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1. Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility

Author

Kuijer, Hendrik N. J., Wang, Jian You, Bougouffa, Salim, Abrouk, Michael, Jamil, Muhammad, Incitti, Roberto, Alam, Intikhab, Balakrishna, Aparna, Alvarez, Derry, Votta, Cristina, Chen, Guan-Ting Erica, Martínez, Claudio, Zuccolo, Andrea, Berqdar, Lamis, Sioud, Salim, Fiorilli, Valentina, de Lera, Angel R., Lanfranco, Luisa, Gojobori, Takashi, Wing, Rod A., Krattinger, Simon G., Gao, Xin, and Al-Babili, Salim

Published
2024
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4. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Author

Zhou, Yong, Yu, Zhichao, Chebotarov, Dmytro, Chougule, Kapeel, Lu, Zhenyuan, Rivera, Luis F., Kathiresan, Nagarajan, Al-Bader, Noor, Mohammed, Nahed, Alsantely, Aseel, Mussurova, Saule, Santos, João, Thimma, Manjula, Troukhan, Maxim, Fornasiero, Alice, Green, Carl D., Copetti, Dario, Kudrna, David, Llaca, Victor, Lorieux, Mathias, Zuccolo, Andrea, Ware, Doreen, McNally, Kenneth, Zhang, Jianwei, and Wing, Rod A.

Published
2023
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6. The Chinese pine genome and methylome unveil key features of conifer evolution

Author

Niu, Shihui, Li, Jiang, Bo, Wenhao, Yang, Weifei, Zuccolo, Andrea, Giacomello, Stefania, Chen, Xi, Han, Fangxu, Yang, Junhe, Song, Yitong, Nie, Yumeng, Zhou, Biao, Wang, Peiyi, Zuo, Quan, Zhang, Hui, Ma, Jingjing, Wang, Jun, Wang, Lvji, Zhu, Qianya, Zhao, Huanhuan, Liu, Zhanmin, Zhang, Xuemei, Liu, Tao, Pei, Surui, Li, Zhimin, Hu, Yao, Yang, Yehui, Li, Wenzhao, Zan, Yanjun, Zhou, Linghua, Lin, Jinxing, Yuan, Tongqi, Li, Wei, Li, Yue, Wei, Hairong, and Wu, Harry X.

Published
2022
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7. Two gap-free reference genomes and a global view of the centromere architecture in rice

Author

Song, Jia-Ming, Xie, Wen-Zhao, Wang, Shuo, Guo, Yi-Xiong, Koo, Dal-Hoe, Kudrna, Dave, Gong, Chenbo, Huang, Yicheng, Feng, Jia-Wu, Zhang, Wenhui, Zhou, Yong, Zuccolo, Andrea, Long, Evan, Lee, Seunghee, Talag, Jayson, Zhou, Run, Zhu, Xi-Tong, Yuan, Daojun, Udall, Joshua, Xie, Weibo, Wing, Rod A., Zhang, Qifa, Poland, Jesse, Zhang, Jianwei, and Chen, Ling-Ling

Published
2021
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8. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Author

Stein, Joshua C, Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J, Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos EM, Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty SS, Talag, Jayson, Danowitz, Ann, Rivera, Luis F, Gschwend, Andrea R, Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel da, da Maia, Luciano Carlos, dos Santos, Railson S, Nyberg, Kevin G, McNally, Kenneth L, Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K, Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C, Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A, Machado, Carlos A, Sanderson, Michael J, Long, Manyuan, Ware, Doreen, and Wing, Rod A

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Conserved Sequence, Crops, Agricultural, Domestication, Evolution, Molecular, Genetic Speciation, Genetic Variation, Genome, Plant, Oryza, Phylogeny, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Published
2018

9. A route to de novo domestication of wild allotetraploid rice

Author

Yu, Hong, Lin, Tao, Meng, Xiangbing, Du, Huilong, Zhang, Jingkun, Liu, Guifu, Chen, Mingjiang, Jing, Yanhui, Kou, Liquan, Li, Xiuxiu, Gao, Qiang, Liang, Yan, Liu, Xiangdong, Fan, Zhilan, Liang, Yuntao, Cheng, Zhukuan, Chen, Mingsheng, Tian, Zhixi, Wang, Yonghong, Chu, Chengcai, Zuo, Jianru, Wan, Jianmin, Qian, Qian, Han, Bin, Zuccolo, Andrea, Wing, Rod A., Gao, Caixia, Liang, Chengzhi, and Li, Jiayang

Published
2021
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10. Transposable Elements in Spruce

Author

Marturano, Giovanni, Canovi, Camilla, Rossi, Federico, Zuccolo, Andrea, Kole, Chittaranjan, Series Editor, Porth, Ilga M., editor, and De la Torre, Amanda R., editor

Published
2020
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11. Chromosome-scale pearl millet genomes reveal aCARLACTONOIC ACID METHYL TRANSFERASEas key determinant of strigolactone pattern and Striga susceptibility

Author

Kuijer, Hendrik NJ, primary, Wang, Jian You, additional, Bougouffa, Salim, additional, Abrouk, Michael, additional, Jamil, Muhammad, additional, Incitti, Roberto, additional, Alam, Intikhab, additional, Balakrishna, Aparna, additional, Alvarez, Derry, additional, Votta, Cristina, additional, Chen, Guan-Ting Erica, additional, Martínez, Claudio, additional, Zuccolo, Andrea, additional, Berqdar, Lamis, additional, Sioud, Salim, additional, Fiorilli, Valentina, additional, de Lera, Angel R, additional, Lanfranco, Luisa, additional, Gojobori, Takashi, additional, Wing, Rod A, additional, Krattinger, Simon G, additional, Gao, Xin, additional, and Al-Babili, Salim, additional

Published
2024
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12. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Author

Wang, Muhua, Yu, Yeisoo, Haberer, Georg, Marri, Pradeep Reddy, Fan, Chuanzhu, Goicoechea, Jose Luis, Zuccolo, Andrea, Song, Xiang, Kudrna, Dave, Ammiraju, Jetty SS, Cossu, Rosa Maria, Maldonado, Carlos, Chen, Jinfeng, Lee, Seunghee, Sisneros, Nick, de Baynast, Kristi, Golser, Wolfgang, Wissotski, Marina, Kim, Woojin, Sanchez, Paul, Ndjiondjop, Marie-Noelle, Sanni, Kayode, Long, Manyuan, Carney, Judith, Panaud, Olivier, Wicker, Thomas, Machado, Carlos A, Chen, Mingsheng, Mayer, Klaus FX, Rounsley, Steve, and Wing, Rod A

Subjects
Africa, Amino Acid Sequence, Base Sequence, Crops, Agricultural, DNA, Plant, Genetic Variation, Genetics, Population, Genome, Plant, Molecular Sequence Data, Oryza, Sequence Analysis, DNA, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

Published
2014

13. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

Author

Wu, G Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Del Fabbro, Cristian, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco R, Estornell, Leandro H, Muñoz-Sanz, Juan V, Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez-Pérez, Julián, Ramón, Daniel, Brunel, Dominique, Luro, François, Chen, Chunxian, Farmerie, William G, Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astúa, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel

Subjects
Base Sequence, Breeding, Citrus, Conserved Sequence, Crops, Agricultural, Evolution, Molecular, Genetic Variation, Genome, Plant, Molecular Sequence Data, Sequence Analysis, DNA, Species Specificity
Abstract

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.

Published
2014

14. Complex history of admixture during citrus domestication revealed by genome analysis

Author

Wu, G. Albert, Prochnik, Simon, Jenkins, Jerry, Salse, Jerome, Hellsten, Uffe, Murat, Florent, Perrier, Xavier, Ruiz, Manuel, Scalabrin, Simone, Terol, Javier, Takita, Marco Aurélio, Labadie, Karine, Poulain, Julie, Couloux, Arnaud, Jabbari, Kamel, Cattonaro, Federica, Fabbro, Cristian Del, Pinosio, Sara, Zuccolo, Andrea, Chapman, Jarrod, Grimwood, Jane, Tadeo, Francisco, Estornell, Leandro H., Mu?oz-Sanz, Juan V., Ibanez, Victoria, Herrero-Ortega, Amparo, Aleza, Pablo, Pérez, Julián Pérez, Ramon, Daniel, Brunel, Dominique, Luro, Francois, Chen, Chunxian, Farmerie, William G., Desany, Brian, Kodira, Chinnappa, Mohiuddin, Mohammed, Harkins, Tim, Fredrikson, Karin, Burns, Paul, Lomsadze, Alexandre, Borodovsky, Mark, Reforgiato, Giuseppe, Freitas-Astua, Juliana, Quetier, Francis, Navarro, Luis, Roose, Mikeal, Wincker, Patrick, Schmutz, Jeremy, Morgante, Michele, Machado, Marcos Antonio, Talon, Manuel, Jaillon, Olivier, Ollitrault, Patrick, Gmitter, Frederick, and Rokhsar, Daniel

Subjects
haploid Clementine mandarin, C. maxima, C. reticulata, Mangshan, China, Huanglongbing, apomixis via nucellar polyembryony, ntrogressive hybridizations
Abstract

Although Citrus is the most globally significant tree fruit, its domestication history is poorlyunderstood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm.Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China showssubstantial sequence divergence from C. reticulata and appears to represent a distinct taxon.Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement.Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources ofvitamin C and other health-promoting compounds. Global production in 2012 exceeded 86million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly vulnerable to disease outbreaks, including citrus greening disease (also known as Huanglongbing) that is rapidly spreading throughout the world's major citrus producing regions1. Understanding the population genomics and domestication of citrus will enable strategies for improvements to citrus including resistance to greening and otherdiseases. The domestication and distribution of edible citrus types began several thousand years ago in Southeast Asia and spread globally following ancient land and sea routes. The lineages that gave rise to most modern cultivated varieties, however, are lost in undocumented antiquity, and their identities remain controversial2, 3. Several features of Citrus biology and cultivation make deciphering these origins difficult. Cultivated varieties are typically propagated clonally by grafting and through asexual seed production (apomixis via nucellar polyembryony) to maintain desirable combinations of traits (Fig. 1). Thus many important cultivar groups have characteristic basic genotypes that presumably arose through interspecific hybridization and/or successive introgressive hybridizations of wild ancestral species. These domestication events predated the global expansion of citrus cultivation by hundreds or perhaps thousands of years, with no record of the domestication process. Diversity within such groups arises through accumulated somatic mutations, generally without sexual recombination, either as limb sports on trees or variants among apomictic seedling progeny.Two wild species are believed to have contributed to domesticated pummelos, mandarins and oranges. Based on morphology and genetic markers, pummelos have generally been identified with the wild species C. maxima (Burm.) Merrill that is indigenous to Southeast Asia. Although mandarins are similarly widely identified with the species C. reticulata Blanco 4-6, wild populations of C. reticulata have not been definitively described. Various authors have taken dif

Published
2014

15. Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Author

Lin, Yao-Cheng, Wang, Jing, Delhomme, Nicolas, Schiffthaler, Bastian, Sundström, Görel, Zuccolo, Andrea, Nystedt, Björn, Hvidsten, Torgeir R., de la Torre, Amanda, Cossu, Rosa M., Hoeppner, Marc P., Lantz, Henrik, Scofield, Douglas G., Zamani, Neda, Johansson, Anna, Mannapperuma, Chanaka, Robinson, Kathryn M., Mähler, Niklas, Leitch, Ilia J., Pellicer, Jaume, Park, Eung-Jun, Van Montagu, Marc, Van de Peer, Yves, Grabherr, Manfred, Jansson, Stefan, Ingvarsson, Pär K., and Street, Nathaniel R.

Published
2018

16. A platinum standard pan-genome resource that represents the population structure of Asian rice

Author

Zhou, Yong, Chebotarov, Dmytro, Kudrna, Dave, Llaca, Victor, Lee, Seunghee, Rajasekar, Shanmugam, Mohammed, Nahed, Al-Bader, Noor, Sobel-Sorenson, Chandler, Parakkal, Praveena, Arbelaez, Lady Johanna, Franco, Natalia, Alexandrov, Nickolai, Hamilton, N. Ruaraidh Sackville, Leung, Hei, Mauleon, Ramil, Lorieux, Mathias, Zuccolo, Andrea, McNally, Kenneth, Zhang, Jianwei, and Wing, Rod A.

Published
2020
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17. Repetitive Sequences

Author

Zuccolo, Andrea, Kole, Chittaranjan, Series editor, Testolin, Raffaele, editor, Huang, Hong-Wen, editor, and Ferguson, Allan Ross, editor

Published
2016
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18. HPC-based genome variant calling workflow (HPC-GVCW)

Author

Zhou, Yong, primary, Kathiresan, Nagarajan, additional, Yu, Zhichao, additional, Rivera, Luis F., additional, Thimma, Manjula, additional, Manickam, Keerthana, additional, Chebotarov, Dmytro, additional, Mauleon, Ramil, additional, Chougule, Kapeel, additional, Wei, Sharon, additional, Gao, Tingting, additional, Green, Carl D., additional, Zuccolo, Andrea, additional, Ware, Doreen, additional, Zhang, Jianwei, additional, McNally, Kenneth L., additional, and Wing, Rod A., additional

Published
2023
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20. The gyrfalcon (Falco rusticolus) genome

Author

Zuccolo, Andrea, primary, Mfarrej, Sara, additional, Celii, Mirko, additional, Mussurova, Saule, additional, Rivera, Luis F, additional, Llaca, Victor, additional, Mohammed, Nahed, additional, Pain, Arnab, additional, Alrefaei, Abdulmajeed Fahad, additional, Alrefaei, Abdulwahed Fahad, additional, and Wing, Rod A, additional

Published
2023
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25. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)

Author

Zhou, Yong, primary, Yu, Zhichao, additional, Chebotarov, Dmytro, additional, Chougule, Kapeel, additional, Lu, Zhenyuan, additional, Rivera, Luis F., additional, Kathiresan, Nagarajan, additional, Al-Bader, Noor, additional, Mohammed, Nahed, additional, Alsantely, Aseel, additional, Mussurova, Saule, additional, Santos, João, additional, Thimma, Manjula, additional, Troukhan, Maxim, additional, Fornasiero, Alice, additional, Green, Carl D., additional, Copetti, Dario, additional, Kudrna, Dave, additional, Llaca, Victor, additional, Lorieux, Mathias, additional, Zuccolo, Andrea, additional, Ware, Doreen, additional, McNally, Kenneth, additional, Zhang, Jianwei, additional, and Wing, Rod A., additional

Published
2022
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26. The B73 Maize Genome: Complexity, Diversity, and Dynamics

Author

Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M., Gillam, Barbara, Chen, Weizu, Yan, Le, Higginbotham, Jamey, Cardenas, Marco, Waligorski, Jason, Applebaum, Elizabeth, Phelps, Lindsey, Falcone, Jason, Kanchi, Krishna, Thane, Thynn, Scimone, Adam, Thane, Nay, Henke, Jessica, Wang, Tom, Ruppert, Jessica, Shah, Neha, Rotter, Kelsi, Hodges, Jennifer, Ingenthron, Elizabeth, Cordes, Matt, Kohlberg, Sara, Sgro, Jennifer, Delgado, Brandon, Mead, Kelly, Chinwalla, Asif, Leonard, Shawn, Crouse, Kevin, Collura, Kristi, Kudrna, Dave, Currie, Jennifer, He, Ruifeng, Angelova, Angelina, Rajasekar, Shanmugam, Mueller, Teri, Lomeli, Rene, Scara, Gabriel, Ko, Ara, Delaney, Krista, Wissotski, Marina, Lopez, Georgina, Campos, David, Braidotti, Michele, Ashley, Elizabeth, Golser, Wolfgang, Kim, HyeRan, Lee, Seunghee, Lin, Jinke, Dujmic, Zeljko, Kim, Woojin, Talag, Jayson, Zuccolo, Andrea, Fan, Chuanzhu, Sebastian, Aswathy, Kramer, Melissa, Spiegel, Lori, Nascimento, Lidia, Zutavern, Theresa, Miller, Beth, Ambroise, Claude, Muller, Stephanie, Spooner, Will, Narechania, Apurva, Ren, Liya, Wei, Sharon, Kumari, Sunita, Faga, Ben, Levy, Michael J., McMahan, Linda, Van Buren, Peter, Vaughn, Matthew W., Ying, Kai, Yeh, Cheng-Ting, Emrich, Scott J., Jia, Yi, Kalyanaraman, Ananth, Hsia, An-Ping, Barbazuk, W. Brad, Baucom, Regina S., Brutnell, Thomas P., Carpita, Nicholas C., Chaparro, Cristian, Chia, Jer-Ming, Deragon, Jean-Marc, Estill, James C., Fu, Yan, Jeddeloh, Jeffrey A., Han, Yujun, Lee, Hyeran, Li, Pinghua, Lisch, Damon R., Liu, Sanzhen, Liu, Zhijie, Nagel, Dawn Holligan, McCann, Maureen C., SanMiguel, Phillip, Myers, Alan M., Nettleton, Dan, Nguyen, John, Penning, Bryan W., Ponnala, Lalit, Schneider, Kevin L., Schwartz, David C., Sharma, Anupma, Soderlund, Carol, Springer, Nathan M., Sun, Qi, Wang, Hao, Waterman, Michael, Westerman, Richard, Wolfgruber, Thomas K., Yang, Lixing, Yu, Yeisoo, Zhang, Lifang, Zhou, Shiguo, Zhu, Qihui, Bennetzen, Jeffrey L., Dawe, R. Kelly, Jiang, Jiming, Jiang, Ning, Presting, Gernot G., Wessler, Susan R., Aluru, Srinivas, Martienssen, Robert A., Clifton, Sandra W., McCombie, W. Richard, Wing, Rod A., and Wilson, Richard K.

Published
2009
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29. The International Oryza Map Alignment Project (IOMAP): the Americas—past achievements and future directions.

Author

Alsantely, Aseel, Gutaker, Rafal, Rodríguez, María E Navarrete, Arrieta-Espinoza, Griselda, Fuchs, Eric J, Oliveira, Antonio Costa de, Tohme, Joe, Zuccolo, Andrea, Wing, Rod A, and Fornasiero, Alice

Subjects
ORYZA, GENETIC variation, BIODIVERSITY conservation, WILD rice, BOTANICAL specimens, RICE, RICE straw
Abstract

The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (O MAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of >600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of 'I O MAP: the Americas' is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas. [ABSTRACT FROM AUTHOR]

Published
2023
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30. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Author

Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, da Rosa Farias, Daniel, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen, and Wing, Rod A.

Published
2018
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36. The Norway spruce genome sequence and conifer genome evolution

Author

Nystedt, Björn, Street, Nathaniel R., Wetterbom, Anna, Zuccolo, Andrea, Lin, Yao-Cheng, Scofield, Douglas G., Vezzi, Francesco, Delhomme, Nicolas, Giacomello, Stefania, Alexeyenko, Andrey, Vicedomini, Riccardo, Sahlin, Kristoffer, Sherwood, Ellen, Elfstrand, Malin, Gramzow, Lydia, Holmberg, Kristina, Hällman, Jimmie, Keech, Olivier, Klasson, Lisa, Koriabine, Maxim, Kucukoglu, Melis, Käller, Max, Luthman, Johannes, Lysholm, Fredrik, Niittylä, Totte, Olson, Åke, Rilakovic, Nemanja, Ritland, Carol, Rosselló, Josep A., Sena, Juliana, Svensson, Thomas, Talavera-López, Carlos, Theien, Günter, Tuominen, Hannele, Vanneste, Kevin, Wu, Zhi-Qiang, Zhang, Bo, Zerbe, Philipp, Arvestad, Lars, Bhalerao, Rishikesh, Bohlmann, Joerg, Bousquet, Jean, Gil, Rosario Garcia, Hvidsten, Torgeir R., de Jong, Pieter, MacKay, John, Morgante, Michele, Ritland, Kermit, Sundberg, Björn, Lee Thompson, Stacey, Van de Peer, Yves, Andersson, Björn, Nilsson, Ove, Ingvarsson, Pär K., Lundeberg, Joakim, and Jansson, Stefan

Published
2013
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37. A physical, genetic and functional sequence assembly of the barley genome

Author

Mayer, Klaus F. X., Waugh, Robbie, Langridge, Peter, Close, Timothy J., Wise, Roger P., Graner, Andreas, Matsumoto, Takashi, Sato, Kazuhiro, Schulman, Alan, Muehlbauer, Gary J., Stein, Nils, Ariyadasa, Ruvini, Schulte, Daniela, Poursarebani, Naser, Zhou, Ruonan, Steuernagel, Burkhard, Mascher, Martin, Scholz, Uwe, Shi, Bujun, Madishetty, Kavitha, Svensson, Jan T., Bhat, Prasanna, Moscou, Matthew, Resnik, Josh, Hedley, Pete, Liu, Hui, Morris, Jenny, Frenkel, Zeev, Korol, Avraham, Bergès, Hélène, Stein, Nils, Taudien, Stefan, Felder, Marius, Groth, Marco, Platzer, Matthias, Himmelbach, Axel, Lonardi, Stefano, Duma, Denisa, Alpert, Matthew, Cordero, Francesa, Beccuti, Marco, Ciardo, Gianfranco, Ma, Yaqin, Wanamaker, Steve, Close, Timothy J., Cattonaro, Federica, Vendramin, Vera, Scalabrin, Simone, Radovic, Slobodanka, Wing, Rod, Morgante, Michele, Waugh, Robbie, Nussbaumer, Thomas, Gundlach, Heidrun, Martis, Mihaela, Poland, Jesse, Mayer, Klaus F. X., Spannagl, Manuel, Pfeifer, Matthias, Moisy, Cédric, Tanskanen, Jaakko, Zuccolo, Andrea, Mayer, Klaus F. X., Schulman, Alan, Russell, Joanne, Druka, Arnis, Marshall, David, Bayer, Micha, Swarbreck, David, Sampath, Dharanya, Ayling, Sarah, Febrer, Melanie, Caccamo, Mario, Tanaka, Tsuyoshi, Wannamaker, Steve, Schmutzer, Thomas, Waugh, Robbie, Brown, John W. S., and Fincher, Geoffrey B.

Published
2012
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38. The Chromosome-Scale Genome and Methylome of Pinus Tabuliformis and the Evolution of Conifers

Author

Niu, Shihui, primary, Li, Jiang, additional, Bo, Wenhao, additional, Yang, Weifei, additional, Zuccolo, Andrea, additional, Giacomello, Stefania, additional, Ma, Jingjing, additional, Han, Fangxu, additional, Chen, Xi, additional, Yang, Junhe, additional, Song, Yitong, additional, Nie, Yumeng, additional, Zhou, Biao, additional, Wang, Peiyi, additional, Zuo, Quan, additional, Zhang, Hui, additional, Wang, Jun, additional, Wang, Lvji, additional, Liu, Zhanmin, additional, Zhang, Xuemei, additional, Liu, Tao, additional, Pei, Surui, additional, Li, Zhimin, additional, Hu, Yao, additional, Yang, Yehui, additional, Li, Wenzhao, additional, Lin, Jinxing, additional, Zan, Yanjun, additional, Zhou, Linghua, additional, Yuan, Tongqi, additional, Li, Wei, additional, Li, Yue, additional, Wei, Hairong, additional, and Wu, Harry X., additional

Published
2021
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39. Assembly and Validation of Two Gap-free Reference Genomes forXian/indicaRice Reveals Insights into Plant Centromere Architecture

Author

Song, Jia-Ming, primary, Xie, Wen-Zhao, additional, Wang, Shuo, additional, Guo, Yi-Xiong, additional, Koo, Dal-Hoe, additional, Kudrna, Dave, additional, Huang, Yicheng, additional, Feng, Jia-Wu, additional, Zhang, Wenhui, additional, Zhou, Yong, additional, Zuccolo, Andrea, additional, Long, Evan, additional, Lee, Seunghee, additional, Talag, Jayson, additional, Zhou, Run, additional, Zhu, Xi-Tong, additional, Yuan, Daojun, additional, Udall, Joshua, additional, Xie, Weibo, additional, Wing, Rod A., additional, Zhang, Qifa, additional, Poland, Jesse, additional, Zhang, Jianwei, additional, and Chen, Ling-Ling, additional

Published
2020
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41. A draft genome of sweet cherry ( Prunus avium L.) reveals genome‐wide and local effects of domestication

Author

Pinosio, Sara, primary, Marroni, Fabio, additional, Zuccolo, Andrea, additional, Vitulo, Nicola, additional, Mariette, Stephanie, additional, Sonnante, Gabriella, additional, Aravanopoulos, Filippos A., additional, Ganopoulos, Ioannis, additional, Palasciano, Marino, additional, Vidotto, Michele, additional, Magris, Gabriele, additional, Iezzoni, Amy, additional, Vendramin, Giovanni G., additional, and Morgante, Michele, additional

Published
2020
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43. The Rice Annotation Project Database (RAP-DB): 2008 update*

Author

Tanaka, Tsuyoshi, Antonio, Baltazar A., Kikuchi, Shoshi, Matsumoto, Takashi, Nagamura, Yoshiaki, Numa, Hisataka, Sakai, Hiroaki, Wu, Jianzhong, Itoh, Takeshi, Sasaki, Takuji, Aono, Ryo, Fujii, Yasuyuki, Habara, Takuya, Harada, Erimi, Kanno, Masako, Kawahara, Yoshihiro, Kawashima, Hiroaki, Kubooka, Hiromi, Matsuya, Akihiro, Nakaoka, Hajime, Saichi, Naomi, Sanbonmatsu, Ryoko, Sato, Yoshiharu, Shinso, Yuji, Suzuki, Mami, Takeda, Jun-ichi, Tanino, Motohiko, Todokoro, Fusano, Yamaguchi, Kaori, Yamamoto, Naoyuki, Yamasaki, Chisato, Imanishi, Tadashi, Okido, Toshihisa, Tada, Masahito, Ikeo, Kazuho, Tateno, Yoshio, Gojobori, Takashi, Lin, Yao-Cheng, Wei, Fu-Jin, Hsing, Yue-ie, Zhao, Qiang, Han, Bin, Kramer, Melissa R., McCombie, Richard W., Lonsdale, David, O’Donovan, Claire C., Whitfield, Eleanor J., Apweiler, Rolf, Koyanagi, Kanako O., Khurana, Jitendra P., Raghuvanshi, Saurabh, Singh, Nagendra K., Tyagi, Akhilesh K., Haberer, Georg, Fujisawa, Masaki, Hosokawa, Satomi, Ito, Yukiyo, Ikawa, Hiroshi, Shibata, Michie, Yamamoto, Mayu, Bruskiewich, Richard M., Hoen, Douglas R., Bureau, Thomas E., Namiki, Nobukazu, Ohyanagi, Hajime, Sakai, Yasumichi, Nobushima, Satoshi, Sakata, Katsumi, Barrero, Roberto A., Sato, Yutaka, Souvorov, Alexandre, Smith-White, Brian, Tatusova, Tatiana, An, Suyoung, An, Gynheung, OOta, Satoshi, Fuks, Galina, Messing, Joachim, Christie, Karen R., Lieberherr, Damien, Kim, HyeRan, Zuccolo, Andrea, Wing, Rod A., Nobuta, Kan, Green, Pamela J., Lu, Cheng, Meyers, Blake C., Chaparro, Cristian, Piegu, Benoit, Panaud, Olivier, and Echeverria, Manuel

Published
2008

46. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

Author

Usai, Gabriele, primary, Mascagni, Flavia, additional, Giordani, Tommaso, additional, Vangelisti, Alberto, additional, Bosi, Emanuele, additional, Zuccolo, Andrea, additional, Ceccarelli, Marilena, additional, King, Robert, additional, Hassani‐Pak, Keywan, additional, Zambrano, Liceth S., additional, Cavallini, Andrea, additional, and Natali, Lucia, additional

Published
2020
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47. Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice

Author

Zhou, Yong, primary, Chebotarov, Dmytro, additional, Kudrna, Dave, additional, Llaca, Victor, additional, Lee, Seunghee, additional, Rajasekar, Shanmugam, additional, Mohammed, Nahed, additional, Al-Bader, Noor, additional, Sobel-Sorenson, Chandler, additional, Parakkal, Praveena, additional, Arbelaez, Lady Johanna, additional, Franco, Natalia, additional, Alexandrov, Nickolai, additional, Hamilton, N. Ruaraidh Sackville, additional, Leung, Hei, additional, Mauleon, Ramil, additional, Lorieux, Mathias, additional, Zuccolo, Andrea, additional, McNally, Kenneth, additional, Zhang, Jianwei, additional, and Wing, Rod A., additional

Published
2019
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48. A draft physical map of a D-genome cotton species (Gossypium raimondii)

Author

Kudrna Dave, Karunakaran Santhosh, Ingles Jennifer, Grover Corrinne, Golser Wolfgang, Epps Ethan, Collura Kristi, Chicola Kristen, Chen Amy H, Braidotti Michele, Wang Xiyin, Tang Haibao, Rong Junkang, Lemke Cornelia, Kim Changsoo, Rainville Lisa K, Compton Rosana O, Estill James C, Bowers John E, Pierce Gary J, Lin Lifeng, Olive Jaime, Tabassum Nabila, Um Eareana, Wissotski Marina, Yu Yeisoo, Zuccolo Andrea, ur Rahman Mehboob, Peterson Daniel G, Wing Rod A, Wendel Jonathan F, and Paterson Andrew H

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. Results A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. Conclusion Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.

Published
2010
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49. Transposable element distribution, abundance and role in genome size variation in the genus Oryza

Author

Collura Kristi, Kim HyeRan, Yu Yeisoo, Talag Jayson, Sebastian Aswathy, Zuccolo Andrea, Kudrna Dave, and Wing Rod A

Subjects
Evolution, QH359-425
Abstract

Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

Published
2007
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50. Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey

Author

Inoko Hidetoshi, Yanagiya Kazuyo, Grim Suzanne M, Buckingham E Bryan, Zuccolo Andrea, Collura Kristi, Mueller Christopher, Lee So-Jeong, Sisneros Nicholas B, Kudrna Dave, Kim HyeRan, Luo Meizhong, Shiina Takashi, Flajnik Martin F, Wing Rod A, and Ohta Yuko

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

Published
2006
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