Colinearity and its exceptions in orthologous adh regions of maize and sorghum.

Orthologous adh regions of the sorghum and maize genomes were sequenced and analyzed. Nine known or candidate genes, including adh1, were found in a 225-kilobase (kb) maize sequence. In a 78-kb space of sorghum, the nine homologues of the maize genes were identified in a colinear order, plus five additional genes. The major fraction of DNA in maize, occupying 166 kb (74%), is represented by 22 long terminal repeat (LTR) retrotransposons. About 6% of the sequence belongs to 33 miniature inverted-repeat transposable elements (MITEs), remnants of DNA transposons, 4 simple sequence repeats, and low-copy-number DNAs of unknown origin. In contrast, no LTR retroelements were detected in the orthologous sorghum region. The unconserved sorghum DNA is composed of 20 putative MITEs, transposon-like elements, 5 simple sequence repeats, and low-copy-number DNAs of unknown origin. No MITEs were discovered in the 166 kb of DNA occupied by the maize LTR retrotransposons. In both species, MITEs were found in the space between genes and inside introns, indicating specific insertion and/or retention for these elements. Two adjacent sorghum genes, including one gene missing in maize, had colinear homologues on Arabidopsis chromosome IV, suggesting two rearrangements in the sorghum and three in the maize genome in comparison to a four-gene region of Arabidopsis. Hence, multiple small rearrangements may be present even in largely colinear genomic regions. These studies revealed a much higher degree of diversity at a microstructural level than predicted by genetic mapping studies for closely related grass species, as well as for comparisons of monocots and dicots.

[1]  J. Bennetzen,et al.  Genetic mapping and characterization of sorghum and related crops by means of maize DNA probes. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[2]  J. Bennetzen,et al.  Nested Retrotransposons in the Intergenic Regions of the Maize Genome , 1996, Science.

[3]  A. Paterson,et al.  Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor. , 1994, Nucleic acids research.

[4]  Michael Y. Galperin,et al.  Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea , 1997, Molecular microbiology.

[5]  J. Bennetzen,et al.  Mu1-related transposable elements of maize preferentially insert into low copy number DNA. , 1995, Genetics.

[6]  P. Piffanelli,et al.  Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana , 1998, Nature.

[7]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[8]  J. Bennetzen,et al.  Microcolinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[9]  S. Tanksley,et al.  Comparative linkage maps of the rice and maize genomes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[10]  B. Sobral,et al.  Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  D. Laurie,et al.  Nuclear DNA content in the genera Zea and Sorghum. Intergeneric, interspecific and intraspecific variation , 1985, Heredity.

[12]  J. Devereux,et al.  A comprehensive set of sequence analysis programs for the VAX , 1984, Nucleic Acids Res..

[13]  J. S. Heslop-Harrison,et al.  Genomes, genes and junk: the large-scale organization of plant chromosomes , 1998 .

[14]  M. Adams,et al.  A tool for analyzing and annotating genomic sequences. , 1997, Genomics.

[15]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[16]  T. Helentjaris,et al.  Was there a single ancestral cereal chromosome? , 1995, Trends in genetics : TIG.

[17]  P. Bork,et al.  Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli , 1996, Current Biology.

[18]  P. Ronald,et al.  Identification and characterization of 14 transposon-like elements in the noncoding regions of members of the Xa21 family of disease resistance genes in rice , 1998, Molecular and General Genetics MGG.

[19]  S. Brenner,et al.  Small is beautiful: comparative genomics with the pufferfish (Fugu rubripes). , 1996, Trends in genetics : TIG.

[20]  S. Wessler,et al.  Retrotransposons in the flanking regions of normal plant genes: a role for copia-like elements in the evolution of gene structure and expression. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[21]  G. Del Sal,et al.  A one-tube plasmid DNA mini-preparation suitable for sequencing. , 1988, Nucleic acids research.

[22]  Phillip SanMiguel,et al.  Evidence that a Recent Increase in Maize Genome Size was Caused by the Massive Amplification of Intergene Retrotransposons , 1998 .

[23]  H. Sambrook.  Molecular cloning : a laboratory manual. Cold Spring Harbor, NY , 1989 .

[24]  P. Schulze-Lefert,et al.  A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome. , 1998, Nucleic acids research.

[25]  J. Bennetzen,et al.  Sequence organization and conservation in sh2/a1-homologous regions of sorghum and rice. , 1998, Genetics.

[26]  L. Hood,et al.  Striking sequence similarity over almost 100 kilobases of human and mouse T–cell receptor DNA , 1994, Nature Genetics.

[27]  J. Bennetzen,et al.  DNA class organization on maize Adh1 yeast artificial chromosomes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[28]  B. Gaut,et al.  DNA sequence evidence for the segmental allotetraploid origin of maize. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[29]  J. Bennetzen,et al.  Characterization of four dispersed repetitive DNA sequences from Zea mays and their use in constructing contiguous DNA fragments using YAC clones. , 1996, Genome.

[30]  J. Bennetzen,et al.  Gene identification in a complex chromosomal continuum by local genomic cross-referencing. , 1996, The Plant journal : for cell and molecular biology.

[31]  M. Palazzolo,et al.  Transposon-facilitated DNA sequencing. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. Bennetzen,et al.  Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adh1. , 1995, The Plant cell.

[33]  J. Bennetzen,et al.  The unified grass genome: synergy in synteny. , 1997, Genome research.

[34]  P. Lu,et al.  Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[35]  D. Soltis,et al.  The dynamic nature of polyploid genomes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[36]  G. Bernardi,et al.  The distribution of genes in the genomes of Gramineae. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[37]  J. Bennetzen,et al.  Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA. , 1994, Genome.

[38]  Phillip SanMiguel,et al.  The paleontology of intergene retrotransposons of maize , 1998, Nature Genetics.

[39]  D. Laurie,et al.  Conservation of fine-scale DNA marker order in the genomes of rice and the Triticeae. , 1995, Nucleic acids research.

[40]  B. Wakimoto,et al.  Beyond the Nucleosome: Epigenetic Aspects of Position–Effect Variegation in Drosophila , 1998, Cell.