Zhang Wen, Sun Xiaoqin, Yuan Huizhong, Araki Hitoshi, Wang Jue, Tian Dacheng
State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093 Nanjing, China.
Mol Genet Genomics. 2008 Oct;280(4):351-61. doi: 10.1007/s00438-008-0370-1. Epub 2008 Aug 9.
Little is known about variation of nucleotide insertion/deletions (indels) within species. In Arabidopsis thaliana, we investigated indel polymorphism patterns between two genome sequences and among 96 accessions at 1215 loci. Our study identified patterns in the variation of indel density, size, GC content and distribution, and a correlation between indels and substitutions. We found that the GC content in indel sequences was lower than that in non-indel sequences and that indels typically occur in regions with lower GC content. Patterns of indel frequency distribution among populations were more consistent with neutral expectation than substitution patterns. We also found that the local level of substitutions is positively correlated with indel density and negatively correlated with their distance to the closed indel, suggesting that indels play an important role in nucleotide variation.
关于物种内核苷酸插入/缺失（indel）的变异，我们了解甚少。在拟南芥中，我们研究了两个基因组序列之间以及96个种质在1215个位点处的indel多态性模式。我们的研究确定了indel密度、大小、GC含量和分布的变异模式，以及indel与替换之间的相关性。我们发现indel序列中的GC含量低于非indel序列，并且indel通常发生在GC含量较低的区域。群体间indel频率分布模式比替换模式更符合中性预期。我们还发现，局部替换水平与indel密度呈正相关，与它们到最近indel的距离呈负相关，这表明indel在核苷酸变异中起重要作用。
