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

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

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Background: Rice 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. Results: We 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. Conclusion: Because 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 envolved 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 peviously suggested. © 2005 Rice Chromosomes 11 and 12 Sequencing Consortia and Messing, licensee BioMed Central Ltd.
Original languageEnglish (US)
JournalBMC Biology
StatePublished - Sep 27 2005
Externally publishedYes


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