Avramova Z, Tikhonov A, SanMiguel P, Jin Y K, Liu C, Woo S S, Wing R A, Bennetzen J L
Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
Plant J. 1996 Dec;10(6):1163-8. doi: 10.1046/j.1365-313x.1996.10061163.x.
Most higher plants have complex genomes containing large quantities of repetitive DNA interspersed with low-copy-number sequences. Many of these repetitive DNAs are mobile and have homology to RNAs in various cell types. This can make it difficult to identify the genes in a long chromosomal continuum. It was decided to use genic sequence conservation and grass genome co-linearity as tools for gene identification. A bacterial artificial chromosome (BAC) clone containing sorghum genomic DNA was selected using a maize Adh1 probe. The 165 kb sorghum BAC was tested for hybridization to a set of clones representing the contiguous 280 kb of DNA flanking maize Adh1. None of the repetitive maize DNAs hybridized, but most of the low-copy-number sequences did. A low-copy-number sequence that did cross-hybridize was found to be a gene, while one that did not was found to be a low-copy-number retrotransposon that was named Reina. Regions of cross-hybridization were co-linear between the two genomes, but closer together in the smaller sorghum genome. These results indicate that local genomic cross-referencing by hybridization of orthologous clones can be an efficient and rapid technique for gene identification and studies of genome organization.
大多数高等植物拥有复杂的基因组，其中包含大量的重复DNA，这些重复DNA与低拷贝数序列相间分布。这些重复DNA中有许多是可移动的，并且与各种细胞类型中的RNA具有同源性。这可能使得在长染色体连续区域中鉴定基因变得困难。因此决定利用基因序列保守性和禾本科植物基因组共线性作为基因鉴定的工具。使用玉米Adh1探针选择了一个包含高粱基因组DNA的细菌人工染色体（BAC）克隆。对这个165 kb的高粱BAC进行测试，以检测其与一组代表玉米Adh1侧翼连续280 kb DNA的克隆的杂交情况。没有重复的玉米DNA发生杂交，但大多数低拷贝数序列发生了杂交。发现一个发生交叉杂交的低拷贝数序列是一个基因，而另一个未发生杂交的是一个低拷贝数反转录转座子，被命名为Reina。两个基因组之间交叉杂交的区域是共线性的，但在较小的高粱基因组中距离更近。这些结果表明，通过直系同源克隆的杂交进行局部基因组交叉参照可以是一种高效、快速地鉴定基因和研究基因组组织的技术。
