Genomic organization of Zea mays and its close relatives
Abstract
The organization of the genomes of higher plants is poorly understood. Higher plant genomes are typified by their large size and extensive repetitive DNA component. In order to formulate a basic picture of genome organization in higher plants, a number of studies were undertaken. The composition and size of modified and repetitive domains in maize and sorghum were investigated. Modified DNA tracts were found to be 30-150 kb in size in both maize and sorghum, despite the three to four fold difference in genome size between the two species. In maize, highly repetitive DNAs were found in these modified tracts. A contiguous interval of 280 kb surrounding the maize Adhl locus was analyzed on two recombinant YACs (yeast artificial chromosomes). A series of overlapping lambda subclones was isolated from the largest YAC, and individual fragments were characterized with respect to their genomic copy number and stability in yeast and E. coli. Cross-hybridization analyses were used to define 37 different repetitive DNA classes within the 280 kb interval, and these were found in a novel organizational pattern. Individual repetitive elements are interspersed with one another in an apparently random fashion, and are spatially separate from single copy number sequences. Extensive tandem arrays were not found. Sequences from one end of the 280 kb interval were used to isolate overlapping YAC clones, representing the first step in a chromosome walk. The structure of the ribosomal DNA (rDNA) repeat from sorghum and several related grasses was compared to the structure of the maize rDNA repeat, in part to analyze the evolutionary relatedness of these species. A high degree of sequence conservation was found within the rDNA repeats of sorghum, sugarcane, and maize. Restriction site and size length variations did allow these related species to be distinguished, however. The organization of modified and unmodified rDNA repeats was investigated in maize seedling leaves, in order to determine the organization of transcriptionally active rDNA genes. Modified rDNA repeats are clustered in 20-150 kb tracts. The presence of a previously undescribed class of under-modified rDNA repeats, that could account for most or all of the 35S rRNA transcription in seedling leaf cells, was also described. These studies have shown that highly repetitive sequences in maize are organized in large tracts, composed of unique combinations of different repetitive elements. The size of these clusters appears to be quite tightly regulated by unknown processes. Highly repetitive DNAs are extensively modified, while single copy, active genes are almost completely unmodified.
Degree
Ph.D.
Advisors
Bennetzen, Purdue University.
Subject Area
Genetics|Molecular biology
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