Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana.
Insertions/Deletions-Associated Nucleotide Polymorphism in Arabidopsis thaliana.
复制标题
拟南芥插入/缺失相关核苷酸多态性
DOI：
10.3389/fpls.2016.01792
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发表时间：
2016
影响因子：
5.6
通讯作者：
Gu T
中科院分区：
文献类型：
--
作者：
Guo C;Du J;Wang L;Yang S;Mauricio R;Tian D;Gu T
尽管普遍观察到高度的种内变异，但对于这种变异的起源仍然缺乏一个普遍的机制。插入和缺失(Indels)是基因组的一种普遍特征，我们假设Indels和核苷酸多态模式之间可能存在关联。在这里，我们研究了大约18个indels(>；100bp)的侧翼序列，这些序列来自拟南芥的大量材料。我们发现两种不同的单倍型，即核苷酸二态，存在于每个INDELs周围，并且二态单倍型总是对应于Indel存在/不存在的模式。此外，两个不同等位基因之间的核苷酸多样性峰值与这些指标密切相关。因此，在indels和二晶性之间存在着密切的联系。进一步的分析表明，Indel相关的替换可能是影响拟南芥核苷酸多态的遗传变异的重要组成部分。最后，我们提出了INDELs可能产生这些高度分化的单倍型的机制。这项研究提供了证据，证明核苷酸二态，通常被认为是频率依赖选择的证据，可以简单地用基因组的结构变异来解释。
Although high levels of within-species variation are commonly observed, a general mechanism for the origin of such variation is still lacking. Insertions and deletions (indels) are a widespread feature of genomes and we hypothesize that there might be an association between indels and patterns of nucleotide polymorphism. Here, we investigate flanking sequences around 18 indels (>100 bp) among a large number of accessions of the plant, Arabidopsis thaliana. We found two distinct haplotypes, i.e., a nucleotide dimorphism, present around each of these indels and dimorphic haplotypes always corresponded to the indel-present/-absent patterns. In addition, the peaks of nucleotide diversity between the two divergent alleles were closely associated with these indels. Thus, there exists a close association between indels and dimorphisms. Further analysis suggests that indel-associated substitutions could be an important component of genetic variation shaping nucleotide polymorphism in Arabidopsis. Finally, we suggest a mechanism by which indels might generate these highly divergent haplotypes. This study provides evidence that nucleotide dimorphisms, which are frequently regarded as evidence of frequency-dependent selection, could be explained simply by structural variation in the genome.