Collinearity of Maize and Sorghum at the DNA Sequence Level

对植物染色体区域进行比较分析，在发现基因、新的移动的DNA种类以及进化变化的性质、速率和机制方面具有特殊的潜力，但这种潜力还没有得到充分的检验。此外，对大小差异很大的密切相关的基因组进行比较分析，可以指出基因组大小差异的起源，同样重要的是，可以确定小基因组是否可以用于大基因组物种中重要基因的图位克隆。在这个项目中，玉米和高粱被选择进行这样的分析，因为它们作为作物和模式遗传系统的重要性。特别是，我们计划（1）发现几个基因丰富区域的基本基因组组成，（2）使用这种双基因组方法来改进和测试注释（包括基因预测）程序，（3）确定高粱基因组的紧密性是否可以用于将已被遗传作图的玉米基因拓扑连接到一个图单元，（4）对玉米染色体组成的基因簇和基因间区进行了分析，并探讨了玉米染色体组成与高粱基因组起源的关系。玉米和高粱中不同染色体位置的连续DNA序列的含量总计为5兆碱基。由于两个基因组的基因密度不同，其特征区域的大小也不同。在玉米中，将使用至少两个BAC克隆，其重叠杂交到指定的成核探针。在高粱中，探针将集中在单个BAC内。通过选择基因序列作为探针，对各基因组的基因区域进行分析，可以得到许多簇，每个簇预测有10-20个基因，以及它们的基因间区域。通过以双基因组方式比较基因簇，预测基因边界和重复元件的更好的计算程序将会出现。在许多情况下，由于遗传和DNA序列数据的整合，基因序列将被发现具有已知表型。目前正在进行的增加玉米和高粱图谱上DNA标记和表型密度的项目也将从这一分析中受益，因为它将为玉米或其近缘植物定位克隆的可行性/困难性提供广泛的证据。基于基因岛的谷物基因组进化研究将通过对基因簇和基因间区的分析得到加强。

Comparative analysis of aligned plant chromosomal regions have exceptional, but largelyuntested, potential for the discovery of genes, new classes of mobile DNAs, and thenature, rates and mechanisms of evolutionary change. Moreover, comparative analysis ofclosely related genomes that differ greatly in size can indicate both the origin(s) of thatgenome size difference and, equally important, determine whether the small genomecould be used for map-based cloning of significant genes in the large genome species. Inthis project, maize and sorghum have been chosen for such an analysis because of theirimportance as crop plants and as model genetic systems. In particular, we plan (1) touncover basic genomic composition of several gene-rich regions, (2) to use this twogenome approach to improve and test annotation (including gene prediction) programs,(3) to determine whether the compactness of the sorghum genome can be used tophysically link maize genes that have been genetically mapped to be as close as one mapunit, and (4) to characterize the chromosomal composition of maize and its relationship tothe origin of the sorghum genome for gene clusters and intergenic regions. The contentof contiguous DNA sequence from different chromosomal locations in maize andsorghum totaling five megabases will be characterized. The size of the regionscharacterized will differ between the two genomes because of their differential genedensity. In maize, a minimum of two BAC clones whose overlap hybridizes to adesignated nucleation probe will be used. In sorghum, the probe will be centered withina single BAC. By selecting gene sequences as probes to genic regions of the respectivegenomes, a number of clusters, each with a predicted 10-20 genes, and their intergenicregions will be obtained. By comparing gene clusters in a bi-genomic fashion, bettercomputational programs for predicting gene boundaries and repeat elements will emerge.In a number of cases, gene sequences will be discovered with known phenotypes becauseof the integration of genetic and DNA sequence data. Current projects to increase thedensity of DNA markers and phenotypes on both maize and sorghum maps will alsobenefit from this analysis because it will provide extensive evidence on thefeasibility/difficulty of positional cloning in maize or its relatives. Evolutionary studiesof cereal genomes based on gene islands will now be enhanced by the analysis of geneclusters and intergenic regions.