{"created":"2024-06-21T06:21:49.577755+00:00","id":2000209,"links":{},"metadata":{"_buckets":{"deposit":"c914a1cc-a401-4b14-9c2a-892f3a92e8ea"},"_deposit":{"created_by":12,"id":"2000209","owner":"12","owners":[12],"pid":{"revision_id":0,"type":"depid","value":"2000209"},"status":"published"},"_oai":{"id":"oai:obihiro.repo.nii.ac.jp:02000209","sets":["5"]},"author_link":["390","404"],"item_2_biblio_info_7":{"attribute_name":"書誌情報","attribute_value_mlt":[{"bibliographicIssueDates":{"bibliographicIssueDateType":"Issued"},"bibliographicIssueNumber":"6","bibliographicPageStart":"jkae080","bibliographicVolumeNumber":"14","bibliographic_titles":[{"bibliographic_title":"G3: Genes, Genomes, Genetics","bibliographic_titleLang":"en"}]}]},"item_2_description_19":{"attribute_name":"フォーマット","attribute_value_mlt":[{"subitem_description":"application/pdf","subitem_description_language":"en","subitem_description_type":"Other"}]},"item_2_description_5":{"attribute_name":"抄録","attribute_value_mlt":[{"subitem_description":"Potato and its wild relatives are distributed mainly in the Mexican highlands and central Andes of South America. The South American A-genome species, including cultivated potatoes, are reproductively isolated from Mexican diploid species. Whole-genome sequencing has disclosed genome structure and similarity, mostly in cultivated potatoes and their closely related species. In this study, we generated a chromosome-scale assembly of the genome of a Mexican diploid species, Solanum bulbocastanum Dun., using PacBio long-read sequencing, optical mapping, and Hi-C scaffolding technologies. The final sequence assembly consisted of 737.9 Mb, among which 647.0 Mb were anchored to the 12 chromosomes. Compared with chromosome-scale assemblies of S. lycopersicum (tomato), S. etuberosum (non-tuber-bearing species with E-genome), S. verrucosum, S. chacoense, S. multidissectum, and S. phureja (all four are A-genome species), the S. bulbocastnum genome was the shortest. It contained fewer transposable elements (56.2%) than A-genome species. A cluster analysis was performed based on pairwise ratios of syntenic regions among the seven chromosome-scale assemblies, showing that the A-genome species were first clustered as a distinct group. Then, this group was clustered with S. bulbocastanum. Sequence similarity in 1,624 single-copy orthologous gene groups among 36 Solanum species and clones separated S. bulbocastanum as a specific group, including other Mexican diploid species, from the A-genome species. Therefore, the S. bulbocastanum genome differs in genome structure and gene sequences from the A-genome species. These findings provide important insights into understanding and utilizing the genetic diversity of S. bulbocastanum and the other Mexican diploid species in potato breeding.","subitem_description_language":"en","subitem_description_type":"Abstract"}]},"item_2_publisher_8":{"attribute_name":"出版者","attribute_value_mlt":[{"subitem_publisher":"Genetics Society of America","subitem_publisher_language":"en"}]},"item_2_relation_13":{"attribute_name":"PubMed番号","attribute_value_mlt":[{"subitem_relation_type":"isIdenticalTo","subitem_relation_type_id":{"subitem_relation_type_id_text":"38608140","subitem_relation_type_select":"PMID"}}]},"item_2_relation_14":{"attribute_name":"DOI","attribute_value_mlt":[{"subitem_relation_type":"isIdenticalTo","subitem_relation_type_id":{"subitem_relation_type_id_text":"http://doi.org/10.1093/g3journal/jkae080","subitem_relation_type_select":"DOI"}}]},"item_2_rights_15":{"attribute_name":"権利","attribute_value_mlt":[{"subitem_rights":"The Author(s)","subitem_rights_language":"en"}]},"item_2_source_id_9":{"attribute_name":"ISSN","attribute_value_mlt":[{"subitem_source_identifier":"21601836","subitem_source_identifier_type":"EISSN"}]},"item_2_subject_21":{"attribute_name":"日本十進分類法","attribute_value_mlt":[{"subitem_subject":"615","subitem_subject_language":"ja","subitem_subject_scheme":"NDC"}]},"item_2_version_type_20":{"attribute_name":"著者版フラグ","attribute_value_mlt":[{"subitem_version_resource":"http://purl.org/coar/version/c_970fb48d4fbd8a85","subitem_version_type":"VoR"}]},"item_creator":{"attribute_name":"著者","attribute_type":"creator","attribute_value_mlt":[{"creatorNames":[{"creatorName":"Hosaka, Awie J.","creatorNameLang":"en"}]},{"creatorNames":[{"creatorName":"Sanetomo, Rena","creatorNameLang":"en"},{"creatorName":"實友, 玲奈","creatorNameLang":"ja"}],"familyNames":[{},{}],"givenNames":[{},{}],"nameIdentifiers":[{}]},{"creatorNames":[{"creatorName":"Hosaka, Kazuyoshi","creatorNameLang":"en"},{"creatorName":"保坂, 和良","creatorNameLang":"ja"}],"familyNames":[{},{}],"givenNames":[{},{}],"nameIdentifiers":[{},{},{}]}]},"item_files":{"attribute_name":"ファイル情報","attribute_type":"file","attribute_value_mlt":[{"accessrole":"open_access","date":[{"dateType":"Available","dateValue":"2024-06-21"}],"filename":"Hosaka_G3_14(6).pdf","filesize":[{"value":"2.6 MB"}],"format":"application/pdf","licensetype":"license_0","url":{"label":"Full Text","url":"https://obihiro.repo.nii.ac.jp/record/2000209/files/Hosaka_G3_14(6).pdf"},"version_id":"00f272f4-0e9f-49c6-b62b-b4a8ab734bff"}]},"item_keyword":{"attribute_name":"キーワード","attribute_value_mlt":[{"subitem_subject":"comparative genomics","subitem_subject_language":"en","subitem_subject_scheme":"Other"}]},"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 de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes","item_titles":{"attribute_name":"タイトル","attribute_value_mlt":[{"subitem_title":"A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes","subitem_title_language":"en"}]},"item_type_id":"2","owner":"12","path":["5"],"pubdate":{"attribute_name":"PubDate","attribute_value":"2024-06-21"},"publish_date":"2024-06-21","publish_status":"0","recid":"2000209","relation_version_is_last":true,"title":["A de novo genome assembly of Solanum bulbocastanum Dun., a Mexican diploid species reproductively isolated from the A-genome species, including cultivated potatoes"],"weko_creator_id":"12","weko_shared_id":-1},"updated":"2024-06-21T06:29:41.369444+00:00"}