Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Author
Abstract
Suggested Citation
DOI: 10.1038/s41467-023-37004-y
Download full text from publisher
References listed on IDEAS
- Yonghui Wu & Prasanna R Bhat & Timothy J Close & Stefano Lonardi, 2008. "Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph," PLOS Genetics, Public Library of Science, vol. 4(10), pages 1-11, October.
- Wensheng Wang & Ramil Mauleon & Zhiqiang Hu & Dmytro Chebotarov & Shuaishuai Tai & Zhichao Wu & Min Li & Tianqing Zheng & Roven Rommel Fuentes & Fan Zhang & Locedie Mansueto & Dario Copetti & Millicen, 2018. "Genomic variation in 3,010 diverse accessions of Asian cultivated rice," Nature, Nature, vol. 557(7703), pages 43-49, May.
- Michal Levy-Sakin & Steven Pastor & Yulia Mostovoy & Le Li & Alden K. Y. Leung & Jennifer McCaffrey & Eleanor Young & Ernest T. Lam & Alex R. Hastie & Karen H. Y. Wong & Claire Y. L. Chung & Walfred M, 2019. "Genome maps across 26 human populations reveal population-specific patterns of structural variation," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
- Daniel C. Jeffares & Clemency Jolly & Mimoza Hoti & Doug Speed & Liam Shaw & Charalampos Rallis & Francois Balloux & Christophe Dessimoz & Jürg Bähler & Fritz J. Sedlazeck, 2017. "Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast," Nature Communications, Nature, vol. 8(1), pages 1-11, April.
- Lun Zhao & Liang Xie & Qing Zhang & Weizhi Ouyang & Li Deng & Pengpeng Guan & Meng Ma & Yue Li & Ying Zhang & Qin Xiao & Jingwen Zhang & Hongmeijuan Li & Shunyao Wang & Jiangwei Man & Zhilin Cao & Qin, 2020. "Integrative analysis of reference epigenomes in 20 rice varieties," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Weixiong Long & Qiang He & Yitao Wang & Yu Wang & Jie Wang & Zhengqing Yuan & Meijia Wang & Wei Chen & Lihua Luo & Laiyang Luo & Weibiao Xu & Yonghui Li & Wei Li & Longan Yan & Yaohui Cai & Huilong Du, 2024. "Genome evolution and diversity of wild and cultivated rice species," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Paris Veltsos & Luis J. Madrigal-Roca & John K. Kelly, 2024. "Testing the evolutionary theory of inversion polymorphisms in the yellow monkeyflower (Mimulus guttatus)," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
- Xuezhu Liao & Dejin Xie & Tingting Bao & Mengmeng Hou & Cheng Li & Bao Nie & Shichao Sun & Dan Peng & Haixiao Hu & Hongru Wang & Yongfu Tao & Yu Zhang & Wei Li & Li Wang, 2024. "Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Zeyu Zheng & Mingjia Zhu & Jin Zhang & Xinfeng Liu & Liqiang Hou & Wenyu Liu & Shuai Yuan & Changhong Luo & Xinhao Yao & Jianquan Liu & Yongzhi Yang, 2024. "A sequence-aware merger of genomic structural variations at population scale," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
- Jin Li & Haifeng Guo & Qijin Lou & Yawen Zeng & Zhenhua Guo & Penghui Xu & Yunsong Gu & Shilei Gao & Bingxia Xu & Shichen Han & Runbin Su & Andong Zou & Wei Ye & Meng Zhang & Yingxiu Li & Xingming Sun, 2025. "Natural variation of indels in the CTB3 promoter confers cold tolerance in japonica rice," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Yingyan Yu & Zhen Zhang & Xiaorui Dong & Ruixin Yang & Zhongqu Duan & Zhen Xiang & Jun Li & Guichao Li & Fazhe Yan & Hongzhang Xue & Du Jiao & Jinyuan Lu & Huimin Lu & Wenmin Zhang & Yangzhen Wei & Sh, 2022. "Pangenomic analysis of Chinese gastric cancer," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
- Heng Du & Lei Zhou & Zhen Liu & Yue Zhuo & Meilin Zhang & Qianqian Huang & Shiyu Lu & Kai Xing & Li Jiang & Jian-Feng Liu, 2024. "The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Siyu Zhang & Zhe Ji & Wu Jiao & Chengbo Shen & Yaojun Qin & Yunzhi Huang & Menghan Huang & Shuming Kang & Xuan Liu & Shunqi Li & Zulong Mo & Ying Yu & Bingyu Jiang & Yanan Tian & Longfei Wang & Qingxi, 2025. "Natural variation of OsWRKY23 drives difference in nitrate use efficiency between indica and japonica rice," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
- Xi Wang & Juan Li & Linqian Han & Chengyong Liang & Jiaxin Li & Xiaoyang Shang & Xinxin Miao & Zi Luo & Wanchao Zhu & Zhao Li & Tianhuan Li & Yongwen Qi & Huihui Li & Xiaoduo Lu & Lin Li, 2023. "QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Liyuan Zhou & Qiongzi Qiu & Qing Zhou & Jianwei Li & Mengqian Yu & Kezhen Li & Lingling Xu & Xiaohui Ke & Haiming Xu & Bingjian Lu & Hui Wang & Weiguo Lu & Pengyuan Liu & Yan Lu, 2022. "Long-read sequencing unveils high-resolution HPV integration and its oncogenic progression in cervical cancer," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
- Taylor, Julian & Butler, David, 2017. "R Package ASMap: Efficient Genetic Linkage Map Construction and Diagnosis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 79(i06).
- Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
- Jinhyun Kim & Sungsik Kim & Huiran Yeom & Seo Woo Song & Kyoungseob Shin & Sangwook Bae & Han Suk Ryu & Ji Young Kim & Ahyoun Choi & Sumin Lee & Taehoon Ryu & Yeongjae Choi & Hamin Kim & Okju Kim & Yu, 2023. "Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
- Rujia Chen & Ning Xiao & Yue Lu & Tianyun Tao & Qianfeng Huang & Shuting Wang & Zhichao Wang & Mingli Chuan & Qing Bu & Zhou Lu & Hanyao Wang & Yanze Su & Yi Ji & Jianheng Ding & Ahmed Gharib & Huixin, 2023. "A de novo evolved gene contributes to rice grain shape difference between indica and japonica," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Tao Zhu & Chunjiao Xia & Ranran Yu & Xinkai Zhou & Xingbing Xu & Lin Wang & Zhanxiang Zong & Junjiao Yang & Yinmeng Liu & Luchang Ming & Yuxin You & Dijun Chen & Weibo Xie, 2024. "Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Huiying He & Yue Leng & Xinglan Cao & Yiwang Zhu & Xiaoxia Li & Qiaoling Yuan & Bin Zhang & Wenchuang He & Hua Wei & Xiangpei Liu & Qiang Xu & Mingliang Guo & Hong Zhang & Longbo Yang & Yang Lv & Xian, 2024. "The pan-tandem repeat map highlights multiallelic variants underlying gene expression and agronomic traits in rice," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Yu Chang & Yujie Fang & Jiahan Liu & Tiantian Ye & Xiaokai Li & Haifu Tu & Ying Ye & Yao Wang & Lizhong Xiong, 2024. "Stress-induced nuclear translocation of ONAC023 improves drought and heat tolerance through multiple processes in rice," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
- Cheng Ding & Guoting Chen & Shiping Luan & Runxin Gao & Yudong Fan & Ying Zhang & Xiaoting Wang & Guoliang Li & Mohamed F. Foda & Jiapei Yan & Xingwang Li, 2025. "Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
- Weixiong Long & Qiang He & Yitao Wang & Yu Wang & Jie Wang & Zhengqing Yuan & Meijia Wang & Wei Chen & Lihua Luo & Laiyang Luo & Weibiao Xu & Yonghui Li & Wei Li & Longan Yan & Yaohui Cai & Huilong Du, 2024. "Genome evolution and diversity of wild and cultivated rice species," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
- Tuomas Hämälä & Christopher Moore & Laura Cowan & Matthew Carlile & David Gopaulchan & Marie K. Brandrud & Siri Birkeland & Matthew Loose & Filip Kolář & Marcus A. Koch & Levi Yant, 2024. "Impact of whole-genome duplications on structural variant evolution in Cochlearia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Xuezhu Liao & Dejin Xie & Tingting Bao & Mengmeng Hou & Cheng Li & Bao Nie & Shichao Sun & Dan Peng & Haixiao Hu & Hongru Wang & Yongfu Tao & Yu Zhang & Wei Li & Li Wang, 2024. "Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Muhammad Junaid Zaghum & Kashir Ali & Sheng Teng, 2022. "Integrated Genetic and Omics Approaches for the Regulation of Nutritional Activities in Rice ( Oryza sativa L.)," Agriculture, MDPI, vol. 12(11), pages 1-17, October.
- Naser Ansari-Pour & Yonglan Zheng & Toshio F. Yoshimatsu & Ayodele Sanni & Mustapha Ajani & Jean-Baptiste Reynier & Avraam Tapinos & Jason J. Pitt & Stefan Dentro & Anna Woodard & Padma Sheila Rajagop, 2021. "Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
- Hongbo Li & Shenhao Wang & Sen Chai & Zhiquan Yang & Qiqi Zhang & Hongjia Xin & Yuanchao Xu & Shengnan Lin & Xinxiu Chen & Zhiwang Yao & Qingyong Yang & Zhangjun Fei & Sanwen Huang & Zhonghua Zhang, 2022. "Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
- Sylvain Aubry, 2023. "Genebanking plant genetic resources in the postgenomic era," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 40(3), pages 961-971, September.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37004-y. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.