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Article(id=1311625833480024599, tenantId=1146029695717560320, journalId=1306273872116547672, issueId=1311625833022845462, articleNumber=null, orderNo=null, doi=10.16819/j.1001-7216.2026.250213, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1740412800000, receivedDateStr=2025-02-25, revisedDate=1741622400000, revisedDateStr=2025-03-11, acceptedDate=null, acceptedDateStr=null, onlineDate=1790645567531, onlineDateStr=2026-09-29, pubDate=1788969600000, pubDateStr=2026-09-10, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1790645567531, onlineIssueDateStr=2026-09-29, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1790645567531, creator=13701087609, updateTime=1790645567531, updator=13701087609, issue=Issue{id=1311625833022845462, tenantId=1146029695717560320, journalId=1306273872116547672, year='2026', volume='40', issue='5', pageStart='569', pageEnd='704', issueExtLink='null', onlineDate='null', pubDate='1788969600000', pubDateStr='2026-09-10', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=1, specialIssue=null, createTime=1790645567421, creator='13701087609', updateTime=1790746157512, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1312047738519384984, tenantId=1146029695717560320, journalId=1306273872116547672, issueId=1311625833022845462, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1312047738519384985, tenantId=1146029695717560320, journalId=1306273872116547672, issueId=1311625833022845462, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=598, endPage=606, ext={EN=ArticleExt(id=1311625833672962584, articleId=1311625833480024599, tenantId=1146029695717560320, journalId=1306273872116547672, language=EN, title=A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima, columnId=1307407385149071973, journalTitle=Chinese Journal of Rice Science, columnName=Research Papers, runingTitle=null, highlight=null, articleAbstract=
Objective

Transposable elements (TEs) are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice. However, due to the highly repetitive nature of TE sequences, their identification typically requires high-quality genome sequences. Currently, the limited genomic resources for African cultivated rice (Oryza glaberrima, Og) hinder systematic investigations into TE diversity and its contributions to the Og domestication process.

Method

We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions (11 Og and 10 Oryza barthii [Ob]). We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.

Result

The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb, with 61.7% of the TE variations larger than 1 kb. The total number of TE variations in the Ob accessions was greater than that in the Og accessions. A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process, which were significantly enriched in biological processes related to basic metabolism. Notably, 30 genes with known functions were involved in the independent domestication of Og.

Conclusion

This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process. The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.

, authors=Xiaoxia LI1, 2, Tianchi ZHANG1, 2, Wenchuang HE2, Huiying HE2, Nan PAN2, Yifan LIU2, Qian QIAN1, 2, 3, Lianguang SHANG2, 3, *, authorsList=Xiaoxia LI, Tianchi ZHANG, Wenchuang HE, Huiying HE, Nan PAN, Yifan LIU, Qian QIAN, Lianguang SHANG, authorCompany=null, correspAuthors=Lianguang SHANG, authorNote=

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These authors contributed equally to this work

, correspAuthorsNote=

*

email:
, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1311625833912037913, articleId=1311625833480024599, tenantId=1146029695717560320, journalId=1306273872116547672, language=CN, title=泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用, columnId=1307407385430090343, journalTitle=中国水稻科学, columnName=研究报告, runingTitle=null, highlight=null, articleAbstract=
目的

转座子（TE）是水稻遗传多样性的重要来源，在亚洲栽培稻（Oryza sativa）的驯化过程中发挥了关键作用。然而，由于TE序列的高度重复性，其鉴定通常依赖于高质量的基因组序列。目前，非洲栽培稻（Oryza glaberrima, Og）的基因组资源有限，导致对其TE的多样性及其在驯化过程中的贡献仍然缺乏系统性研究。

方法

本研究基于11份Og和10份短舌野生稻（Oryza barthii, Ob）的染色体级别的基因组序列，构建了Og和Ob群体的高精度泛TE变异图谱。通过对该图谱进行选择性分析，鉴定了854个在Og驯化过程中受到选择的TE变异。

结果

该泛TE图谱共包含17, 097个高质量的TE变异，覆盖基因组总长度39.1 Mb，其中61.7%的TE变异长度超过1 kb。Ob群体的TE变异总数高于Og群体。在Og驯化过程中，共鉴定出658个含受选择TE变异的基因，这些基因显著富集于基础代谢相关的生物过程，其中包括30个在Og独立驯化过程中发挥作用的已知功能基因。

结论

本研究揭示了TE变异是Og驯化过程中表型变异的重要来源，构建的高质量泛TE变异图谱不仅丰富了水稻育种的可用变异库，也为Og种质资源的遗传改良提供了重要的理论依据和资源支持。

, authors=李笑霞1, 2, 张天驰1, 2, 贺文闯2, 贺慧英2, 盘楠2, 刘祎凡2, 钱前1, 2, 3, 商连光2, 3, *, authorsList=李笑霞, 张天驰, 贺文闯, 贺慧英, 盘楠, 刘祎凡, 钱前, 商连光, authorCompany=null, correspAuthors=商连光, authorNote=

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共同第一作者

, correspAuthorsNote=

*

email:
, copyrightStatement=作者同意论文在本刊发表,论文的数字化复制权、发行权、汇编权及信息网络传播权即转让本刊编辑部。论文的著作权转让费在本刊稿酬中一次性支付。, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=ZB4PWsd/ezZYUx7/bvcGQQ==, magXml=JzORCfVFFtT8VcZcB4Fyfg==, pdfUrl=null, pdf=nndwBO08NdVARdOkaYQcPQ==, pdfFileSize=847852, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=b48prTM60BdeXjFgN2K4OQ==, mapNumber=null, fund=null)}, authors=[Author(id=1312069793126122092, tenantId=1146029695717560320, journalId=1306273872116547672, articleId=1311625833480024599, orderNo=0, firstName=null, middleName=null, lastName=null, nameCn=null, orcid=null, stid=null, country=null, authorPic=null, dead=0, email=null, emailSecond=null, emailThird=null, correspondingAuthor=0, authorType=1, ext={EN=AuthorExt(id=1312069793210008175, tenantId=1146029695717560320, journalId=1306273872116547672, articleId=1311625833480024599, authorId=1312069793126122092, language=EN, stringName=Xiaoxia LI, firstName=Xiaoxia, middleName=null, lastName=LI, prefix=null, suffix=null, authorComment=null, nameInitials=null, affiliation=null, department=null, xref=1, 2, address=1Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
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泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用
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李笑霞 1, 2 , 张天驰 1, 2 , 贺文闯 2 , 贺慧英 2 , 盘楠 2 , 刘祎凡 2 , 钱前 1, 2, 3 , 商连光 2, 3, *
中国水稻科学 | 研究报告 2026,40(5): 598-606
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中国水稻科学 |研究报告 2026 , 40 (5) : 598 -606
泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用
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李笑霞1, 2, 张天驰1, 2, 贺文闯2, 贺慧英2, 盘楠2, 刘祎凡2, 钱前1, 2, 3, 商连光2, 3, *
作者信息
  • 1沈阳农业大学 水稻研究所，沈阳 110161
  • 2中国农业科学院 深圳农业基因组研究所（岭南现代农业科学与技术广东省实验室深圳分中心），深圳 518120
  • 3崖州湾国家实验室，三亚 572024
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#

共同第一作者

A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima
Xiaoxia LI1, 2, Tianchi ZHANG1, 2, Wenchuang HE2, Huiying HE2, Nan PAN2, Yifan LIU2, Qian QIAN1, 2, 3, Lianguang SHANG2, 3, *
Affiliations
  • 1Rice Research Institute, Shenyang Agricultural University, Shenyang 110161, China
  • 2Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
  • 3Yazhouwan National Laboratory, Sanya 572024, China
    • Corresponding Author:

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出版时间: 2026-09-10 doi: 10.16819/j.1001-7216.2026.250213
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摘要
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目的

转座子（TE）是水稻遗传多样性的重要来源，在亚洲栽培稻（Oryza sativa）的驯化过程中发挥了关键作用。然而，由于TE序列的高度重复性，其鉴定通常依赖于高质量的基因组序列。目前，非洲栽培稻（Oryza glaberrima, Og）的基因组资源有限，导致对其TE的多样性及其在驯化过程中的贡献仍然缺乏系统性研究。

方法

本研究基于11份Og和10份短舌野生稻（Oryza barthii, Ob）的染色体级别的基因组序列，构建了Og和Ob群体的高精度泛TE变异图谱。通过对该图谱进行选择性分析，鉴定了854个在Og驯化过程中受到选择的TE变异。

结果

该泛TE图谱共包含17, 097个高质量的TE变异，覆盖基因组总长度39.1 Mb，其中61.7%的TE变异长度超过1 kb。Ob群体的TE变异总数高于Og群体。在Og驯化过程中，共鉴定出658个含受选择TE变异的基因，这些基因显著富集于基础代谢相关的生物过程，其中包括30个在Og独立驯化过程中发挥作用的已知功能基因。

结论

本研究揭示了TE变异是Og驯化过程中表型变异的重要来源，构建的高质量泛TE变异图谱不仅丰富了水稻育种的可用变异库，也为Og种质资源的遗传改良提供了重要的理论依据和资源支持。

非洲栽培稻  /  短舌野生稻  /  转座子  /  泛基因组  /  驯化
Objective

Transposable elements (TEs) are a significant source of genetic diversity in rice and play a crucial role in the domestication process of Asian cultivated rice. However, due to the highly repetitive nature of TE sequences, their identification typically requires high-quality genome sequences. Currently, the limited genomic resources for African cultivated rice (Oryza glaberrima, Og) hinder systematic investigations into TE diversity and its contributions to the Og domestication process.

Method

We constructed a high-resolution pan-TE variation map using the chromosome-level genomes of 21 accessions (11 Og and 10 Oryza barthii [Ob]). We estimated the divergence of each TE variation across the genome using FST analysis and identified 854 selected TE variations putatively involved in the Og domestication process.

Result

The pan-TE variation map comprises 17,097 non-redundant high-quality TE variations with a total length of 39.1 Mb, with 61.7% of the TE variations larger than 1 kb. The total number of TE variations in the Ob accessions was greater than that in the Og accessions. A total of 658 genes harboring selected TE variations were identified as potentially involved in the Og domestication process, which were significantly enriched in biological processes related to basic metabolism. Notably, 30 genes with known functions were involved in the independent domestication of Og.

Conclusion

This study highlights the significant role of TE variations as a source of phenotypic diversity during the Og domestication process. The high-quality pan-TE variation map not only enriches the available variation library for rice breeding but also provides critical theoretical foundations and resource support for the genetic improvement of Og germplasm.

Oryza glaberrima  /  Oryza barthii  /  transposable element  /  pan-genome  /  domestication
李笑霞, 张天驰, 贺文闯, 贺慧英, 盘楠, 刘祎凡, 钱前, 商连光. 泛基因组图谱揭示转座子在非洲栽培稻驯化中的作用. 中国水稻科学, 2026 , 40 (5) : 598 -606 . DOI: 10.16819/j.1001-7216.2026.250213
Xiaoxia LI, Tianchi ZHANG, Wenchuang HE, Huiying HE, Nan PAN, Yifan LIU, Qian QIAN, Lianguang SHANG. A Pan-genome Map Reveals the Contribution of Transposable Elements to Domestication of Oryza glaberrima[J]. Chinese Journal of Rice Science, 2026 , 40 (5) : 598 -606 . DOI: 10.16819/j.1001-7216.2026.250213
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  • 国家重点研发计划资助项目(2024YFF1000400)
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doi: 10.16819/j.1001-7216.2026.250213
  • 接收时间：2025-02-25
  • 首发时间：2026-09-29
  • 出版时间：2026-09-10
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  • 收稿日期：2025-02-25
  • 修回日期：2025-03-11
基金
国家重点研发计划资助项目(2024YFF1000400)
作者信息
    1沈阳农业大学 水稻研究所，沈阳 110161
    2中国农业科学院 深圳农业基因组研究所（岭南现代农业科学与技术广东省实验室深圳分中心），深圳 518120
    3崖州湾国家实验室，三亚 572024

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2种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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