In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.

^* Consortium Members (corresponding authors): Arizona Genomics Institute, Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, University of Wisconsin (ACWW) Rice Genome Sequencing Consortium: ¹Arizona Genomics Institute, ²Arizona Genomics Computational Laboratory, Department of Plant Sciences, 303 Forbes Building, The University of Arizona, Tucson, AZ 85721, USA. ³Clemson University Genomics Institute, 100 Jordan Hall, Clemson University, Clemson, SC 29634, USA. ⁴Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. ⁵Washington University School of Medicine Genome Sequencing Center, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA. ⁶University of Wisconsin-Madison, Department of Horticulture, Madison, WI 53706: Yeisoo Yu,^1,3 Teri Rambo,^1,3 Jennifer Currie,^1,3 Christopher Saski,^1,3 Hye Ran Kim,^1,3 Kristi Collura,^1,3 Shelly Thompson,^1,3 Jessica Simmons,³ Tae-Jin Yang,^1,3 Gyoungju Nah,^1,3 Ami J. Patel,³ Scheen Thurmond,^1,3 David Henry,³ Ryan Oates,³ Michael Palmer,³ Gina Pries,³ Jennifer Gibson,³ Heidi Anderson,³ Manjiri Paradkar,³ Lindsay Crane,³ Jeff Dale,³ Megan B.-Carver,³ Todd Wood,³ David Frisch,³ Friedrich Engler,^2,3 Cari Soderlund,^2,3 Lance E. Palmer,⁴ Leonid Tetylman,⁴ Lidia Nascimento,⁴ Melissa de la Bastide,⁴ Lori Spiegel,⁴ Doreen Ware,⁴ Andrew O'Shaughnessy,⁴ Sujit Dike,⁴ Neilay Dedhia,⁴ Raymond Preston,⁴ Emily Huang,⁴ Kristin Ferraro,⁴ Kathy Kuit,⁴ Beth Miller,⁴ Theresa Zutavern,⁴ Frederick Katzenberger,⁴ Stephanie Muller,⁴ Vivekanand Balija,⁴ Robert A. Martienssen,⁴ Lincoln Stein,⁴ Pat Minx,⁵ Doug Johnson,⁵ Holly Cordum,⁵ Elaine Mardis,⁵ Zhukuan Cheng,⁶ Jiming Jiang,⁶ Richard Wilson,⁵ W. Richard McCombie,⁴ and Rod A. Wing.^1,3 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA, and ⁷Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21218, USA.: Qiaoping Yuan, Shu Ouyang, Jia Liu, Kristine M. Jones, Kristen Gansberger, Kelly Moffat, Jessica Hill, Tamara Tsitrin, Larry Overton, Jyati Bera, Mary Kim, Shaohua Jin, Luke Tallon, Anne Ciecko, Grace Pai, Susan Van Aken, Terry Utterback, Steve Reidmuller, Jon Bormann, Tamara Feldblyum, Joseph Hsiao, Victoria Zismann, Stacey Blunt, Aymeric de Vazeilles, Tristan Shaffer, Hean Koo, Bernard Suh, Qi Yang, Brian Haas, Jeremy Peterson, Mihaela Pertea, Natalia Volfovsky⁷ (Present address: Advanced Biomedical Computer Center, National Cancer Institute–Frederick/SAIC, Frederick, MD 21702, USA), Jennifer Wortman, Owen White, Steven L. Salzberg,⁷ Claire M. Fraser, and C. Robin Buell. PGIR-Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA: Joachim Messing, Rentao Song, Galina Fuks, Victor Llaca, Steve Kovchak, and Steve Young. Plant Genome Mapping Laboratory, University of Georgia, Athens GA 30602, USA: John E. Bowers and Andrew H. Paterson. Department of Biological Sciences, Montgomery Hall, Northern Illinois University, DeKalb, IL 60115, USA: Mitrick A. Johns and Long Mao. Center for Integrated Fungal Research, Box 7251, 840 Main Campus Drive, Suite 1200, North Carolina State University, Raleigh, NC 27695–7251, USA: Huaqin Pan and Ralph A. Dean. To whom correspondence should be addressed. E-mail: rbuell{at}tigr.org (C.R.B.); messing{at}waksman.rutgers.edu (J.M.); mccombie{at}cshl.edu (W.R.M.); rwing{at}ag.arizona.edu (R.A.W.)