Sequence composition and genome organization of maize.

Zea mays L. ssp. mays, or corn, one of the most important crops and a model for plant genetics, has a genome approximately 80% the size of the human genome. To gain global insight into the organization of its genome, we have sequenced the ends of large insert clones, yielding a cumulative length of one-eighth of the genome with a DNA sequence read every 6.2 kb, thereby describing a large percentage of the genes and transposable elements of maize in an unbiased approach. Based on the accumulative 307 Mb of sequence, repeat sequences occupy 58% and genic regions occupy 7.5%. A conservative estimate predicts approximately 59,000 genes, which is higher than in any other organism sequenced so far. Because the sequences are derived from bacterial artificial chromosome clones, which are ordered in overlapping bins, tagged genes are also ordered along continuous chromosomal segments. Based on this positional information, roughly one-third of the genes appear to consist of tandemly arrayed gene families. Although the ancestor of maize arose by tetraploidization, fewer than half of the genes appear to be present in two orthologous copies, indicating that the maize genome has undergone significant gene loss since the duplication event.

[1]  B. Mcclintock.  A CYTOLOGICAL DEMONSTRATION OF THE LOCATION OF AN INTERCHANGE BETWEEN TWO NON-HOMOLOGOUS CHROMOSOMES OF ZEA MAYS. , 1930, Proceedings of the National Academy of Sciences of the United States of America.

[2]  M. Rhoades.  Duplicate Genes in Maize , 1951, The American Naturalist.

[3]  T. Helentjaris,et al.  Identification of the genomic locations of duplicate nucleotide sequences in maize by analysis of restriction fragment length polymorphisms. , 1988, Genetics.

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

[5]  R. Flavell,et al.  A family of retrotransposons and associated genomic variation in wheat. , 1991, Genomics.

[6]  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.

[7]  D. Laurie,et al.  Chromosome size in maize and sorghum using EM serial section reconstructed nuclei , 1995 .

[8]  J. Bennetzen,et al.  The contributions of retroelements to plant genome organization, function and evolution. , 1996, Trends in microbiology.

[9]  K. Devos,et al.  Comparative genetics in the grasses. , 1998, Plant molecular biology.

[10]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[11]  J. Messing.  Do plants have more genes than humans? , 2001, Trends in plant science.

[12]  E. Kellogg,et al.  Evolutionary history of the grasses. , 2001, Plant physiology.

[13]  Hui-Hsien Chou,et al.  DNA sequence quality trimming and vector removal , 2001, Bioinform..

[14]  A. Schulman,et al.  Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. , 2001, Genome research.

[15]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[16]  Ngozi A. Duru,et al.  Construction and characterization of a deep-coverage bacterial artificial chromosome library for maize , 2002 .

[17]  V. Walbot,et al.  Progress in maize gene discovery: a project update , 2003, Functional & Integrative Genomics.

[18]  Ngozi A. Duru,et al.  Characterization of Three Maize Bacterial Artificial Chromosome Libraries toward Anchoring of the Physical Map to the Genetic Map Using High-Density Bacterial Artificial Chromosome Filter Hybridization1 , 2002, Plant Physiology.

[19]  J. Messing,et al.  Contiguous Genomic DNA Sequence Comprising the 19-kD Zein Gene Family from Maize1 , 2002, Plant Physiology.

[20]  Cédric Feschotte,et al.  Plant transposable elements: where genetics meets genomics , 2002, Nature Reviews Genetics.

[21]  V. Chandler,et al.  Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. , 2002, Genes & development.

[22]  J Quackenbush,et al.  Enrichment of Gene-Coding Sequences in Maize by Genome Filtration , 2003, Science.

[23]  S. Dike,et al.  Maize Genome Sequencing by Methylation Filtration , 2003, Science.

[24]  Hans-Werner Mewes,et al.  Sputnik: a database platform for comparative plant genomics , 2003, Nucleic Acids Res..

[25]  J. Volff,et al.  Diversity of retrotransposable elements in compact pufferfish genomes. , 2003, Trends in genetics : TIG.

[26]  Cari Soderlund,et al.  In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10 , 2003, Science.

[27]  H. Kazazian.  Mobile Elements: Drivers of Genome Evolution , 2004, Science.

[28]  J. Bennetzen,et al.  Gene loss and movement in the maize genome. , 2004, Genome research.

[29]  Hans-Werner Mewes,et al.  MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics , 2004, Nucleic Acids Res..

[30]  R. B. Flavell,et al.  Genome size and the proportion of repeated nucleotide sequence DNA in plants , 1974, Biochemical Genetics.

[31]  Jianxin Ma,et al.  Close split of sorghum and maize genome progenitors. , 2004, Genome research.

[32]  Jianxin Ma,et al.  Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. , 2004, Genome research.

[33]  Joachim Messing,et al.  Pattern of diversity in the genomic region near the maize domestication gene tb1. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Mari Nakamura,et al.  Composition and Structure of the Centromeric Region of Rice Chromosome 8 , 2004, The Plant Cell Online.

[35]  B. Birren,et al.  Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.

[36]  B. Larkins,et al.  Characterization of the maize endosperm transcriptome and its comparison to the rice genome. , 2004, Genome research.