Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.Maize (Zea mays or corn) has a wide variety of uses and broad economic impact. It is a significant food source for humans, a chief ingredient in livestock feed, and is the source of a wide range of manufactured products, including sweeteners, fuel, and adhesives. It also has a long and storied history as a model organism in genetic studies. The combination of its genetic and economic importance has made maize a prime organism for genomic studies (for review, see Messing, 2005). Despite its evident value, progress toward generating a whole-genome sequence of maize has been held back by the cost and complexity of such a project. Although it is a medium-sized grass genome, at 2.4 Gb the maize genome is large compared to other sequenced plants and so will require significant funding to sequence. On top of this, its high repeat content poses computational challenges for accurately assembling a genome sequence.In the absence of a genome sequence, studies of selected regions of the maize genome and comparisons to related species have been carried out. Comparative genetic analyses (Hulbert et al., 1990;Ahn and Tanksley, 1993;Moore et al., 1995;Gale and Devos, 1998) have suggested that significant portions of grass genomes are conserved (collinear). It has been proposed that, aside from polyploidization, large genome sizes in the grasses are caused primarily by the high content of repetitive elements (SanMiguel and Bennetzen, 1998;Meyers et al., 2001;Song et al., 2002). Several studies have investigated the local structure of orthologous regions in various grass species (Chen et al., 1997;Feuillet and Keller, 1999;Tikhonov et al., 1999;Tarchini et al...

Maize (Zea mays L.) is one of the most important cereal crops and a model for the study of genetics, evolution, and domestication. To better understand maize genome organization and to build a framework for genome sequencing, we constructed a sequence-ready fingerprinted contig-based physical map that covers 93.5% of the genome, of which 86.1% is aligned to the genetic map. The fingerprinted contig map contains 25,908 genic markers that enabled us to align nearly 73% of the anchored maize genome to the rice genome. The distribution pattern of expressed sequence tags correlates to that of recombination. In collinear regions, 1 kb in rice corresponds to an average of 3.2 kb in maize, yet maize has a 6-fold genome size expansion. This can be explained by the fact that most rice regions correspond to two regions in maize as a result of its recent polyploid origin. Inversions account for the majority of chromosome structural variations during subsequent maize diploidization. We also find clear evidence of ancient genome duplication predating the divergence of the progenitors of maize and rice. Reconstructing the paleoethnobotany of the maize genome indicates that the progenitors of modern maize contained ten chromosomes.