Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes

Japanese chestnut ( Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar 'Tsukuba' by combining Nanopore long reads and Hi-C sequencing. The final as...

Full description

Saved in:
Bibliographic Details
Published in:Frontiers in plant science 2022-11, Vol.13, p.1049253-1049253
Main Authors: Wang, Jiawei, Hong, Po, Qiao, Qian, Zhu, Dongzi, Zhang, Lisi, Lin, Ke, Sun, Shan, Jiang, Shuna, Shen, Bingxue, Zhang, Shizhong, Liu, Qingzhong
Format: Article
Language:English
Subjects:
evolution
genome sequencing
Hi-C
japanese chestnut
nanopore
Plant Science
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3
cites cdi_FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3
container_end_page 1049253
container_issue
container_start_page 1049253
container_title Frontiers in plant science
container_volume 13
creator Wang, Jiawei
Hong, Po
Qiao, Qian
Zhu, Dongzi
Zhang, Lisi
Lin, Ke
Sun, Shan
Jiang, Shuna
Shen, Bingxue
Zhang, Shizhong
Liu, Qingzhong
description Japanese chestnut ( Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar 'Tsukuba' by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.
doi_str_mv 10.3389/fpls.2022.1049253
format article
fullrecord <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_aaedfa235f264e3a8b603dac3765471a</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_aaedfa235f264e3a8b603dac3765471a</doaj_id><sourcerecordid>2754856577</sourcerecordid><originalsourceid>FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3</originalsourceid><addsrcrecordid>eNpVkU1v1DAQhi0EolXpD-CCfCyHLI6_4lyQ0IqPokpcQOJmTZzJblZOHGzvVv33eNmlan3xzHjex_a8hLyt2UoI034YFp9WnHG-qplsuRIvyGWttayk5r9fPokvyHVKO1aWYqxtm9fkQmhVG8X0JdmttzFMIYUJK48H9HSDc0kopIRT5x_oEsNh7DHRGe_pOKdxs82pBDnQ77DAjAmp22LK8z7TG7qGlEsRqIs4Qwb6_kxMb8irAXzC6_N-RX59-fxz_a26-_H1dv3prnJSq1w5UYtaKomIynGJbWek6xol-kEbVMAbGExvmBnKHzrdD9AqaAdg2kgQfS-uyO2J2wfY2SWOE8QHG2C0_wohbizEPDqPFgCLngs1cC1RQOEx0YMTjVayqaGwPp5Yy76bsHc45wj-GfT5yTxu7SYcbNtILrUogJszIIY_-zIlO43JofdlRmGfLG-UNEqrpimt9anVxZBSxOHxmprZo-X2aLk9Wm7PlhfNu6fve1T8N1j8BYMFqxc</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2754856577</pqid></control><display><type>article</type><title>Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes</title><source>PMC (PubMed Central)</source><creator>Wang, Jiawei ; Hong, Po ; Qiao, Qian ; Zhu, Dongzi ; Zhang, Lisi ; Lin, Ke ; Sun, Shan ; Jiang, Shuna ; Shen, Bingxue ; Zhang, Shizhong ; Liu, Qingzhong</creator><creatorcontrib>Wang, Jiawei ; Hong, Po ; Qiao, Qian ; Zhu, Dongzi ; Zhang, Lisi ; Lin, Ke ; Sun, Shan ; Jiang, Shuna ; Shen, Bingxue ; Zhang, Shizhong ; Liu, Qingzhong</creatorcontrib><description>Japanese chestnut ( Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar 'Tsukuba' by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.</description><identifier>ISSN: 1664-462X</identifier><identifier>EISSN: 1664-462X</identifier><identifier>DOI: 10.3389/fpls.2022.1049253</identifier><identifier>PMID: 36518506</identifier><language>eng</language><publisher>Switzerland: Frontiers Media S.A</publisher><subject>evolution ; genome sequencing ; Hi-C ; japanese chestnut ; nanopore ; Plant Science</subject><ispartof>Frontiers in plant science, 2022-11, Vol.13, p.1049253-1049253</ispartof><rights>Copyright © 2022 Wang, Hong, Qiao, Zhu, Zhang, Lin, Sun, Jiang, Shen, Zhang and Liu.</rights><rights>Copyright © 2022 Wang, Hong, Qiao, Zhu, Zhang, Lin, Sun, Jiang, Shen, Zhang and Liu 2022 Wang, Hong, Qiao, Zhu, Zhang, Lin, Sun, Jiang, Shen, Zhang and Liu</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3</citedby><cites>FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9742463/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9742463/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36518506$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Jiawei</creatorcontrib><creatorcontrib>Hong, Po</creatorcontrib><creatorcontrib>Qiao, Qian</creatorcontrib><creatorcontrib>Zhu, Dongzi</creatorcontrib><creatorcontrib>Zhang, Lisi</creatorcontrib><creatorcontrib>Lin, Ke</creatorcontrib><creatorcontrib>Sun, Shan</creatorcontrib><creatorcontrib>Jiang, Shuna</creatorcontrib><creatorcontrib>Shen, Bingxue</creatorcontrib><creatorcontrib>Zhang, Shizhong</creatorcontrib><creatorcontrib>Liu, Qingzhong</creatorcontrib><title>Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes</title><title>Frontiers in plant science</title><addtitle>Front Plant Sci</addtitle><description>Japanese chestnut ( Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar 'Tsukuba' by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.</description><subject>evolution</subject><subject>genome sequencing</subject><subject>Hi-C</subject><subject>japanese chestnut</subject><subject>nanopore</subject><subject>Plant Science</subject><issn>1664-462X</issn><issn>1664-462X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNpVkU1v1DAQhi0EolXpD-CCfCyHLI6_4lyQ0IqPokpcQOJmTZzJblZOHGzvVv33eNmlan3xzHjex_a8hLyt2UoI034YFp9WnHG-qplsuRIvyGWttayk5r9fPokvyHVKO1aWYqxtm9fkQmhVG8X0JdmttzFMIYUJK48H9HSDc0kopIRT5x_oEsNh7DHRGe_pOKdxs82pBDnQ77DAjAmp22LK8z7TG7qGlEsRqIs4Qwb6_kxMb8irAXzC6_N-RX59-fxz_a26-_H1dv3prnJSq1w5UYtaKomIynGJbWek6xol-kEbVMAbGExvmBnKHzrdD9AqaAdg2kgQfS-uyO2J2wfY2SWOE8QHG2C0_wohbizEPDqPFgCLngs1cC1RQOEx0YMTjVayqaGwPp5Yy76bsHc45wj-GfT5yTxu7SYcbNtILrUogJszIIY_-zIlO43JofdlRmGfLG-UNEqrpimt9anVxZBSxOHxmprZo-X2aLk9Wm7PlhfNu6fve1T8N1j8BYMFqxc</recordid><startdate>20221128</startdate><enddate>20221128</enddate><creator>Wang, Jiawei</creator><creator>Hong, Po</creator><creator>Qiao, Qian</creator><creator>Zhu, Dongzi</creator><creator>Zhang, Lisi</creator><creator>Lin, Ke</creator><creator>Sun, Shan</creator><creator>Jiang, Shuna</creator><creator>Shen, Bingxue</creator><creator>Zhang, Shizhong</creator><creator>Liu, Qingzhong</creator><general>Frontiers Media S.A</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20221128</creationdate><title>Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes</title><author>Wang, Jiawei ; Hong, Po ; Qiao, Qian ; Zhu, Dongzi ; Zhang, Lisi ; Lin, Ke ; Sun, Shan ; Jiang, Shuna ; Shen, Bingxue ; Zhang, Shizhong ; Liu, Qingzhong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>evolution</topic><topic>genome sequencing</topic><topic>Hi-C</topic><topic>japanese chestnut</topic><topic>nanopore</topic><topic>Plant Science</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Jiawei</creatorcontrib><creatorcontrib>Hong, Po</creatorcontrib><creatorcontrib>Qiao, Qian</creatorcontrib><creatorcontrib>Zhu, Dongzi</creatorcontrib><creatorcontrib>Zhang, Lisi</creatorcontrib><creatorcontrib>Lin, Ke</creatorcontrib><creatorcontrib>Sun, Shan</creatorcontrib><creatorcontrib>Jiang, Shuna</creatorcontrib><creatorcontrib>Shen, Bingxue</creatorcontrib><creatorcontrib>Zhang, Shizhong</creatorcontrib><creatorcontrib>Liu, Qingzhong</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Frontiers in plant science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Jiawei</au><au>Hong, Po</au><au>Qiao, Qian</au><au>Zhu, Dongzi</au><au>Zhang, Lisi</au><au>Lin, Ke</au><au>Sun, Shan</au><au>Jiang, Shuna</au><au>Shen, Bingxue</au><au>Zhang, Shizhong</au><au>Liu, Qingzhong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes</atitle><jtitle>Frontiers in plant science</jtitle><addtitle>Front Plant Sci</addtitle><date>2022-11-28</date><risdate>2022</risdate><volume>13</volume><spage>1049253</spage><epage>1049253</epage><pages>1049253-1049253</pages><issn>1664-462X</issn><eissn>1664-462X</eissn><abstract>Japanese chestnut ( Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar 'Tsukuba' by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.</abstract><cop>Switzerland</cop><pub>Frontiers Media S.A</pub><pmid>36518506</pmid><doi>10.3389/fpls.2022.1049253</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1664-462X
ispartof Frontiers in plant science, 2022-11, Vol.13, p.1049253-1049253
issn 1664-462X
1664-462X
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_aaedfa235f264e3a8b603dac3765471a
source PMC (PubMed Central)
subjects evolution
genome sequencing
Hi-C
japanese chestnut
nanopore
Plant Science
title Chromosome-level genome assembly provides new insights into Japanese chestnut ( Castanea crenata ) genomes
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-23T04%3A39%3A43IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Chromosome-level%20genome%20assembly%20provides%20new%20insights%20into%20Japanese%20chestnut%20(%20Castanea%20crenata%20)%20genomes&rft.jtitle=Frontiers%20in%20plant%20science&rft.au=Wang,%20Jiawei&rft.date=2022-11-28&rft.volume=13&rft.spage=1049253&rft.epage=1049253&rft.pages=1049253-1049253&rft.issn=1664-462X&rft.eissn=1664-462X&rft_id=info:doi/10.3389/fpls.2022.1049253&rft_dat=%3Cproquest_doaj_%3E2754856577%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c465t-c3131454eee5c24e9b84cb753df68e5a27af8d808f518b6dfa95a9fa0684a3dd3%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2754856577&rft_id=info:pmid/36518506&rfr_iscdi=true