Sequence Organization and Conservation in sh2/a1-Homologous Regions of Sorghum and Rice

Corresponding author: Jeffrey L. Bennetzen, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, maize{at}bilbo.bio.purdue.edu (E-mail).

Communicating editor: J. A. BIRCHLER

Previously, we have demonstrated microcolinearity of gene composition and orientation in sh2/a1-homologous regions of the rice, sorghum, and maize genomes. However, the sh2 and a1 homologues are only about 20 kb apart in both rice and sorghum, while they are separated by about 140 kb in maize. In order to further define sequence organization and conservation in sh2/a1-homologous regions, we have completely sequenced a 42,446-bp segment of sorghum DNA. Four genes were identified: a homologue of sh2, two homologues of a1, and a putative transcriptional regulatory gene. A solo long terminal repeat of the retroelement Leviathan was detected between the two a1 homologues, and eight miniature inverted repeat transposable elements were found in this region. Comparison of the sorghum sequence with the sequence of the homologous segment from rice indicated that only the identified genes were evolutionarily conserved between these two species, which have evolved independently for over 50 million years. The introns of the a1 homologues have evolved faster than the introns of the sh2 homologue. The a1 tandem duplication appears to be an ancient event that may have preceded the ancestral divergence of maize, sorghum, and rice.

This article has been cited by other articles:

				H. Kim, P. S. Miguel, W. Nelson, K. Collura, M. Wissotski, J. G. Walling, J. P. Kim, S. A. Jackson, C. Soderlund, and R. A. Wing Comparative Physical Mapping Between Oryza sativa (AA Genome Type) and O. punctata (BB Genome Type) Genetics, May 1, 2007; 176(1): 379 - 390. [Abstract] [Full Text] [PDF]

				J. S. Hawkins, H. Kim, J. D. Nason, R. A. Wing, and J. F. Wendel Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium Genome Res., October 1, 2006; 16(10): 1252 - 1261. [Abstract] [Full Text] [PDF]

				S. Goel, Z. Chen, Y. Akiyama, J. A. Conner, M. Basu, G. Gualtieri, W. W. Hanna, and P. Ozias-Akins Comparative Physical Mapping of the Apospory-Specific Genomic Region in Two Apomictic Grasses: Pennisetum squamulatum and Cenchrus ciliaris Genetics, May 1, 2006; 173(1): 389 - 400. [Abstract] [Full Text] [PDF]

				N. Shimada, R. Sasaki, S. Sato, T. Kaneko, S. Tabata, T. Aoki, and S.-i. Ayabe A comprehensive analysis of six dihydroflavonol 4-reductases encoded by a gene cluster of the Lotus japonicus genome J. Exp. Bot., September 1, 2005; 56(419): 2573 - 2585. [Abstract] [Full Text] [PDF]

				H. Yao and P. S. Schnable Cis-effects on Meiotic Recombination Across Distinct a1-sh2 Intervals in a Common Zea Genetic Background Genetics, August 1, 2005; 170(4): 1929 - 1944. [Abstract] [Full Text] [PDF]

				H. M. Li, D. Rotter, S. A. Bonos, W. A. Meyer, and F. C. Belanger Identification of a Gene in the Process of Being Lost from the Genus Agrostis Plant Physiology, August 1, 2005; 138(4): 2386 - 2395. [Abstract] [Full Text] [PDF]

				Z. Swigonova, J. L. Bennetzen, and J. Messing Structure and Evolution of the r/b Chromosomal Regions in Rice, Maize and Sorghum Genetics, February 1, 2005; 169(2): 891 - 906. [Abstract] [Full Text] [PDF]

				K. S. Caldwell, P. Langridge, and W. Powell Comparative Sequence Analysis of the Region Harboring the Hardness Locus in Barley and Its Colinear Region in Rice Plant Physiology, October 1, 2004; 136(2): 3177 - 3190. [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]

				D.-Y. Xie, L. A. Jackson, J. D. Cooper, D. Ferreira, and N. L. Paiva Molecular and Biochemical Analysis of Two cDNA Clones Encoding Dihydroflavonol-4-Reductase from Medicago truncatula Plant Physiology, March 1, 2004; 134(3): 979 - 994. [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]

				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]

				W. Ramakrishna, J. Emberton, P. SanMiguel, M. Ogden, V. Llaca, J. Messing, and J. L. Bennetzen Comparative Sequence Analysis of the Sorghum Rph Region and the Maize Rp1 Resistance Gene Complex Plant Physiology, December 1, 2002; 130(4): 1728 - 1738. [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]

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

				H. Fu and H. K. Dooner From the Cover: Intraspecific violation of genetic colinearity and its implications in maize PNAS, July 9, 2002; 99(14): 9573 - 9578. [Abstract] [Full Text] [PDF]

				J. Salse, B. Piegu, R. Cooke, and M. Delseny Synteny between Arabidopsis thaliana and rice at the genome level: a tool to identify conservation in the ongoing rice genome sequencing project Nucleic Acids Res., June 1, 2002; 30(11): 2316 - 2328. [Abstract] [Full Text] [PDF]

				J. P. Tomkins, G. Davis, D. Main, Y. Yim, N. Duru, T. Musket, J. L. Goicoechea, D. A. Frisch, E. H. Coe Jr., and R. A. Wing Construction and Characterization of a Deep-Coverage Bacterial Artificial Chromosome Library for Maize Crop Sci., May 1, 2002; 42(3): 928 - 933. [Abstract] [Full Text] [PDF]

				Z. V. Avramova Heterochromatin in Animals and Plants. Similarities and Differences Plant Physiology, May 1, 2002; 129(1): 40 - 49. [Full Text] [PDF]

				H. Yao, Q. Zhou, J. Li, H. Smith, M. Yandeau, B. J. Nikolau, and P. S. Schnable From the Cover: Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize PNAS, April 30, 2002; 99(9): 6157 - 6162. [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]

				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]

				Z. Cheng, C. R. Buell, R. A. Wing, M. Gu, and J. Jiang Toward a Cytological Characterization of the Rice Genome Genome Res., December 1, 2001; 11(12): 2133 - 2141. [Abstract] [Full Text] [PDF]

				S. A. Jackson, Z. Cheng, M. L. Wang, H. M. Goodman, and J. Jiang Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome Genetics, October 1, 2000; 156(2): 833 - 838. [Abstract] [Full Text]

				A. H. Paterson, J. E. Bowers, M. D. Burow, X. Draye, C. G. Elsik, C.-X. Jiang, C. S. Katsar, T.-H. Lan, Y.-R. Lin, R. Ming, et al. Comparative Genomics of Plant Chromosomes PLANT CELL, September 1, 2000; 12(9): 1523 - 1540. [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]

				A. P. Tikhonov, J. L. Bennetzen, and Z. V. Avramova Structural Domains and Matrix Attachment Regions along Colinear Chromosomal Segments of Maize and Sorghum PLANT CELL, February 1, 2000; 12(2): 249 - 264. [Abstract] [Full Text]

				A. P. Tikhonov, P. J. SanMiguel, Y. Nakajima, N. M. Gorenstein, J. L. Bennetzen, and Z. Avramova Colinearity and its exceptions in orthologous adh regions of maize and sorghum PNAS, June 22, 1999; 96(13): 7409 - 7414. [Abstract] [Full Text] [PDF]

				H. Yao, Q. Zhou, J. Li, H. Smith, M. Yandeau, B. J. Nikolau, and P. S. Schnable From the Cover: Molecular characterization of meiotic recombination across the 140-kb multigenic a1-sh2 interval of maize PNAS, April 30, 2002; 99(9): 6157 - 6162. [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]

				B. C. Meyers, S. V. Tingey, and M. Morgante Abundance, Distribution, and Transcriptional Activity of Repetitive Elements in the Maize Genome Genome Res., October 1, 2001; 11(10): 1660 - 1676. [Abstract] [Full Text] [PDF]