Morton B R
Department of Botany and Plant Sciences, University of California, Riverside 92521, USA.
Proc Natl Acad Sci U S A. 1995 Oct 10;92(21):9717-21. doi: 10.1073/pnas.92.21.9717.
The correspondence between the transversion/transition ratio and the neighboring base composition in chloroplast DNA is examined. For 18 noncoding regions of the chloroplast genome, alignments between rice (Oryza sativa) and maize (Zea mays) were generated by two different methods. Difficulties of aligning noncoding DNA are discussed, and the alignments are analyzed in a manner that reduces alignment artifacts. Sequence divergence is < 10%, so multiple substitutions at a site are assumed to be rare. Observed substitutions were analyzed with respect to the A+T content of the two immediately flanking bases. It is shown that as this content increases, the proportion of transversions also increases. When both the 5'- and 3'-flanking nucleotides are G or C (A+T content of 0), only 25% of the observed substitutions are transversions. However, when both the 5'- and 3'-flanking nucleotides are A or T (A+T content of 2), 57% of the observed substitutions are transversions. Therefore, the influence of flanking base composition on substitutions, previously reported for a single noncoding region, is a general feature of the chloroplast genome.
本文研究了叶绿体DNA中颠换/转换比率与相邻碱基组成之间的对应关系。针对叶绿体基因组的18个非编码区域，通过两种不同方法生成了水稻（Oryza sativa）和玉米（Zea mays）之间的比对。讨论了非编码DNA比对的困难之处，并以减少比对假象的方式对这些比对进行了分析。序列分歧小于10%，因此假定一个位点上的多重替换很少见。针对紧邻的两个碱基的A+T含量，分析了观察到的替换情况。结果表明，随着该含量的增加，颠换的比例也会增加。当5'和3'侧翼核苷酸均为G或C（A+T含量为0）时，观察到的替换中只有25%是颠换。然而，当5'和3'侧翼核苷酸均为A或T（A+T含量为2）时，观察到的替换中有57%是颠换。因此，先前在单个非编码区域报道的侧翼碱基组成对替换的影响是叶绿体基因组的一个普遍特征。
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