by/4.0/)", "licensetype": "license_free", "mimetype": "application/pdf", "size": 2200000.0, "url": {"label": "Wallberg-2019-A hybrid de novo genome assembly", "url": "https://oist.repo.nii.ac.jp/record/1036/files/Wallberg-2019-A hybrid de novo genome assembly.pdf"}, "version_id": "d3e40d89-7a3e-4c6f-a472-d69e23cb2187"}]}, "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": "A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds", "item_titles": {"attribute_name": "タイトル", "attribute_value_mlt": [{"subitem_title": "A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds", "subitem_title_language": "en"}]}, "item_type_id": "10001", "owner": "28", "path": ["44"], "permalink_uri": "https://oist.repo.nii.ac.jp/records/1036", "pubdate": {"attribute_name": "公開日", "attribute_value": "2019-07-26"}, "publish_date": "2019-07-26", "publish_status": "0", "recid": "1036", "relation": {}, "relation_version_is_last": true, "title": ["A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds"], "weko_shared_id": 28}
A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds
https://oist.repo.nii.ac.jp/records/1036
https://oist.repo.nii.ac.jp/records/103617432346-72a4-4799-a59c-748898e4b8c1
名前 / ファイル | ライセンス | アクション |
---|---|---|
Wallberg-2019-A hybrid de novo genome assembly (2.2 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 | 2019-07-26 | |||||
タイトル | ||||||
言語 | en | |||||
タイトル | A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds | |||||
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) |
Wallberg, Andreas
× Wallberg, Andreas× Bunikis, Ignas× Pettersson, Olga Vinnere× Mosbech, Mai-Britt× Childers, Anna K.× Evans, Jay D.× Mikheyev, Alexander S.× Robertson, Hugh M.× Robinson, Gene E.× Webster, Matthew T. |
|||||
書誌情報 |
en : BMC Genomics 巻 20, 号 1, p. 275, 発行日 2019-04-08 |
|||||
抄録 | ||||||
内容記述タイプ | Other | |||||
内容記述 | Background: The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map. Results: Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor >98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features. Conclusions: The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics. |
|||||
出版者 | ||||||
出版者 | BioMed Central Ltd | |||||
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/30961563 | |||||
DOI | ||||||
関連タイプ | isIdenticalTo | |||||
識別子タイプ | DOI | |||||
関連識別子 | info:doi/10.1186/s12864-019-5642-0 | |||||
権利 | ||||||
権利情報 | © 2019 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/s12864-019-5642-0 | |||||
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 |