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1. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

Author

Ying Wang, Chantal Schenowitz, Jeffrey P. Tomkins, Claudine Médigue, Luis Gabriel Wall, Claudio Valverde, Benoit Cournoyer, Nadia Demange, Philippe Normand, Alison M. Berry, Louis S. Tisa, Juliana E. Mastronunzio, David Vallenet, David R. Benson, Pascal Lapierre, Emilie Bagnarol, Tania Rawnsley, Nathalie Choisne, Zoé Rouy, Johann Peter Gogarten, Céline Lavire, Alla Lapidus, Nicole Alloisio, Vincent Daubin, Arnaud Couloux, Stéphane Cruveiller, Ying Huang, Carla A. Bassi, James Niemann, Maria Pilar Francino, Derek M. Bickhart, J Maréchal, Laurent Labarre, Beth C. Mullin, Fernando Tavares, Olga R. Kopp, Michele Martinez, Eugene Goltsman, Anita Sellstedt, Pierre Pujic, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Department of Molecular and Cell Biology, University of Connecticut (UCONN), Department of Microbiology, University of New Hampshire (UNH), Department of Plant Sciences [Davis, CA], University of California [Davis] (UC Davis), University of California-University of California, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Department of Biochemistry & Cellular & Molecular Biology and the Genome Science & Technology Program, The University of Tennessee [Knoxville], Department of Biochemistry & Cellular 1 Molecular Biology and The Genome Science & Technology Program, Department of Plant Physiology, Umeå University, Genomics Institute, Clemson University, Departamento de Ciencia y Tecnología [Buenos Aires], Universidad Nacional de Quilmes (UNQ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), University of Connecticut ( UCONN ), University of New Hampshire ( UNH ), University of California [Davis] ( UC Davis ), Unité de recherche en génomique végétale ( URGV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biométrie et Biologie Evolutive ( LBBE ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique ( Inria ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Energy / Joint Genome Institute ( DOE ), Los Alamos National Laboratory ( LANL ), Programa Interacciones Biologicas, Departamento de Cienca y Tecnologia, Universidad Nacional de Quilmes, Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Sciences [Univ California Davis] (Plant - UC Davis), and University of California (UC)-University of California (UC)

Subjects
DNA, Bacterial, Root nodule, Prophages, [SDE.BE.ECOM]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Molecular Sequence Data, Frankia, Plant Roots, Genome, Article, Actinobacteria, Evolution, Molecular, Magnoliopsida, 03 medical and health sciences, Symbiosis, Gene Duplication, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, Phylogeny, Genetics (clinical), 030304 developmental biology, 2. Zero hunger, Frankia alni, [ SDE.BE ] Environmental Sciences/Biodiversity and Ecology, 0303 health sciences, Facultative, Geography, biology, 030306 microbiology, fungi, food and beverages, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], DNA Transposable Elements, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Actinorhizal plant, [ SDE.BE.ECOM ] Environmental Sciences/Biodiversity and Ecology/domain_sde.be.ecom, Gene Deletion, Genome, Bacterial
Abstract

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the “actinorhizal” symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.

Published
2006
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2. The map-based sequence of the rice genome

Author

Shu Mei Liu, Hong-Hwa Chen, Kiran Kumar, Aki Iwabuchi, Luke J. Tallon, Yasuyuki Fujii, Yuichi Ito, Jennifer Currie, Douglas Fadrosh, Bruce Weaver, Hisakazu Iwama, Nahoko Fujitsuka, Arvind K. Bharti, Vivek Dalal, Eric Pelletier, Wataru Karasawa, Carol Soderlund, Masako Okamoto, Ajit K. Pal, Lei Zhang, Tomoko Maehara, Anupama Gaur, Tomotaro Nishikawa, Michiko Ikeda, Jingjie Zhu, Meizhong Luo, Yoshiharu Sato, Dibyendu Kumar, Mikiko Honda, Takuya Habara, Jianyu Song, Yuka Takazaki, Alok Singh, Ari Kikuta, Neilay Dedhia, Thomas E. Bureau, Eric Linton Victor Llaca, Nadia Demange, Yoshiaki Nagamura, Koh Ichi Kadowaki, Takanori Shimokawa, Kohei Arita, Patrick Wincker, Saori Hijishita, Kai Ying, Takahito Bito, Tae-Jin Yang, Mayu Yamamoto, Masahiro Yano, Paulo Dejalma Zimmer, Nagendra K. Singh, Atsuko Idonuma, Jia Liu, Anne Ciecko, Friedrich Engler, Shinji Naito, Pei Fang Lee, Hideki Nagasaki, Jianping Guan, Yoko Ichikawa, Sujit Dike, Shu Ouyang, Yuko Nakama, Masao Hamada, Saurabh Raghuvanshi, Ching San Chen, Teh Yuan Chow, Joseph Hsiao, Béatrice Segurens, Hiroaki Sakai, W. Richard McCombie, Nobukazu Namiki, Hiroyuki Kanamori, Mei-Chu Chung, Yiqi Lu, Claude Scarpelli, Kelly Moffat, Yoshino Chiden, Baltazar A. Antonio, Susan R. McCouch, Paramjit Khurana, Amy Bronzino Nelson, Tamara Feldblyum, Hiroshi Mizuno, Masatoshi Masukawa, Yoshihito Niimura, Tomoya Ohta, Joachim Messing, Yukiyo Ito, Lance E. Palmer, Antonio Costa de Oliveira, Nozomi Ono, Ai Ling Hour, Kumiko Tsuji, Qijun Weng, Michael W. Bevan, Guofan Hong, C. Robin Buell, Subodh K. Srivastava, Atul Bhargava, Galina Fuks, Masahiro Sugiura, Akio Miyao, Kristine Jones, John Yu Liou, Ayano Meguro, Aymeric R. De Vazeille, Mika Tsugane, Xiaohui Liu, Rie Fukunaka, Jean Weissenbach, Shu Jen Lin, Jayati Bera, Tomoya Baba, Yao-Cheng Lin, Lori Spiegel, Laurence Cattolico, Irfan Ahmad Ghazi, Shoko Saji, Jianzhong Wu, Danlin Fan, Takashi Gojobori, Rod A. Wing, Harumi Yamagata, Koji Arikawa, Shuliang Yu, Marcel Salanoubat, Yumi Nakamichi, Kristi Collura, Jetty S.S. Ammiraju, Vipin Gupta, Stephen I. Wright, Y. Huang, Qiang Zhao, Yuichi Katayose, Tingting Lu, Stacey E. Iobst, Akhilesh K. Tyagi, A. O'Shaughnessy, Tilak Raj Sharma, Hiroyoshi Aoki, Kazue Ito, Marina Nakashima, Vydianathan Ravi, J. F. Shaw, Takashi Matsumoto, Tamara Tsitrin, Yoshiyuki Mukai, Steve Reidmuller, Steve Young, Kozue Kamiya, Lidia Nascimento, Qi Feng, Shivani Johri, Kazuko Yukawa, Sylvie Samain, Hirohiko Hirochika, Kimiko Yamamoto, Matthew Reardon, Holly Cordum, Mu Kuei Chu, Kim Yul Ho, Victoria Zismann, Jessica Hill, Tomoko Ito, Gregory Wilson, Isamu Ohta, Bahattin Tanyolac, Amitabh Mohanty, Rie Yoshihara, Nikoleta Juretic, Bin Han, Jie Mu, Susan Van Aken, Satomi Hosokawa, Kayo Machita, Shaohua Jin, Odir Antônio Dellagostin, Satoshi Katagiri, Apichart Vanavichit, Takuji Sasaki, Douglas R. Hoen, Richard K. Wilson, Patrick Minx, Larry Overton, Rentao Song, Kimihiro Terasawa, Jang Ho Hahn, Steve Kavchok, Hiroko Yamane, Parul Khurana, Melissa De La Bastide, Gisela Orjeda, Francis Quetier, Katsumi Sakata, Anita Kapur, Hyeran Kim, Grace Pai, Ian Bancroft, Trilochan Mohapatra, Manami Negishi, Ya Ting Chao, Kanako Kurita, Mari Nakamura, Masaki Fujisawa, Maiko Ikeno, Yu Zhang, Miyuki Sakaguchi, Yuko Nagata, Harumi Kobayashi, Kamlesh Batra, Huisun Zhong, Mary Kim, T. Utterback, Shoji Yoshiki, A. Pandit, Chizuko Harada, Benjamin Burr, Jacqueline Jackson, Jitendra P. Khurana, Michie Shibata, Jiming Jiang, Hue Vuong, Chia Hsiung Cheng, Sachie Ito, Zhukuan Cheng, Qiaoping Yuan, Akiko Hayashi, Tatsumi Mizubayashi, Yeisoo Yu, Nathalie Choisne, Shubha Vij, Noriko Kobayashi, Vivekanand Balija, Hong Pang Wu, K. Sureshbabu, Ying Li, Theresa Zutavern, G. Sangsakoo, Kristen Gansberger, Yujun Zhang, Kazunori Waki, Weiwei Jin, R. Preston, Shigenori Ueda, Yilei Liu, Angélique D'Hont, Kwang-Jen Hsiao, Kumiko Sakai, Richard Bruskiewich, Luiz Anderson Teixeira de Mattos, Teri Rambo, Yue-Ie C. Hsing, Mahavir Yadav, Shinichi Yamamoto, Arnaud Couloux, Sally A. Leong, Kishor Gaikwad, Masumi Iijima, Takeshi Itoh, Gaspar Malone, Gladys Keizer, and Anupam Dixit

Subjects
Transposable element, Identification, RNA, Untranslated, Euchromatin, International Cooperation, Centromere, Molecular Sequence Data, Arabidopsis, Oryza sativa, Biology, Genes, Plant, Zea mays, Genome, Chromosomes, Plant, F30 - Génétique et amélioration des plantes, Gene family, Cloning, Molecular, Gene, Sorghum, Synteny, Cell Nucleus, Organelles, Genetics, Polymorphism, Genetic, Génome, Multidisciplinary, Computational Biology, food and beverages, Oryza, Genomics, Sequence Analysis, DNA, Tandem Repeat Sequences, Gène, Multigene Family, Proteome, DNA Transposable Elements, Carte génétique, Genome, Plant, Caractère agronomique
Abstract

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Published
2005
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3. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Author

Wei Zhu, Jitendra P. Khurana, Wenming Wang, Paramjit Khurana, Kamlesh Batra, Ashutosh Bhargava, Victoria Zismann, Mary Kim, Teri Rambo, Alok Singh, K. Sureshbabu, Laurence Cattolico, Teresa Utterback, Tilak Raj Sharma, Joachim Messing, Patrick Wincker, Theresa Zutavern, Jia Liu, Susan Van Aken, Steven L. Salzberg, Douglas Fadrosh, Subodh K. Srivastava, Tamara Feldblyum, Mahavir Yadav, C. Robin Buell, Arnaud Couloux, Shuba Vij, Gisela Orjeda, Matthew R. Lewis, Jennifer Currie, Christopher Mueller, Lori Spiegel, Irfan Ahmad Ghazi, Matt Reardon, Sylvie Samain, Dave Kudrna, Larry Overton, Rod A. Wing, Anupama Gaur, Kishor Gaikwad, Vikrant Gupta, Ravi Vydianathan, Nathalie Choisne, Trilochan Mohapatra, Anita Kapur, Hyeran Kim, Luke J. Tallon, Rekha Dixit, Nadia Demange, Parul Khurana, Jennifer R. Wortman, Claire M. Fraser, Jayati Bera, M. Ragiba, John P. Hamilton, Owen White, Bruce Weaver, Kristine Jones, Qiaoping Yuan, Anupam Dixit, Sulabha Sharma, Shivani Johri, Lidia Nascimento, Sangeeta D. Mendiratta, Claude Scarpelli, Dibyendu Kumar, Hue Vuong, Haining Lin, Aymeric R. De Vazeille, Diana Stum, Awadhesh Pandit, Brian J. Haas, Harvinder Singh, Yeisoo Yu, Jean Weissenbach, Vibha Singhal, Amitabh Mohanty, Shaohua Jin, Vivek Dalal, Saurabh Raghuvanshi, Joseph Hsiao, Béatrice Segurens, Melissa Kramer, Marcel Salanoubat, Stacey E. Iobst, Akhilesh K. Tyagi, Kristi Collura, Arvind K. Bharti, Eric Pelletier, Ajit K. Pal, Nagendra K. Singh, Shu Ouyang, Pradeep K. Singh, Tamara Tsitrin, R. Preston, Angélique D'Hont, Suresh C. Swain, Aihui Wang, and Sumita Pal

Subjects
0106 biological sciences, Physiology, Oryza sativa, Plant Science, Paralogous Gene, Biology, 01 natural sciences, Genome, Chromosomes, Plant, General Biochemistry, Genetics and Molecular Biology, F30 - Génétique et amélioration des plantes, 03 medical and health sciences, Structural Biology, Gene Duplication, Chromosome 19, Gene duplication, Gene family, Triticum, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Repetitive Sequences, Nucleic Acid, 030304 developmental biology, Segmental duplication, Synteny, 2. Zero hunger, Genetics, 0303 health sciences, Chromosome Mapping, food and beverages, Oryza, Cell Biology, Genome project, Immunity, Innate, General Agricultural and Biological Sciences, Genome, Plant, Research Article, 010606 plant biology & botany, Developmental Biology, Biotechnology
Abstract

BackgroundRice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals.ResultsWe have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes.ConclusionBecause the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested.

Published
2005
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