Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
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DOI：
10.1186/s12862-014-0268-y
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发表时间：
2014-12-24
影响因子：
3.4
通讯作者：
Galloway, Laura F.
中科院分区：
文献类型：
--
作者：
Barnard-Kubow, Karen B.;Sloan, Daniel B.;Galloway, Laura F.
背景资料：虽然质体基因组在大多数被子植物中是高度保守的，但多个谱系的结构重排和核苷酸取代率增加。这些谱系表现出过量的非同义取代（即，dN/dS比值升高），表明类似的机制可能导致对这些基因的放松和/或阳性选择。然而，关于这些机制是否继续在种内水平塑造序列多样性，人们知之甚少。结果：我们检查了美洲钟花质体基因组中种间分歧和种内多态性的模式，并且跨质体基因发现dN/dS和pN/pS之间存在显着相关性（即，dN/dS的种内当量）。许多基因，包括ycf 1，ycf 2，clpP，和核糖体蛋白基因表现出高dN/dS比。McDonald-Kreitman测试检测到很少的证据积极选择作用于这些基因，可能是由于存在大量的种内divergence.Conclusions：这些结果表明，机制导致增加的核苷酸取代率在质体基因组中继续作用于种内水平。加速质体基因组进化可能增加种内细胞核遗传不相容性的可能性，从而有助于物种形成过程的早期阶段。
Background: Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in similar subsets of plastid genes, suggesting that similar mechanisms may be leading to relaxed and/or positive selection on these genes. However, little is known regarding whether these mechanisms continue to shape sequence diversity at the intraspecific level.Results: We examined patterns of interspecific divergence and intraspecific polymorphism in the plastid genome of Campanulastrum americanum, and across plastid genes found a significant correlation between dN/dS and pN/pS (i.e., the within-species equivalent of dN/dS). A number of genes including ycf1, ycf2, clpP, and ribosomal protein genes exhibited high dN/dS ratios. McDonald-Kreitman tests detected little evidence for positive selection acting on these genes, likely due to the presence of substantial intraspecific divergence.Conclusions: These results suggest that mechanisms leading to increased nucleotide substitution rates in the plastid genome are continuing to act at the intraspecific level. Accelerated plastid genome evolution may increase the likelihood of intraspecific cytonuclear genetic incompatibilities, and thereby contribute to the early stages of the speciation process.