Collinearity of Maize and Sorghum at the DNA Sequence Level

比对植物染色体区域的比较分析具有发现基因、新的可移动DNA类别以及进化变化的性质、速率和机制的特殊的、但在很大程度上未经测试的潜力。此外，对大小差异很大的密切相关基因组的比较分析不仅可以指出基因组大小差异的来源(S)，而且同样重要的是，确定小基因组是否可以用于基于图谱的大基因组物种中重要基因的克隆。在这个项目中，玉米和高粱被选为这样的分析对象，因为它们作为农作物和模式遗传系统具有重要意义。具体地说，我们计划(1)揭示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凑性是否可以用于从表面上连接已被遗传定位为接近一个图谱单位的玉米基因，以及(4)表征玉米的染色体组成及其与高粱基因组起源之间的基因簇和基因间隔区的关系。玉米和高粱不同染色体位置的相邻DNA序列总计5兆碱基的含量将被表征。由于这两个基因组的基因密度不同，其特征区域的大小也会有所不同。在玉米中，将使用至少两个重叠杂交到指定成核探针的BAC克隆。在高粱中，探头将以单一生物活性物质为中心。通过选择基因序列作为各自基因组基因区域的探针，将获得若干簇，每个簇预测有10-20个基因，以及它们的基因间区。通过以双基因组方式比较基因簇，将出现更好的计算程序来预测基因边界和重复元件。在许多情况下，由于遗传和DNA序列数据的整合，将发现具有已知表型的基因序列。目前在玉米和高粱图谱上增加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种定位克隆的可行性/难度提供广泛的证据。基于基因岛的谷物基因组的进化研究现在将通过基因簇和基因间隔区的分析而得到加强。

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.