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