Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations
Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic reso...
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| Published in | Cell Vol. 184; no. 13; pp. 3542 - 3558.e16 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
24.06.2021
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.
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•De novo assembly of 31 high-quality genomes for genetically diverse accessions•Pan-genome-scale resources and a graph-based genome reveal hidden SVs and gCNVs•The derived state of O. sativa SVs was inferred using the O. glaberrima assembly•SVs and gCNVs have shaped gene expression profiles and agronomic trait variations
A high-quality rice pan-genome of genetically diverse rice accessions is constructed through de novo genome assemblies, demonstrating the impact of structural variation and gene copy number variations on environmental adaptations and agronomic traits. |
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| AbstractList | Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research. Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research. Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research. [Display omitted] •De novo assembly of 31 high-quality genomes for genetically diverse accessions•Pan-genome-scale resources and a graph-based genome reveal hidden SVs and gCNVs•The derived state of O. sativa SVs was inferred using the O. glaberrima assembly•SVs and gCNVs have shaped gene expression profiles and agronomic trait variations A high-quality rice pan-genome of genetically diverse rice accessions is constructed through de novo genome assemblies, demonstrating the impact of structural variation and gene copy number variations on environmental adaptations and agronomic traits. |
| Author | Chen, Zhuo Li, Weitao Du, Huilong Liao, Yi Li, Xuanzhao He, Min Qin, Peng Li, Yan He, Qiang Wang, Yuping Li, Ting Chen, Weilan Fan, Shijun Yin, Junjie Gao, Qiang Chen, Xuewei Tu, Bin Zhang, Hongyu Li, Shigui Ou, Shujun Liang, Chengzhi Qian, Yangwen Jiang, Ning Wang, Jing Li, Xiuxiu Yuan, Hua Lu, Hongwei Ma, Bingtian Wang, Hao |
| Author_xml | – sequence: 1 givenname: Peng surname: Qin fullname: Qin, Peng email: qinpeng@sicau.edu.cn organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 2 givenname: Hongwei surname: Lu fullname: Lu, Hongwei organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 3 givenname: Huilong surname: Du fullname: Du, Huilong organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 4 givenname: Hao surname: Wang fullname: Wang, Hao organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 5 givenname: Weilan surname: Chen fullname: Chen, Weilan organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 6 givenname: Zhuo surname: Chen fullname: Chen, Zhuo organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 7 givenname: Qiang surname: He fullname: He, Qiang organization: School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China – sequence: 8 givenname: Shujun surname: Ou fullname: Ou, Shujun organization: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA – sequence: 9 givenname: Hongyu surname: Zhang fullname: Zhang, Hongyu organization: School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China – sequence: 10 givenname: Xuanzhao surname: Li fullname: Li, Xuanzhao organization: School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China – sequence: 11 givenname: Xiuxiu surname: Li fullname: Li, Xiuxiu organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 12 givenname: Yan surname: Li fullname: Li, Yan organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 13 givenname: Yi orcidid: 0000-0002-7724-1799 surname: Liao fullname: Liao, Yi organization: Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA – sequence: 14 givenname: Qiang surname: Gao fullname: Gao, Qiang organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 15 givenname: Bin surname: Tu fullname: Tu, Bin organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 16 givenname: Hua surname: Yuan fullname: Yuan, Hua organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 17 givenname: Bingtian surname: Ma fullname: Ma, Bingtian organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 18 givenname: Yuping surname: Wang fullname: Wang, Yuping organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 19 givenname: Yangwen surname: Qian fullname: Qian, Yangwen organization: Biogle Genome Editing Center, Changzhou, Jiangsu, China – sequence: 20 givenname: Shijun surname: Fan fullname: Fan, Shijun organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 21 givenname: Weitao surname: Li fullname: Li, Weitao organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 22 givenname: Jing surname: Wang fullname: Wang, Jing organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 23 givenname: Min surname: He fullname: He, Min organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 24 givenname: Junjie surname: Yin fullname: Yin, Junjie organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 25 givenname: Ting surname: Li fullname: Li, Ting organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 26 givenname: Ning surname: Jiang fullname: Jiang, Ning organization: Department of Horticulture, Michigan State University, East Lansing, MI, USA – sequence: 27 givenname: Xuewei surname: Chen fullname: Chen, Xuewei organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China – sequence: 28 givenname: Chengzhi orcidid: 0000-0001-8913-3552 surname: Liang fullname: Liang, Chengzhi email: cliang@genetics.ac.cn organization: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China – sequence: 29 givenname: Shigui surname: Li fullname: Li, Shigui email: lishigui@sicau.edu.cn organization: State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34051138$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1186/s13100-019-0193-0 10.1038/s41576-018-0024-z 10.1038/s41588-018-0040-0 10.1016/j.molp.2019.02.008 10.1186/s13059-019-1911-0 10.1073/pnas.0403715101 10.1093/bioinformatics/btv351 10.1038/s41477-019-0507-8 10.1038/s41477-019-0577-7 10.1038/s41586-020-2961-x 10.1038/ncomms15324 10.1038/s41588-018-0182-0 10.1073/pnas.1317360111 10.1038/s41467-019-13355-3 10.1093/bioinformatics/btu031 10.1186/s12284-018-0207-4 10.1093/nar/gkr1293 10.1038/nplants.2017.43 10.1105/tpc.15.00310 10.1186/s13059-019-1905-y 10.1038/nmeth.3317 10.1038/s41467-019-14197-9 10.1093/nar/gki458 10.1038/ng.548 10.1186/1939-8433-6-4 10.1038/nbt.4227 10.1371/journal.pcbi.1005944 10.1038/s41587-019-0201-4 10.1038/s41588-018-0041-z 10.1016/j.cell.2018.12.019 10.1186/s13059-020-1941-7 10.1016/j.cels.2015.07.012 10.1093/bioinformatics/btu077 10.1093/bioinformatics/btp352 10.1038/s41592-018-0001-7 10.1038/sdata.2018.79 10.1038/s41467-020-14779-y 10.1038/nplants.2015.124 10.1101/gr.241240.118 10.1073/pnas.1410068111 10.1007/s00299-015-1931-5 10.1038/nature03608 10.1038/s41588-018-0316-4 10.1101/gr.215087.116 10.1146/annurev-arplant-050718-100320 10.1016/j.molp.2018.11.005 10.1038/s41586-020-2947-8 10.1016/j.jgg.2017.05.003 10.1038/ng0508-491 10.1104/pp.20.00253 10.1534/genetics.105.044891 10.1038/nrg3373 10.1186/s12870-016-0711-x 10.3390/ijms21041344 10.1038/ng.3346 10.1038/s41467-017-01400-y 10.1104/pp.16.01177 10.1038/nrg.2015.25 10.1038/416701a 10.1038/s41588-018-0282-x 10.1038/s41586-018-0063-9 10.1038/s41597-020-0438-2 10.1016/j.cell.2010.10.027 10.1038/nbt.1621 10.1038/s41588-019-0427-6 10.1016/j.jgg.2018.10.007 10.1016/j.cell.2020.05.023 10.1111/tpj.13925 10.1093/jxb/erz198 10.1016/j.molp.2017.03.009 10.1126/science.aal3327 10.1038/s41576-019-0180-9 10.1104/pp.19.00386 10.1093/gigascience/gix119 10.1186/1471-2105-9-18 10.1101/gr.088997.108 10.1016/j.jgg.2020.10.006 10.1146/annurev-phyto-073009-114453 10.1093/bioinformatics/btp324 10.1104/pp.17.01310 10.1093/bib/bbs017 10.1270/jsbbs.18172 10.1016/j.cell.2013.04.010 10.1186/1471-2164-14-649 10.1016/j.cell.2020.05.021 10.1038/s41467-019-10820-x 10.1093/nar/gkq862 10.1016/j.tplants.2019.01.003 10.1007/s11103-016-0544-x 10.1101/gr.094052.109 10.1038/ng.806 |
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| References | Ma, Bennetzen (bib49) 2004; 101 Ou, Chen, Jiang (bib55) 2018; 46 Fuentes, Chebotarov, Duitama, Smith, De la Hoz, Mohiyuddin, Wing, McNally, Tatarinova, Grigoriev (bib19) 2019; 29 Kawahara, de la Bastide, Hamilton, Kanamori, McCombie, Ouyang, Schwartz, Tanaka, Wu, Zhou (bib34) 2013; 6 Hickey, Heller, Monlong, Sibbesen, Sirén, Eizenga, Dawson, Garrison, Novak, Paten (bib24) 2020; 21 Xie, Yoneyama, Yoneyama (bib84) 2010; 48 Ellinghaus, Kurtz, Willhoeft (bib18) 2008; 9 Kang, Sul, Service, Zaitlen, Kong, Freimer, Sabatti, Eskin (bib33) 2010; 42 Shen, Wang, Liu, Wu, Jin, Zhao, Xie, Zhu, Tang, Li (bib63) 2017; 8 Sasaki, Ashikari, Ueguchi-Tanaka, Itoh, Nishimura, Swapan, Ishiyama, Saito, Kobayashi, Khush (bib60) 2002; 416 Kidd, Graves, Newman, Fulton, Hayden, Malig, Kallicki, Kaul, Wilson, Eichler (bib36) 2010; 143 Wang, Mauleon, Hu, Chebotarov, Tai, Wu, Li, Zheng, Fuentes, Zhang (bib78) 2018; 557 Yao, Li, Yu, Ouyang (bib90) 2018; 7 Du, Liang (bib13) 2019; 10 Stanke, Morgenstern (bib68) 2005; 33 Alonge, Wang, Benoit, Soyk, Pereira, Zhang, Suresh, Ramakrishnan, Maumus, Ciren (bib3) 2020; 182 Yu, Wang, Xu, Feng, Yuan, Yu, Wang, Tang, Wei (bib92) 2013; 14 Du, Yu, Ma, Gao, Cao, Chen, Ma, Qi, Li, Zhao (bib14) 2017; 8 Walkowiak, Gao, Monat, Haberer, Kassa, Brinton, Ramirez-Gonzalez, Kolodziej, Delorean, Thambugala (bib74) 2020; 588 Stein, Yu, Copetti, Zwickl, Zhang, Zhang, Chougule, Gao, Iwata, Goicoechea (bib69) 2018; 50 Liu, Du, Li, Shen, Peng, Liu, Zhou, Zhang, Liu, Shi (bib47) 2020; 182 Goel, Sun, Jiao, Schneeberger (bib21) 2019; 20 Zhao, Feng, Lu, Li, Wang, Tian, Zhan, Lu, Zhang, Huang (bib96) 2018; 50 Jukes, Cantor (bib32) 1969 Wang, Tang, Debarry, Tan, Li, Wang, Lee, Jin, Marler, Guo (bib75) 2012; 40 Li, Handsaker, Wysoker, Fennell, Ruan, Homer, Marth, Abecasis, Durbin (bib43) 2009; 25 Garrison, Sirén, Novak, Hickey, Eizenga, Dawson, Jones, Garg, Markello, Lin (bib20) 2018; 36 Li, Durbin (bib42) 2009; 25 Weischenfeldt, Symmons, Spitz, Korbel (bib81) 2013; 14 Hu, Wang, Wu, Sun, Li, Lu, Fu, Shi, Xu, Ruan (bib26) 2018; 5 Lye, Purugganan (bib48) 2019; 24 Zhang, Chen, Xing, Kudrna, Yao, Copetti, Mu, Li, Song, Xie (bib94) 2016; 113 Delteil, Gobbato, Cayrol, Estevan, Michel-Romiti, Dievart, Kroj, Morel (bib10) 2016; 16 Jones, Binns, Chang, Fraser, Li, McAnulla, McWilliam, Maslen, Mitchell, Nuka (bib31) 2014; 30 Simão, Waterhouse, Ioannidis, Kriventseva, Zdobnov (bib65) 2015; 31 Wang, Xiong, Hu, Jiang, Yu, Xu, Fang, Zeng, Xu, Xu (bib76) 2015; 47 Shi, Liang (bib64) 2019; 180 Yang, Ge, Yang, Qin, Sun, Wang, Li, Liu, Wu, Wang (bib89) 2019; 10 Yang, Liu, Gao, Gui, Chen, Yang, Huang, Deng, Luo, He (bib88) 2019; 51 Sun, Zhou, Chen, Shi, Zhao, Zhao, Song, Zhang, Cui, Dong (bib71) 2018; 50 Su, Gu, Peterson (bib70) 2019; 12 Thorvaldsdóttir, Robinson, Mesirov (bib72) 2013; 14 He, Wang, Wu, Chen, Lin, Cheng, Liu, Chen, Liao (bib23) 2014; 20 Chen, Huang, Tian, Wing, Han (bib8) 2019; 70 Kim, Paggi, Park, Bennett, Salzberg (bib38) 2019; 37 Marçais, Delcher, Phillippy, Coston, Salzberg, Zimin (bib50) 2018; 14 Ou, Jiang (bib53) 2018; 176 Audano, Sulovari, Graves-Lindsay, Cantsilieris, Sorensen, Welch, Dougherty, Nelson, Shah, Dutcher (bib4) 2019; 176 Duan, Xu, Zeng, Zhang, Geng, Zhang, Huang, Huang, Xu, Ge (bib15) 2017; 10 Yang, Luquette, Gehlenborg, Xi, Haseley, Hsieh, Zhang, Ren, Protopopov, Chin (bib87) 2013; 153 Oikawa, Maeda, Oguchi, Yamaguchi, Tanabe, Ebana, Yano, Ebitani, Izawa (bib52) 2015; 27 Rakocevic, Semenyuk, Lee, Spencer, Browning, Johnson, Arsenijevic, Nadj, Ghose, Suciu (bib58) 2019; 51 Dudchenko, Batra, Omer, Nyquist, Hoeger, Durand, Shamim, Machol, Lander, Aiden, Aiden (bib16) 2017; 356 Zhou, Chebotarov, Kudrna, Llaca, Lee, Rajasekar, Mohammed, Al-Bader, Sobel-Sorenson, Parakkal (bib98) 2020; 7 Zhou, Minio, Massonnet, Solares, Lv, Beridze, Cantu, Gaut (bib97) 2019; 5 Wing, Purugganan, Zhang (bib82) 2018; 19 Xiong, He, Lai, Dooner, Du (bib86) 2014; 111 Wang, Zhang, Xiao, Zhang, Wang, Chen, Fang (bib80) 2020; 183 Kent (bib35) 2002; 12 Trapnell, Williams, Pertea, Mortazavi, Kwan, van Baren, Salzberg, Wold, Pachter (bib73) 2010; 28 Jiao, Schneeberger (bib30) 2020; 11 Kretzschmar, Pelayo, Trijatmiko, Gabunada, Alam, Jimenez, Mendioro, Slamet-Loedin, Sreenivasulu, Bailey-Serres (bib41) 2015; 1 Alexander, Novembre, Lange (bib2) 2009; 19 Qu, Liu, Zhou, Bellizzi, Zeng, Dai, Han, Wang (bib57) 2006; 172 Sedlazeck, Rescheneder, Smolka, Fang, Nattestad, von Haeseler, Schatz (bib62) 2018; 15 Chen, Zhao, Zhu, Zou, Yin, Chern, Zhou, Ying, Jiang, Li (bib7) 2018; 45 Reich, Price, Patterson (bib59) 2008; 40 Han, Wessler (bib22) 2010; 38 Durand, Robinson, Shamim, Machol, Mesirov, Lander, Aiden (bib17) 2016; 3 Wang, Tu, Yuan, Zhu, Shen, Li, Liu, Pei, Wang, Zhao (bib79) 2019; 51 DePristo, Banks, Poplin, Garimella, Maguire, Hartl, Philippakis, del Angel, Rivas, Hanna (bib11) 2011; 43 Chen, Li, Lu, Gao, Du, Peng, Qin, Liang (bib9) 2020; 47 Carvalho, Lupski (bib6) 2016; 17 Schatz, Maron, Stein, Hernandez Wences, Gurtowski, Biggers, Lee, Kramer, Antoniou, Ghiban (bib61) 2014; 15 Hufnagel, Marques, Soriano, Marquès, Divol, Doumas, Sallet, Mancinotti, Carrere, Marande (bib27) 2020; 11 Jayakodi, Padmarasu, Haberer, Bonthala, Gundlach, Monat, Lux, Kamal, Lang, Himmelbach (bib28) 2020; 588 Li, Han, Chen, Yang, Liu, Li, Ding, Chu (bib44) 2017; 93 Xia, Zou, Sang, Xu, Yin, Li, Wu, Hu, Hao, Zhang (bib83) 2017; 44 Cardoso, Zhang, Jamil, Hepworth, Charnikhova, Dimkpa, Meharg, Wright, Liu, Meng (bib5) 2014; 111 Dong, Li, Li, Yuan, Xie, Wang, Li, Yu, Wang, Ding (bib12) 2018; 94 Xie, Wu, Tang, Luo, Patterson, Liu, Huang, He, Gu, Li (bib85) 2014; 30 Nonoue, Hori, Ono, Shibaya, Ogiso-Tanaka, Mizobuchi, Fukuoka, Yano (bib51) 2019; 69 Zhang, Liang, Cui, Ji, Li, Zhang, Liu, Riaz, Yao, Liu (bib95) 2018; 11 Song, Guan, Hu, Guo, Yang, Wang, Liu, Wang, Lu, Zhou (bib67) 2020; 6 Ou, Jiang (bib54) 2019; 10 Kim, Langmead, Salzberg (bib37) 2015; 12 Ou, Su, Liao, Chougule, Agda, Hellinga, Lugo, Elliott, Ware, Peterson (bib56) 2019; 20 Ho, Urban, Mills (bib25) 2020; 21 Liu, Chen, Zheng, Wu, Lin, Heng, Tian, Cheng, Yu, Zhou (bib46) 2017; 3 Akiyama, Matsuzaki, Hayashi (bib1) 2005; 435 Koren, Walenz, Berlin, Miller, Bergman, Phillippy (bib40) 2017; 27 Smit, Hubley, Green (bib66) 2013-2015 Jeong, Yang, Cho, An (bib29) 2016; 35 Liang, Mao, Ware, Stein (bib45) 2009; 19 Yin, Liu, Xu, Lu, Dong, Yang, Ye, Feng, Wu (bib91) 2019; 70 Kobayashi, Hori, Yamamoto, Yano (bib39) 2018; 11 Yuan, Wang, Zhang, He, Yu (bib93) 2020; 21 Wang, Tao, Marowsky, Fan (bib77) 2016; 172 Hickey (10.1016/j.cell.2021.04.046_bib24) 2020; 21 Weischenfeldt (10.1016/j.cell.2021.04.046_bib81) 2013; 14 Reich (10.1016/j.cell.2021.04.046_bib59) 2008; 40 Ou (10.1016/j.cell.2021.04.046_bib56) 2019; 20 Kent (10.1016/j.cell.2021.04.046_bib35) 2002; 12 Goel (10.1016/j.cell.2021.04.046_bib21) 2019; 20 Wing (10.1016/j.cell.2021.04.046_bib82) 2018; 19 Koren (10.1016/j.cell.2021.04.046_bib40) 2017; 27 Du (10.1016/j.cell.2021.04.046_bib13) 2019; 10 Li (10.1016/j.cell.2021.04.046_bib42) 2009; 25 Kretzschmar (10.1016/j.cell.2021.04.046_bib41) 2015; 1 Chen (10.1016/j.cell.2021.04.046_bib8) 2019; 70 Marçais (10.1016/j.cell.2021.04.046_bib50) 2018; 14 Wang (10.1016/j.cell.2021.04.046_bib78) 2018; 557 Xie (10.1016/j.cell.2021.04.046_bib84) 2010; 48 Dudchenko (10.1016/j.cell.2021.04.046_bib16) 2017; 356 Zhao (10.1016/j.cell.2021.04.046_bib96) 2018; 50 Kang (10.1016/j.cell.2021.04.046_bib33) 2010; 42 Yang (10.1016/j.cell.2021.04.046_bib88) 2019; 51 Ou (10.1016/j.cell.2021.04.046_bib55) 2018; 46 Yin (10.1016/j.cell.2021.04.046_bib91) 2019; 70 Yu (10.1016/j.cell.2021.04.046_bib92) 2013; 14 Ou (10.1016/j.cell.2021.04.046_bib54) 2019; 10 Ou (10.1016/j.cell.2021.04.046_bib53) 2018; 176 Jiao (10.1016/j.cell.2021.04.046_bib30) 2020; 11 Ma (10.1016/j.cell.2021.04.046_bib49) 2004; 101 Sedlazeck (10.1016/j.cell.2021.04.046_bib62) 2018; 15 Han (10.1016/j.cell.2021.04.046_bib22) 2010; 38 Jones (10.1016/j.cell.2021.04.046_bib31) 2014; 30 Qu (10.1016/j.cell.2021.04.046_bib57) 2006; 172 Yuan (10.1016/j.cell.2021.04.046_bib93) 2020; 21 Li (10.1016/j.cell.2021.04.046_bib43) 2009; 25 Zhou (10.1016/j.cell.2021.04.046_bib98) 2020; 7 Chen (10.1016/j.cell.2021.04.046_bib7) 2018; 45 Audano (10.1016/j.cell.2021.04.046_bib4) 2019; 176 Shi (10.1016/j.cell.2021.04.046_bib64) 2019; 180 Hu (10.1016/j.cell.2021.04.046_bib26) 2018; 5 Hufnagel (10.1016/j.cell.2021.04.046_bib27) 2020; 11 Wang (10.1016/j.cell.2021.04.046_bib79) 2019; 51 Stanke (10.1016/j.cell.2021.04.046_bib68) 2005; 33 Walkowiak (10.1016/j.cell.2021.04.046_bib74) 2020; 588 Song (10.1016/j.cell.2021.04.046_bib67) 2020; 6 Sun (10.1016/j.cell.2021.04.046_bib71) 2018; 50 Liu (10.1016/j.cell.2021.04.046_bib46) 2017; 3 Nonoue (10.1016/j.cell.2021.04.046_bib51) 2019; 69 Yang (10.1016/j.cell.2021.04.046_bib89) 2019; 10 Stein (10.1016/j.cell.2021.04.046_bib69) 2018; 50 Delteil (10.1016/j.cell.2021.04.046_bib10) 2016; 16 Oikawa (10.1016/j.cell.2021.04.046_bib52) 2015; 27 Akiyama (10.1016/j.cell.2021.04.046_bib1) 2005; 435 Kobayashi (10.1016/j.cell.2021.04.046_bib39) 2018; 11 Cardoso (10.1016/j.cell.2021.04.046_bib5) 2014; 111 Lye (10.1016/j.cell.2021.04.046_bib48) 2019; 24 Simão (10.1016/j.cell.2021.04.046_bib65) 2015; 31 Ellinghaus (10.1016/j.cell.2021.04.046_bib18) 2008; 9 Smit (10.1016/j.cell.2021.04.046_bib66) 2013 Thorvaldsdóttir (10.1016/j.cell.2021.04.046_bib72) 2013; 14 Sasaki (10.1016/j.cell.2021.04.046_bib60) 2002; 416 Wang (10.1016/j.cell.2021.04.046_bib76) 2015; 47 Carvalho (10.1016/j.cell.2021.04.046_bib6) 2016; 17 Trapnell (10.1016/j.cell.2021.04.046_bib73) 2010; 28 Duan (10.1016/j.cell.2021.04.046_bib15) 2017; 10 Li (10.1016/j.cell.2021.04.046_bib44) 2017; 93 Xiong (10.1016/j.cell.2021.04.046_bib86) 2014; 111 DePristo (10.1016/j.cell.2021.04.046_bib11) 2011; 43 Alonge (10.1016/j.cell.2021.04.046_bib3) 2020; 182 Du (10.1016/j.cell.2021.04.046_bib14) 2017; 8 Dong (10.1016/j.cell.2021.04.046_bib12) 2018; 94 Ho (10.1016/j.cell.2021.04.046_bib25) 2020; 21 Jayakodi (10.1016/j.cell.2021.04.046_bib28) 2020; 588 Chen (10.1016/j.cell.2021.04.046_bib9) 2020; 47 Durand (10.1016/j.cell.2021.04.046_bib17) 2016; 3 Yang (10.1016/j.cell.2021.04.046_bib87) 2013; 153 Kawahara (10.1016/j.cell.2021.04.046_bib34) 2013; 6 Kim (10.1016/j.cell.2021.04.046_bib38) 2019; 37 Shen (10.1016/j.cell.2021.04.046_bib63) 2017; 8 Wang (10.1016/j.cell.2021.04.046_bib77) 2016; 172 Su (10.1016/j.cell.2021.04.046_bib70) 2019; 12 Alexander (10.1016/j.cell.2021.04.046_bib2) 2009; 19 Jukes (10.1016/j.cell.2021.04.046_bib32) 1969 Fuentes (10.1016/j.cell.2021.04.046_bib19) 2019; 29 Jeong (10.1016/j.cell.2021.04.046_bib29) 2016; 35 Kim (10.1016/j.cell.2021.04.046_bib37) 2015; 12 Xie (10.1016/j.cell.2021.04.046_bib85) 2014; 30 Zhang (10.1016/j.cell.2021.04.046_bib95) 2018; 11 Wang (10.1016/j.cell.2021.04.046_bib75) 2012; 40 Kidd (10.1016/j.cell.2021.04.046_bib36) 2010; 143 Liang (10.1016/j.cell.2021.04.046_bib45) 2009; 19 Xia (10.1016/j.cell.2021.04.046_bib83) 2017; 44 Garrison (10.1016/j.cell.2021.04.046_bib20) 2018; 36 He (10.1016/j.cell.2021.04.046_bib23) 2014; 20 Rakocevic (10.1016/j.cell.2021.04.046_bib58) 2019; 51 Liu (10.1016/j.cell.2021.04.046_bib47) 2020; 182 Wang (10.1016/j.cell.2021.04.046_bib80) 2020; 183 Yao (10.1016/j.cell.2021.04.046_bib90) 2018; 7 Schatz (10.1016/j.cell.2021.04.046_bib61) 2014; 15 Zhou (10.1016/j.cell.2021.04.046_bib97) 2019; 5 Zhang (10.1016/j.cell.2021.04.046_bib94) 2016; 113 |
| References_xml | – volume: 30 start-page: 1660 year: 2014 end-page: 1666 ident: bib85 article-title: SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads publication-title: Bioinformatics – volume: 10 start-page: 48 year: 2019 ident: bib54 article-title: LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons publication-title: Mob. DNA – volume: 51 start-page: 1052 year: 2019 end-page: 1059 ident: bib88 article-title: Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement publication-title: Nat. Genet. – volume: 47 start-page: 637 year: 2020 end-page: 649 ident: bib9 article-title: Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice publication-title: J. Genet. Genomics – volume: 435 start-page: 824 year: 2005 end-page: 827 ident: bib1 article-title: Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi publication-title: Nature – volume: 48 start-page: 93 year: 2010 end-page: 117 ident: bib84 article-title: The strigolactone story publication-title: Annu. Rev. Phytopathol. – volume: 46 start-page: e126 year: 2018 ident: bib55 article-title: Assessing genome assembly quality using the LTR Assembly Index (LAI) publication-title: Nucleic Acids Res. – volume: 47 start-page: 944 year: 2015 end-page: 948 ident: bib76 article-title: Copy number variation at the GL7 locus contributes to grain size diversity in rice publication-title: Nat. Genet. – volume: 172 start-page: 1901 year: 2006 end-page: 1914 ident: bib57 article-title: The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice publication-title: Genetics – volume: 6 start-page: 34 year: 2020 end-page: 45 ident: bib67 article-title: Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus publication-title: Nat. Plants – volume: 70 start-page: 639 year: 2019 end-page: 665 ident: bib8 article-title: The Genomics of publication-title: Annu. Rev. Plant Biol. – volume: 50 start-page: 1289 year: 2018 end-page: 1295 ident: bib71 article-title: Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes publication-title: Nat. Genet. – volume: 588 start-page: 284 year: 2020 end-page: 289 ident: bib28 article-title: The barley pan-genome reveals the hidden legacy of mutation breeding publication-title: Nature – volume: 101 start-page: 12404 year: 2004 end-page: 12410 ident: bib49 article-title: Rapid recent growth and divergence of rice nuclear genomes publication-title: Proc. Natl. Acad. Sci. USA – volume: 20 start-page: 275 year: 2019 ident: bib56 article-title: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline publication-title: Genome Biol. – volume: 44 start-page: 235 year: 2017 end-page: 241 ident: bib83 article-title: Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice publication-title: J. Genet. Genomics – volume: 14 start-page: e1005944 year: 2018 ident: bib50 article-title: MUMmer4: A fast and versatile genome alignment system publication-title: PLoS Comput. Biol. – volume: 11 start-page: 492 year: 2020 ident: bib27 article-title: High-quality genome sequence of white lupin provides insight into soil exploration and seed quality publication-title: Nat. Commun. – volume: 94 start-page: 1141 year: 2018 end-page: 1156 ident: bib12 article-title: Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice publication-title: Plant J. – volume: 11 start-page: 1492 year: 2018 end-page: 1508 ident: bib95 article-title: N publication-title: Mol. Plant – volume: 11 start-page: 15 year: 2018 ident: bib39 article-title: Koshihikari: a premium short-grain rice cultivar - its expansion and breeding in Japan publication-title: Rice (N. Y.) – volume: 111 start-page: 2379 year: 2014 end-page: 2384 ident: bib5 article-title: Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs publication-title: Proc. Natl. Acad. Sci. USA – volume: 15 start-page: 506 year: 2014 ident: bib61 article-title: Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica publication-title: Genome Biol. – volume: 36 start-page: 875 year: 2018 end-page: 879 ident: bib20 article-title: Variation graph toolkit improves read mapping by representing genetic variation in the reference publication-title: Nat. Biotechnol. – volume: 12 start-page: 447 year: 2019 end-page: 460 ident: bib70 article-title: TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome publication-title: Mol. Plant – volume: 27 start-page: 722 year: 2017 end-page: 736 ident: bib40 article-title: Canu: scalable and accurate long-read assembly via adaptive publication-title: Genome Res. – volume: 3 start-page: 99 year: 2016 end-page: 101 ident: bib17 article-title: Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom publication-title: Cell Syst. – volume: 12 start-page: 357 year: 2015 end-page: 360 ident: bib37 article-title: HISAT: a fast spliced aligner with low memory requirements publication-title: Nat. Methods – volume: 27 start-page: 2401 year: 2015 end-page: 2414 ident: bib52 article-title: The Birth of a Black Rice Gene and Its Local Spread by Introgression publication-title: Plant Cell – year: 2013-2015 ident: bib66 article-title: RepeatMasker Open-4.0 – volume: 182 start-page: 162 year: 2020 end-page: 176.e13 ident: bib47 article-title: Pan-Genome of Wild and Cultivated Soybeans publication-title: Cell – volume: 25 start-page: 2078 year: 2009 end-page: 2079 ident: bib43 article-title: The sequence alignment/map format and SAMtools publication-title: Bioinformatics – volume: 7 start-page: 1 year: 2018 end-page: 9 ident: bib90 article-title: funRiceGenes dataset for comprehensive understanding and application of rice functional genes publication-title: Gigascience – volume: 7 start-page: 113 year: 2020 ident: bib98 article-title: A platinum standard pan-genome resource that represents the population structure of Asian rice publication-title: Sci. Data – volume: 176 start-page: 663 year: 2019 end-page: 675.e19 ident: bib4 article-title: Characterizing the Major Structural Variant Alleles of the Human Genome publication-title: Cell – volume: 19 start-page: 1912 year: 2009 end-page: 1923 ident: bib45 article-title: Evidence-based gene predictions in plant genomes publication-title: Genome Res. – volume: 19 start-page: 505 year: 2018 end-page: 517 ident: bib82 article-title: The rice genome revolution: from an ancient grain to Green Super Rice publication-title: Nat. Rev. Genet. – volume: 42 start-page: 348 year: 2010 end-page: 354 ident: bib33 article-title: Variance component model to account for sample structure in genome-wide association studies publication-title: Nat. Genet. – volume: 29 start-page: 870 year: 2019 end-page: 880 ident: bib19 article-title: Structural variants in 3000 rice genomes publication-title: Genome Res. – volume: 11 start-page: 989 year: 2020 ident: bib30 article-title: Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics publication-title: Nat. Commun. – volume: 33 start-page: W465-7 year: 2005 ident: bib68 article-title: AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints publication-title: Nucleic Acids Res. – volume: 416 start-page: 701 year: 2002 end-page: 702 ident: bib60 article-title: Green revolution: a mutant gibberellin-synthesis gene in rice publication-title: Nature – volume: 588 start-page: 277 year: 2020 end-page: 283 ident: bib74 article-title: Multiple wheat genomes reveal global variation in modern breeding publication-title: Nature – volume: 3 start-page: 17043 year: 2017 ident: bib46 article-title: GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice publication-title: Nat. Plants – volume: 183 start-page: 1157 year: 2020 end-page: 1170 ident: bib80 article-title: Rice publication-title: Plant Physiol. – volume: 21 start-page: 35 year: 2020 ident: bib24 article-title: Genotyping structural variants in pangenome graphs using the vg toolkit publication-title: Genome Biol. – volume: 28 start-page: 511 year: 2010 end-page: 515 ident: bib73 article-title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nat. Biotechnol. – volume: 557 start-page: 43 year: 2018 end-page: 49 ident: bib78 article-title: Genomic variation in 3,010 diverse accessions of Asian cultivated rice publication-title: Nature – volume: 35 start-page: 905 year: 2016 end-page: 920 ident: bib29 article-title: OsVIL1 controls flowering time in rice by suppressing OsLF under short days and by inducing Ghd7 under long days publication-title: Plant Cell Rep. – volume: 143 start-page: 837 year: 2010 end-page: 847 ident: bib36 article-title: A human genome structural variation sequencing resource reveals insights into mutational mechanisms publication-title: Cell – volume: 17 start-page: 224 year: 2016 end-page: 238 ident: bib6 article-title: Mechanisms underlying structural variant formation in genomic disorders publication-title: Nat. Rev. Genet. – volume: 172 start-page: 427 year: 2016 end-page: 440 ident: bib77 article-title: Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes publication-title: Plant Physiol. – volume: 21 start-page: 1344 year: 2020 ident: bib93 article-title: Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice ( publication-title: Int. J. Mol. Sci. – volume: 5 start-page: 965 year: 2019 end-page: 979 ident: bib97 article-title: The population genetics of structural variants in grapevine domestication publication-title: Nat. Plants – volume: 180 start-page: 1803 year: 2019 end-page: 1815 ident: bib64 article-title: Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection publication-title: Plant Physiol. – volume: 8 start-page: 1310 year: 2017 ident: bib63 article-title: Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice publication-title: Nat. Commun. – volume: 356 start-page: 92 year: 2017 end-page: 95 ident: bib16 article-title: De novo assembly of the publication-title: Science – volume: 153 start-page: 919 year: 2013 end-page: 929 ident: bib87 article-title: Diverse mechanisms of somatic structural variations in human cancer genomes publication-title: Cell – volume: 24 start-page: 352 year: 2019 end-page: 365 ident: bib48 article-title: Copy Number Variation in Domestication publication-title: Trends Plant Sci. – volume: 14 start-page: 649 year: 2013 ident: bib92 article-title: Genome-wide copy number variations in Oryza sativa L publication-title: BMC Genomics – volume: 10 start-page: 685 year: 2017 end-page: 694 ident: bib15 article-title: Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice publication-title: Mol. Plant – volume: 40 start-page: 491 year: 2008 end-page: 492 ident: bib59 article-title: Principal component analysis of genetic data publication-title: Nat. Genet. – volume: 31 start-page: 3210 year: 2015 end-page: 3212 ident: bib65 article-title: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs publication-title: Bioinformatics – volume: 10 start-page: 2989 year: 2019 ident: bib89 article-title: Extensive intraspecific gene order and gene structural variations in upland cotton cultivars publication-title: Nat. Commun. – volume: 38 start-page: e199 year: 2010 ident: bib22 article-title: MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences publication-title: Nucleic Acids Res. – volume: 45 start-page: 663 year: 2018 end-page: 672 ident: bib7 article-title: Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis publication-title: J. Genet. Genomics – volume: 50 start-page: 285 year: 2018 end-page: 296 ident: bib69 article-title: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza publication-title: Nat. Genet. – volume: 14 start-page: 125 year: 2013 end-page: 138 ident: bib81 article-title: Phenotypic impact of genomic structural variation: insights from and for human disease publication-title: Nat. Rev. Genet. – volume: 8 start-page: 15324 year: 2017 ident: bib14 article-title: Sequencing and de novo assembly of a near complete indica rice genome publication-title: Nat. Commun. – volume: 43 start-page: 491 year: 2011 end-page: 498 ident: bib11 article-title: A framework for variation discovery and genotyping using next-generation DNA sequencing data publication-title: Nat. Genet. – volume: 14 start-page: 178 year: 2013 end-page: 192 ident: bib72 article-title: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration publication-title: Brief. Bioinform. – volume: 16 start-page: 17 year: 2016 ident: bib10 article-title: Several wall-associated kinases participate positively and negatively in basal defense against rice blast fungus publication-title: BMC Plant Biol. – volume: 21 start-page: 171 year: 2020 end-page: 189 ident: bib25 article-title: Structural variation in the sequencing era publication-title: Nat. Rev. Genet. – volume: 10 start-page: 5360 year: 2019 ident: bib13 article-title: Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads publication-title: Nat. Commun. – volume: 25 start-page: 1754 year: 2009 end-page: 1760 ident: bib42 article-title: Fast and accurate short read alignment with Burrows-Wheeler transform publication-title: Bioinformatics – volume: 5 start-page: 180079 year: 2018 ident: bib26 article-title: Novel sequences, structural variations and gene presence variations of Asian cultivated rice publication-title: Sci. Data – volume: 37 start-page: 907 year: 2019 end-page: 915 ident: bib38 article-title: Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype publication-title: Nat. Biotechnol. – volume: 93 start-page: 21 year: 2017 end-page: 34 ident: bib44 article-title: Overexpression of OsDT11, which encodes a novel cysteine-rich peptide, enhances drought tolerance and increases ABA concentration in rice publication-title: Plant Mol. Biol. – volume: 182 start-page: 145 year: 2020 end-page: 161.e23 ident: bib3 article-title: Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato publication-title: Cell – volume: 40 start-page: e49 year: 2012 ident: bib75 article-title: MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity publication-title: Nucleic Acids Res. – volume: 12 start-page: 656 year: 2002 end-page: 664 ident: bib35 article-title: BLAT--the BLAST-like alignment tool publication-title: Genome Res. – volume: 176 start-page: 1410 year: 2018 end-page: 1422 ident: bib53 article-title: LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons publication-title: Plant Physiol. – volume: 6 start-page: 4 year: 2013 ident: bib34 article-title: Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data publication-title: Rice (N. Y.) – volume: 113 start-page: E5163 year: 2016 end-page: E5171 ident: bib94 article-title: Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63 publication-title: Proc. Natl. Acad. Sci. USA – volume: 9 start-page: 18 year: 2008 ident: bib18 article-title: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons publication-title: BMC Bioinformatics – volume: 15 start-page: 461 year: 2018 end-page: 468 ident: bib62 article-title: Accurate detection of complex structural variations using single-molecule sequencing publication-title: Nat. Methods – volume: 1 start-page: 15124 year: 2015 ident: bib41 article-title: A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice publication-title: Nat. Plants – volume: 51 start-page: 354 year: 2019 end-page: 362 ident: bib58 article-title: Fast and accurate genomic analyses using genome graphs publication-title: Nat. Genet. – volume: 20 start-page: 417 year: 2014 end-page: 425 ident: bib23 article-title: The progress of mapping, isolation of the genes resisting to blast and their breeding application in rice publication-title: Zhongguo Nongxue Tongbao – volume: 30 start-page: 1236 year: 2014 end-page: 1240 ident: bib31 article-title: InterProScan 5: genome-scale protein function classification publication-title: Bioinformatics – volume: 51 start-page: 224 year: 2019 end-page: 229 ident: bib79 article-title: Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense publication-title: Nat. Genet. – start-page: 21 year: 1969 end-page: 132 ident: bib32 article-title: Evolution of protein molecules publication-title: Mammalian Protein Metabolism – volume: 70 start-page: 3895 year: 2019 end-page: 3909 ident: bib91 article-title: OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice publication-title: J. Exp. Bot. – volume: 19 start-page: 1655 year: 2009 end-page: 1664 ident: bib2 article-title: Fast model-based estimation of ancestry in unrelated individuals publication-title: Genome Res. – volume: 111 start-page: 10263 year: 2014 end-page: 10268 ident: bib86 article-title: HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes publication-title: Proc. Natl. Acad. Sci. USA – volume: 69 start-page: 352 year: 2019 end-page: 358 ident: bib51 article-title: Detection of heading date QTLs in advanced-backcross populations of an elite publication-title: Breed. Sci. – volume: 50 start-page: 278 year: 2018 end-page: 284 ident: bib96 article-title: Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice publication-title: Nat. Genet. – volume: 20 start-page: 277 year: 2019 ident: bib21 article-title: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies publication-title: Genome Biol. – volume: 10 start-page: 48 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib54 article-title: LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons publication-title: Mob. DNA doi: 10.1186/s13100-019-0193-0 – volume: 19 start-page: 505 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib82 article-title: The rice genome revolution: from an ancient grain to Green Super Rice publication-title: Nat. Rev. Genet. doi: 10.1038/s41576-018-0024-z – volume: 50 start-page: 285 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib69 article-title: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza publication-title: Nat. Genet. doi: 10.1038/s41588-018-0040-0 – volume: 12 start-page: 447 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib70 article-title: TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome publication-title: Mol. Plant doi: 10.1016/j.molp.2019.02.008 – volume: 20 start-page: 277 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib21 article-title: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies publication-title: Genome Biol. doi: 10.1186/s13059-019-1911-0 – volume: 101 start-page: 12404 year: 2004 ident: 10.1016/j.cell.2021.04.046_bib49 article-title: Rapid recent growth and divergence of rice nuclear genomes publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.0403715101 – volume: 31 start-page: 3210 year: 2015 ident: 10.1016/j.cell.2021.04.046_bib65 article-title: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs publication-title: Bioinformatics doi: 10.1093/bioinformatics/btv351 – volume: 5 start-page: 965 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib97 article-title: The population genetics of structural variants in grapevine domestication publication-title: Nat. Plants doi: 10.1038/s41477-019-0507-8 – volume: 6 start-page: 34 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib67 article-title: Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus publication-title: Nat. Plants doi: 10.1038/s41477-019-0577-7 – volume: 588 start-page: 277 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib74 article-title: Multiple wheat genomes reveal global variation in modern breeding publication-title: Nature doi: 10.1038/s41586-020-2961-x – volume: 8 start-page: 15324 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib14 article-title: Sequencing and de novo assembly of a near complete indica rice genome publication-title: Nat. Commun. doi: 10.1038/ncomms15324 – volume: 50 start-page: 1289 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib71 article-title: Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes publication-title: Nat. Genet. doi: 10.1038/s41588-018-0182-0 – volume: 111 start-page: 2379 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib5 article-title: Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1317360111 – volume: 10 start-page: 5360 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib13 article-title: Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads publication-title: Nat. Commun. doi: 10.1038/s41467-019-13355-3 – volume: 30 start-page: 1236 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib31 article-title: InterProScan 5: genome-scale protein function classification publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu031 – volume: 11 start-page: 15 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib39 article-title: Koshihikari: a premium short-grain rice cultivar - its expansion and breeding in Japan publication-title: Rice (N. Y.) doi: 10.1186/s12284-018-0207-4 – volume: 40 start-page: e49 year: 2012 ident: 10.1016/j.cell.2021.04.046_bib75 article-title: MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkr1293 – volume: 3 start-page: 17043 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib46 article-title: GW5 acts in the brassinosteroid signalling pathway to regulate grain width and weight in rice publication-title: Nat. Plants doi: 10.1038/nplants.2017.43 – volume: 27 start-page: 2401 year: 2015 ident: 10.1016/j.cell.2021.04.046_bib52 article-title: The Birth of a Black Rice Gene and Its Local Spread by Introgression publication-title: Plant Cell doi: 10.1105/tpc.15.00310 – volume: 20 start-page: 275 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib56 article-title: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline publication-title: Genome Biol. doi: 10.1186/s13059-019-1905-y – volume: 12 start-page: 357 year: 2015 ident: 10.1016/j.cell.2021.04.046_bib37 article-title: HISAT: a fast spliced aligner with low memory requirements publication-title: Nat. Methods doi: 10.1038/nmeth.3317 – volume: 11 start-page: 492 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib27 article-title: High-quality genome sequence of white lupin provides insight into soil exploration and seed quality publication-title: Nat. Commun. doi: 10.1038/s41467-019-14197-9 – volume: 33 start-page: W465-7 year: 2005 ident: 10.1016/j.cell.2021.04.046_bib68 article-title: AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints publication-title: Nucleic Acids Res. doi: 10.1093/nar/gki458 – volume: 42 start-page: 348 year: 2010 ident: 10.1016/j.cell.2021.04.046_bib33 article-title: Variance component model to account for sample structure in genome-wide association studies publication-title: Nat. Genet. doi: 10.1038/ng.548 – volume: 6 start-page: 4 year: 2013 ident: 10.1016/j.cell.2021.04.046_bib34 article-title: Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data publication-title: Rice (N. Y.) doi: 10.1186/1939-8433-6-4 – volume: 36 start-page: 875 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib20 article-title: Variation graph toolkit improves read mapping by representing genetic variation in the reference publication-title: Nat. Biotechnol. doi: 10.1038/nbt.4227 – volume: 12 start-page: 656 year: 2002 ident: 10.1016/j.cell.2021.04.046_bib35 article-title: BLAT--the BLAST-like alignment tool publication-title: Genome Res. – volume: 14 start-page: e1005944 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib50 article-title: MUMmer4: A fast and versatile genome alignment system publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.1005944 – volume: 37 start-page: 907 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib38 article-title: Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype publication-title: Nat. Biotechnol. doi: 10.1038/s41587-019-0201-4 – volume: 50 start-page: 278 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib96 article-title: Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice publication-title: Nat. Genet. doi: 10.1038/s41588-018-0041-z – volume: 176 start-page: 663 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib4 article-title: Characterizing the Major Structural Variant Alleles of the Human Genome publication-title: Cell doi: 10.1016/j.cell.2018.12.019 – volume: 21 start-page: 35 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib24 article-title: Genotyping structural variants in pangenome graphs using the vg toolkit publication-title: Genome Biol. doi: 10.1186/s13059-020-1941-7 – volume: 3 start-page: 99 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib17 article-title: Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom publication-title: Cell Syst. doi: 10.1016/j.cels.2015.07.012 – volume: 30 start-page: 1660 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib85 article-title: SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu077 – volume: 25 start-page: 2078 year: 2009 ident: 10.1016/j.cell.2021.04.046_bib43 article-title: The sequence alignment/map format and SAMtools publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp352 – volume: 15 start-page: 461 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib62 article-title: Accurate detection of complex structural variations using single-molecule sequencing publication-title: Nat. Methods doi: 10.1038/s41592-018-0001-7 – volume: 5 start-page: 180079 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib26 article-title: Novel sequences, structural variations and gene presence variations of Asian cultivated rice publication-title: Sci. Data doi: 10.1038/sdata.2018.79 – volume: 11 start-page: 989 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib30 article-title: Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics publication-title: Nat. Commun. doi: 10.1038/s41467-020-14779-y – volume: 1 start-page: 15124 year: 2015 ident: 10.1016/j.cell.2021.04.046_bib41 article-title: A trehalose-6-phosphate phosphatase enhances anaerobic germination tolerance in rice publication-title: Nat. Plants doi: 10.1038/nplants.2015.124 – volume: 29 start-page: 870 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib19 article-title: Structural variants in 3000 rice genomes publication-title: Genome Res. doi: 10.1101/gr.241240.118 – volume: 111 start-page: 10263 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib86 article-title: HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1410068111 – volume: 35 start-page: 905 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib29 article-title: OsVIL1 controls flowering time in rice by suppressing OsLF under short days and by inducing Ghd7 under long days publication-title: Plant Cell Rep. doi: 10.1007/s00299-015-1931-5 – volume: 20 start-page: 417 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib23 article-title: The progress of mapping, isolation of the genes resisting to blast and their breeding application in rice publication-title: Zhongguo Nongxue Tongbao – volume: 435 start-page: 824 year: 2005 ident: 10.1016/j.cell.2021.04.046_bib1 article-title: Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi publication-title: Nature doi: 10.1038/nature03608 – volume: 51 start-page: 354 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib58 article-title: Fast and accurate genomic analyses using genome graphs publication-title: Nat. Genet. doi: 10.1038/s41588-018-0316-4 – volume: 27 start-page: 722 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib40 article-title: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation publication-title: Genome Res. doi: 10.1101/gr.215087.116 – volume: 70 start-page: 639 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib8 article-title: The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis publication-title: Annu. Rev. Plant Biol. doi: 10.1146/annurev-arplant-050718-100320 – volume: 11 start-page: 1492 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib95 article-title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses publication-title: Mol. Plant doi: 10.1016/j.molp.2018.11.005 – volume: 588 start-page: 284 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib28 article-title: The barley pan-genome reveals the hidden legacy of mutation breeding publication-title: Nature doi: 10.1038/s41586-020-2947-8 – volume: 44 start-page: 235 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib83 article-title: Rice Expression Database (RED): An integrated RNA-Seq-derived gene expression database for rice publication-title: J. Genet. Genomics doi: 10.1016/j.jgg.2017.05.003 – volume: 40 start-page: 491 year: 2008 ident: 10.1016/j.cell.2021.04.046_bib59 article-title: Principal component analysis of genetic data publication-title: Nat. Genet. doi: 10.1038/ng0508-491 – volume: 183 start-page: 1157 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib80 article-title: Rice GERMIN-LIKE PROTEIN 2-1 Functions in Seed Dormancy under the Control of Abscisic Acid and Gibberellic Acid Signaling Pathways publication-title: Plant Physiol. doi: 10.1104/pp.20.00253 – volume: 172 start-page: 1901 year: 2006 ident: 10.1016/j.cell.2021.04.046_bib57 article-title: The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat protein and is a member of a multigene family in rice publication-title: Genetics doi: 10.1534/genetics.105.044891 – volume: 14 start-page: 125 year: 2013 ident: 10.1016/j.cell.2021.04.046_bib81 article-title: Phenotypic impact of genomic structural variation: insights from and for human disease publication-title: Nat. Rev. Genet. doi: 10.1038/nrg3373 – volume: 16 start-page: 17 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib10 article-title: Several wall-associated kinases participate positively and negatively in basal defense against rice blast fungus publication-title: BMC Plant Biol. doi: 10.1186/s12870-016-0711-x – volume: 21 start-page: 1344 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib93 article-title: Genetic Dissection of Seed Dormancy using Chromosome Segment Substitution Lines in Rice (Oryza sativa L.) publication-title: Int. J. Mol. Sci. doi: 10.3390/ijms21041344 – volume: 47 start-page: 944 year: 2015 ident: 10.1016/j.cell.2021.04.046_bib76 article-title: Copy number variation at the GL7 locus contributes to grain size diversity in rice publication-title: Nat. Genet. doi: 10.1038/ng.3346 – volume: 8 start-page: 1310 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib63 article-title: Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice publication-title: Nat. Commun. doi: 10.1038/s41467-017-01400-y – volume: 172 start-page: 427 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib77 article-title: Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes publication-title: Plant Physiol. doi: 10.1104/pp.16.01177 – volume: 17 start-page: 224 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib6 article-title: Mechanisms underlying structural variant formation in genomic disorders publication-title: Nat. Rev. Genet. doi: 10.1038/nrg.2015.25 – start-page: 21 year: 1969 ident: 10.1016/j.cell.2021.04.046_bib32 article-title: Evolution of protein molecules – volume: 113 start-page: E5163 year: 2016 ident: 10.1016/j.cell.2021.04.046_bib94 article-title: Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63 publication-title: Proc. Natl. Acad. Sci. USA – volume: 416 start-page: 701 year: 2002 ident: 10.1016/j.cell.2021.04.046_bib60 article-title: Green revolution: a mutant gibberellin-synthesis gene in rice publication-title: Nature doi: 10.1038/416701a – volume: 51 start-page: 224 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib79 article-title: Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense publication-title: Nat. Genet. doi: 10.1038/s41588-018-0282-x – volume: 557 start-page: 43 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib78 article-title: Genomic variation in 3,010 diverse accessions of Asian cultivated rice publication-title: Nature doi: 10.1038/s41586-018-0063-9 – volume: 7 start-page: 113 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib98 article-title: A platinum standard pan-genome resource that represents the population structure of Asian rice publication-title: Sci. Data doi: 10.1038/s41597-020-0438-2 – volume: 143 start-page: 837 year: 2010 ident: 10.1016/j.cell.2021.04.046_bib36 article-title: A human genome structural variation sequencing resource reveals insights into mutational mechanisms publication-title: Cell doi: 10.1016/j.cell.2010.10.027 – volume: 28 start-page: 511 year: 2010 ident: 10.1016/j.cell.2021.04.046_bib73 article-title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation publication-title: Nat. Biotechnol. doi: 10.1038/nbt.1621 – volume: 51 start-page: 1052 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib88 article-title: Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement publication-title: Nat. Genet. doi: 10.1038/s41588-019-0427-6 – volume: 45 start-page: 663 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib7 article-title: Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis publication-title: J. Genet. Genomics doi: 10.1016/j.jgg.2018.10.007 – volume: 182 start-page: 162 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib47 article-title: Pan-Genome of Wild and Cultivated Soybeans publication-title: Cell doi: 10.1016/j.cell.2020.05.023 – volume: 94 start-page: 1141 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib12 article-title: Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice publication-title: Plant J. doi: 10.1111/tpj.13925 – volume: 70 start-page: 3895 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib91 article-title: OsMADS18, a membrane-bound MADS-box transcription factor, modulates plant architecture and the abscisic acid response in rice publication-title: J. Exp. Bot. doi: 10.1093/jxb/erz198 – volume: 10 start-page: 685 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib15 article-title: Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice publication-title: Mol. Plant doi: 10.1016/j.molp.2017.03.009 – volume: 356 start-page: 92 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib16 article-title: De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds publication-title: Science doi: 10.1126/science.aal3327 – volume: 21 start-page: 171 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib25 article-title: Structural variation in the sequencing era publication-title: Nat. Rev. Genet. doi: 10.1038/s41576-019-0180-9 – volume: 15 start-page: 506 year: 2014 ident: 10.1016/j.cell.2021.04.046_bib61 article-title: Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica publication-title: Genome Biol. – volume: 180 start-page: 1803 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib64 article-title: Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection publication-title: Plant Physiol. doi: 10.1104/pp.19.00386 – volume: 7 start-page: 1 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib90 article-title: funRiceGenes dataset for comprehensive understanding and application of rice functional genes publication-title: Gigascience doi: 10.1093/gigascience/gix119 – volume: 9 start-page: 18 year: 2008 ident: 10.1016/j.cell.2021.04.046_bib18 article-title: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-18 – volume: 19 start-page: 1912 year: 2009 ident: 10.1016/j.cell.2021.04.046_bib45 article-title: Evidence-based gene predictions in plant genomes publication-title: Genome Res. doi: 10.1101/gr.088997.108 – volume: 47 start-page: 637 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib9 article-title: Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice publication-title: J. Genet. Genomics doi: 10.1016/j.jgg.2020.10.006 – volume: 48 start-page: 93 year: 2010 ident: 10.1016/j.cell.2021.04.046_bib84 article-title: The strigolactone story publication-title: Annu. Rev. Phytopathol. doi: 10.1146/annurev-phyto-073009-114453 – volume: 25 start-page: 1754 year: 2009 ident: 10.1016/j.cell.2021.04.046_bib42 article-title: Fast and accurate short read alignment with Burrows-Wheeler transform publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 176 start-page: 1410 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib53 article-title: LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons publication-title: Plant Physiol. doi: 10.1104/pp.17.01310 – volume: 14 start-page: 178 year: 2013 ident: 10.1016/j.cell.2021.04.046_bib72 article-title: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration publication-title: Brief. Bioinform. doi: 10.1093/bib/bbs017 – volume: 69 start-page: 352 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib51 article-title: Detection of heading date QTLs in advanced-backcross populations of an elite indica rice cultivar, IR64 publication-title: Breed. Sci. doi: 10.1270/jsbbs.18172 – volume: 153 start-page: 919 year: 2013 ident: 10.1016/j.cell.2021.04.046_bib87 article-title: Diverse mechanisms of somatic structural variations in human cancer genomes publication-title: Cell doi: 10.1016/j.cell.2013.04.010 – volume: 14 start-page: 649 year: 2013 ident: 10.1016/j.cell.2021.04.046_bib92 article-title: Genome-wide copy number variations in Oryza sativa L publication-title: BMC Genomics doi: 10.1186/1471-2164-14-649 – volume: 182 start-page: 145 year: 2020 ident: 10.1016/j.cell.2021.04.046_bib3 article-title: Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato publication-title: Cell doi: 10.1016/j.cell.2020.05.021 – volume: 10 start-page: 2989 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib89 article-title: Extensive intraspecific gene order and gene structural variations in upland cotton cultivars publication-title: Nat. Commun. doi: 10.1038/s41467-019-10820-x – volume: 38 start-page: e199 year: 2010 ident: 10.1016/j.cell.2021.04.046_bib22 article-title: MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq862 – volume: 24 start-page: 352 year: 2019 ident: 10.1016/j.cell.2021.04.046_bib48 article-title: Copy Number Variation in Domestication publication-title: Trends Plant Sci. doi: 10.1016/j.tplants.2019.01.003 – volume: 93 start-page: 21 year: 2017 ident: 10.1016/j.cell.2021.04.046_bib44 article-title: Overexpression of OsDT11, which encodes a novel cysteine-rich peptide, enhances drought tolerance and increases ABA concentration in rice publication-title: Plant Mol. Biol. doi: 10.1007/s11103-016-0544-x – volume: 46 start-page: e126 year: 2018 ident: 10.1016/j.cell.2021.04.046_bib55 article-title: Assessing genome assembly quality using the LTR Assembly Index (LAI) publication-title: Nucleic Acids Res. – year: 2013 ident: 10.1016/j.cell.2021.04.046_bib66 – volume: 19 start-page: 1655 year: 2009 ident: 10.1016/j.cell.2021.04.046_bib2 article-title: Fast model-based estimation of ancestry in unrelated individuals publication-title: Genome Res. doi: 10.1101/gr.094052.109 – volume: 43 start-page: 491 year: 2011 ident: 10.1016/j.cell.2021.04.046_bib11 article-title: A framework for variation discovery and genotyping using next-generation DNA sequencing data publication-title: Nat. Genet. doi: 10.1038/ng.806 |
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| Snippet | Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31... |
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| SubjectTerms | Adaptation, Physiological - genetics Agriculture Domestication Ecotype evolution Gene copy number variation gene expression Gene Expression Profiling Gene Expression Regulation, Plant Genes, Plant Genetic Variation genome Genome, Plant genome-wide association study Genomic Structural Variation genomics Graph-based genome High-quality assembly Molecular Sequence Annotation Oryza - genetics Oryza glaberrima Oryza sativa Pan-genome Phenotype Rice Structural variation |
| Title | Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations |
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