The Complete Sequence of 340 kb of DNA around the Rice Adh1–Adh2 Region Reveals Interrupted Colinearity with Maize Chromosome 4

Correspondence to: Antoni Rafalski, j-antoni.rafalski{at}usa.dupont.com (E-mail), 302-631-2607 (fax)

A 2.3-centimorgan (cM) segment of rice chromosome 11 consisting of 340 kb of DNA sequence around the alcohol dehydrogenase Adh1 and Adh2 loci was completely sequenced, revealing the presence of 33 putative genes, including several apparently involved in disease resistance. Fourteen of the genes were confirmed by identifying the corresponding transcripts. Five genes, spanning 1.9 cM of the region, cross-hybridized with maize genomic DNA and were genetically mapped in maize, revealing a stretch of colinearity with maize chromosome 4. The Adh1 gene marked one significant interruption. This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. Several other genes, most notably genes similar to known disease resistance genes, showed no cross-hybridization with maize genomic DNA, suggesting sequence divergence or absence of these sequences in maize, which is in contrast to several other well-conserved genes, including Adh1 and Adh2. These findings indicate that the use of rice as the model system for other cereals may sometimes be complicated by the presence of rapidly evolving gene families and microtranslocations. Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner–like element, which is new to rice. In contrast to maize, retroelements are less frequent in rice. Only 14.4% of this genome segment consist of retroelements. Miniature inverted repeat transposable elements were found to be the most frequently occurring class of repetitive elements, accounting for 18.8% of the total repetitive DNA.

This article has been cited by other articles:

				R. Terada, Y. Johzuka-Hisatomi, M. Saitoh, H. Asao, and S. Iida Gene Targeting by Homologous Recombination as a Biotechnological Tool for Rice Functional Genomics Plant Physiology, June 1, 2007; 144(2): 846 - 856. [Abstract] [Full Text] [PDF]

				L.-B. Zhang and S. Ge Multilocus Analysis of Nucleotide Variation and Speciation in Oryza officinalis and Its Close Relatives Mol. Biol. Evol., March 1, 2007; 24(3): 769 - 783. [Abstract] [Full Text] [PDF]

				W. Odland, A. Baumgarten, and R. Phillips Ancestral Rice Blocks Define Multiple Related Regions in the Maize Genome Crop Sci., November 1, 2006; 46(Supplement_1): S-41 - S-48. [Abstract] [Full Text] [PDF]

				G. Yang, C. F. Weil, and S. R. Wessler A Rice Tc1/Mariner-Like Element Transposes in Yeast PLANT CELL, October 1, 2006; 18(10): 2469 - 2478. [Abstract] [Full Text] [PDF]

				L. Timms, R. Jimenez, M. Chase, D. Lavelle, L. McHale, A. Kozik, Z. Lai, A. Heesacker, S. Knapp, L. Rieseberg, et al. Analyses of Synteny Between Arabidopsis thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements Genetics, August 1, 2006; 173(4): 2227 - 2235. [Abstract] [Full Text] [PDF]

				J. S.S. Ammiraju, M. Luo, J. L. Goicoechea, W. Wang, D. Kudrna, C. Mueller, J. Talag, H. Kim, N. B. Sisneros, B. Blackmon, et al. The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza Genome Res., January 1, 2006; 16(1): 140 - 147. [Abstract] [Full Text] [PDF]

				G. Haberer, S. Young, A. K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R. A. Wing, S. Rounsley, B. Birren, et al. Structure and Architecture of the Maize Genome Plant Physiology, December 1, 2005; 139(4): 1612 - 1624. [Abstract] [Full Text] [PDF]

				C. Feschotte, M. T. Osterlund, R. Peeler, and S. R. Wessler DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs Nucleic Acids Res., April 14, 2005; 33(7): 2153 - 2165. [Abstract] [Full Text] [PDF]

				S. Brunner, K. Fengler, M. Morgante, S. Tingey, and A. Rafalski Evolution of DNA Sequence Nonhomologies among Maize Inbreds PLANT CELL, February 1, 2005; 17(2): 343 - 360. [Abstract] [Full Text] [PDF]

				C. E. Grover, H. Kim, R. A. Wing, A. H. Paterson, and J. F. Wendel Incongruent Patterns of Local and Global Genome Size Evolution in Cotton Genome Res., August 1, 2004; 14(8): 1474 - 1482. [Abstract] [Full Text] [PDF]

				X. Zhang, N. Jiang, C. Feschotte, and S. R. Wessler PIF- and Pong-Like Transposable Elements: Distribution, Evolution and Relationship With Tourist-Like Miniature Inverted-Repeat Transposable Elements Genetics, February 1, 2004; 166(2): 971 - 986. [Abstract] [Full Text] [PDF]

				K. Ilic, P. J. SanMiguel, and J. L. Bennetzen A complex history of rearrangement in an orthologous region of the maize, sorghum, and rice genomes PNAS, October 14, 2003; 100(21): 12265 - 12270. [Abstract] [Full Text] [PDF]

				K. Vandepoele, C. Simillion, and Y. Van de Peer Evidence That Rice and Other Cereals Are Ancient Aneuploids PLANT CELL, September 1, 2003; 15(9): 2192 - 2202. [Abstract] [Full Text] [PDF]

				M. E. Sorrells, M. La Rota, C. E. Bermudez-Kandianis, R. A. Greene, R. Kantety, J. D. Munkvold, Miftahudin, A. Mahmoud, X. Ma, P. J. Gustafson, et al. Comparative DNA Sequence Analysis of Wheat and Rice Genomes Genome Res., August 1, 2003; 13(8): 1818 - 1827. [Abstract] [Full Text] [PDF]

				R. Song and J. Messing Gene expression of a gene family in maize based on noncollinear haplotypes PNAS, July 22, 2003; 100(15): 9055 - 9060. [Abstract] [Full Text] [PDF]

				S. Brunner, B. Keller, and C. Feuillet A Large Rearrangement Involving Genes and Low-Copy DNA Interrupts the Microcollinearity Between Rice and Barley at the Rph7 Locus Genetics, June 1, 2003; 164(2): 673 - 683. [Abstract] [Full Text] [PDF]

				H. Guo and S. P. Moose Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution PLANT CELL, May 1, 2003; 15(5): 1143 - 1158. [Abstract] [Full Text]

				C. Vitte and O. Panaud Formation of Solo-LTRs Through Unequal Homologous Recombination Counterbalances Amplifications of LTR Retrotransposons in Rice Oryza sativa L. Mol. Biol. Evol., April 1, 2003; 20(4): 528 - 540. [Abstract] [Full Text] [PDF]

				C. Feschotte, L. Swamy, and S. R. Wessler Genome-Wide Analysis of mariner-Like Transposable Elements in Rice Reveals Complex Relationships With Stowaway Miniature Inverted Repeat Transposable Elements (MITEs) Genetics, February 1, 2003; 163(2): 747 - 758. [Abstract] [Full Text] [PDF]

				Z.-N. Yang, X.-R. Ye, J. Molina, M. L. Roose, and T. E. Mirkov Sequence Analysis of a 282-Kilobase Region Surrounding the Citrus Tristeza Virus Resistance Gene (Ctv) Locus in Poncirus trifoliata L. Raf. Plant Physiology, February 1, 2003; 131(2): 482 - 492. [Abstract] [Full Text] [PDF]

				N. Jiang, I. K. Jordan, and S. R. Wessler Dasheng and RIRE2. A Nonautonomous Long Terminal Repeat Element and Its Putative Autonomous Partner in the Rice Genome Plant Physiology, December 1, 2002; 130(4): 1697 - 1705. [Abstract] [Full Text] [PDF]

				D. T. Morishige, K. L. Childs, L. D. Moore, and J. E. Mullet Targeted Analysis of Orthologous Phytochrome A Regions of the Sorghum, Maize, and Rice Genomes using Comparative Gene-Island Sequencing Plant Physiology, December 1, 2002; 130(4): 1614 - 1625. [Abstract] [Full Text] [PDF]

				K. Vandepoele, Y. Saeys, C. Simillion, J. Raes, and Y. Van de Peer The Automatic Detection of Homologous Regions (ADHoRe) and Its Application to Microcolinearity Between Arabidopsis and Rice Genome Res., November 1, 2002; 12(11): 1792 - 1801. [Abstract] [Full Text] [PDF]

				W. Ramakrishna, J. Dubcovsky, Y.-J. Park, C. Busso, J. Emberton, P. SanMiguel, and J. L. Bennetzen Different Types and Rates of Genome Evolution Detected by Comparative Sequence Analysis of Orthologous Segments From Four Cereal Genomes Genetics, November 1, 2002; 162(3): 1389 - 1400. [Abstract] [Full Text] [PDF]

				R. Song, V. Llaca, and J. Messing Mosaic Organization of Orthologous Sequences in Grass Genomes Genome Res., October 1, 2002; 12(10): 1549 - 1555. [Abstract] [Full Text] [PDF]

				X. Niu, T. Helentjaris, and N. J. Bate Maize ABI4 Binds Coupling Element1 in Abscisic Acid and Sugar Response Genes PLANT CELL, October 1, 2002; 14(10): 2565 - 2575. [Abstract] [Full Text] [PDF]

				F. Xu, E. S. Lagudah, S. P. Moose, and D. E. Riechers Tandemly Duplicated Safener-Induced Glutathione S-Transferase Genes from Triticum tauschii Contribute to Genome- and Organ-Specific Expression in Hexaploid Wheat Plant Physiology, September 1, 2002; 130(1): 362 - 373. [Abstract] [Full Text] [PDF]

				J. L. Bennetzen and W. Ramakrishna Exceptional haplotype variation in maize PNAS, July 9, 2002; 99(14): 9093 - 9095. [Full Text] [PDF]

				N. Jiang, Z. Bao, S. Temnykh, Z. Cheng, J. Jiang, R. A. Wing, S. R. McCouch, and S. R. Wessler Dasheng: A Recently Amplified Nonautonomous Long Terminal Repeat Element That Is a Major Component of Pericentromeric Regions in Rice Genetics, July 1, 2002; 161(3): 1293 - 1305. [Abstract] [Full Text] [PDF]

				C. Vieira, C. Nardon, C. Arpin, D. Lepetit, and C. Biemont Evolution of Genome Size in Drosophila. Is the Invader's Genome Being Invaded by Transposable Elements? Mol. Biol. Evol., July 1, 2002; 19(7): 1154 - 1161. [Abstract] [Full Text] [PDF]

				J. Yu, S. Hu, J. Wang, G. K.-S. Wong, S. Li, B. Liu, Y. Deng, L. Dai, Y. Zhou, X. Zhang, et al. A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) Science, April 5, 2002; 296(5565): 79 - 92. [Abstract] [Full Text] [PDF]

				W. Li and B. S. Gill The Colinearity of the Sh2/A1 Orthologous Region in Rice, Sorghum and Maize Is Interrupted and Accompanied by Genome Expansion in the Triticeae Genetics, March 1, 2002; 160(3): 1153 - 1162. [Abstract] [Full Text] [PDF]

				D. Sandhu and K. S. Gill Gene-Containing Regions of Wheat and the Other Grass Genomes Plant Physiology, March 1, 2002; 128(3): 803 - 811. [Abstract] [Full Text] [PDF]

				D. Ware, P. Jaiswal, J. Ni, X. Pan, K. Chang, K. Clark, L. Teytelman, S. Schmidt, W. Zhao, S. Cartinhour, et al. Gramene: a resource for comparative grass genomics Nucleic Acids Res., January 1, 2002; 30(1): 103 - 105. [Abstract] [Full Text] [PDF]

				C. FEUILLET and B. KELLER Comparative Genomics in the Grass Family: Molecular Characterization of Grass Genome Structure and Evolution Ann. Bot., January 1, 2002; 89(1): 3 - 10. [Abstract] [Full Text] [PDF]

				C. Feschotte and S. R. Wessler Mariner-like transposases are widespread and diverse in flowering plants PNAS, December 21, 2001; (2001) 22626699. [Abstract] [Full Text] [PDF]

				H. Liu, R. Sachidanandam, and L. Stein Comparative Genomics Between Rice and Arabidopsis Shows Scant Collinearity in Gene Order Genome Res., December 1, 2001; 11(12): 2020 - 2026. [Abstract] [Full Text] [PDF]

				H. Shao and Z. Tu Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons Genetics, November 1, 2001; 159(3): 1103 - 1115. [Abstract] [Full Text] [PDF]

				N. Jiang and S. R. Wessler Insertion Preference of Maize and Rice Miniature Inverted Repeat Transposable Elements as Revealed by the Analysis of Nested Elements PLANT CELL, November 1, 2001; 13(11): 2553 - 2564. [Abstract] [Full Text] [PDF]

				X. Zhang, C. Feschotte, Q. Zhang, N. Jiang, W. B. Eggleston, and S. R. Wessler P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases PNAS, September 26, 2001; (2001) 211442198. [Abstract] [Full Text] [PDF]

				T. Wiehe, S. Gebauer-Jung, T. Mitchell-Olds, and R. Guigo SGP-1: Prediction and Validation of Homologous Genes Based on Sequence Alignments Genome Res., September 1, 2001; 11(9): 1574 - 1583. [Abstract] [Full Text] [PDF]

				N. A. Eckardt Everything in Its Place: Conservation of Gene Order among Distantly Related Plant Species PLANT CELL, April 1, 2001; 13(4): 723 - 725. [Full Text]

				M. Freeling Grasses as a Single Genetic System. Reassessment 2001 Plant Physiology, March 1, 2001; 125(3): 1191 - 1197. [Full Text]

				B. S. Gaut Patterns of Chromosomal Duplication in Maize and Their Implications for Comparative Maps of the Grasses Genome Res., January 1, 2001; 11(1): 55 - 66. [Abstract] [Full Text]

				N. Stein, C. Feuillet, T. Wicker, E. Schlagenhauf, and B. Keller Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.) PNAS, November 8, 2000; (2000) 230361597. [Abstract] [Full Text]

				G. T. Bryan, K.-S. Wu, L. Farrall, Y. Jia, H. P. Hershey, S. A. McAdams, K. N. Faulk, G. K. Donaldson, R. Tarchini, and B. Valent tA Single Amino Acid Difference Distinguishes Resistant and Susceptible Alleles of the Rice Blast Resistance Gene Pi-ta PLANT CELL, November 1, 2000; 12(11): 2033 - 2046. [Abstract] [Full Text]

				A. M. Casa, C. Brouwer, A. Nagel, L. Wang, Q. Zhang, S. Kresovich, and S. R. Wessler Inaugural Article: The MITE family Heartbreaker (Hbr): Molecular markers in maize PNAS, August 29, 2000; 97(18): 10083 - 10089. [Abstract] [Full Text] [PDF]

				L. Mao, T. C. Wood, Y. Yu, M. A. Budiman, J. Tomkins, S.-s. Woo, M. Sasinowski, G. Presting, D. Frisch, S. Goff, et al. Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors Genome Res., July 1, 2000; 10(7): 982 - 990. [Abstract] [Full Text]

				J. L. Bennetzen Comparative Sequence Analysis of Plant Nuclear Genomes: Microcolinearity and Its Many Exceptions PLANT CELL, July 1, 2000; 12(7): 1021 - 1030. [Abstract] [Full Text]

				J. F. Wendel and S. R. Wessler Retrotransposon-mediated genome evolution on a local ecological scale PNAS, June 6, 2000; 97(12): 6250 - 6252. [Full Text] [PDF]

				C. Feschotte and S. R. Wessler Mariner-like transposases are widespread and diverse in flowering plants PNAS, January 8, 2002; 99(1): 280 - 285. [Abstract] [Full Text] [PDF]

				X. Zhang, C. Feschotte, Q. Zhang, N. Jiang, W. B. Eggleston, and S. R. Wessler From the Cover: P instability factor: An active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases PNAS, October 23, 2001; 98(22): 12572 - 12577. [Abstract] [Full Text] [PDF]

				N. Stein, C. Feuillet, T. Wicker, E. Schlagenhauf, and B. Keller Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.) PNAS, November 21, 2000; 97(24): 13436 - 13441. [Abstract] [Full Text] [PDF]

				K. Mayer, G. Murphy, R. Tarchini, R. Wambutt, G. Volckaert, T. Pohl, A. Dusterhoft, W. Stiekema, K.-D. Entian, N. Terryn, et al. Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana Genome Res., July 1, 2001; 11(7): 1167 - 1174. [Abstract] [Full Text] [PDF]