Dynamics of copy number variation in host races of the pea aphid.
Dynamics of copy number variation in host races of the pea aphid.
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DOI：
10.1093/molbev/msu266
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发表时间：
2015-01
影响因子：
10.7
通讯作者：
Butlin RK
中科院分区：
文献类型：
--
作者：
Duvaux L;Geissmann Q;Gharbi K;Zhou JJ;Ferrari J;Smadja CM;Butlin RK
拷贝数变异(CNV)对整体遗传变异有重要贡献，并被认为在适应中起重要作用。然而，除了少数模式物种外，CNV在自然种群中的传播范围很少被研究。在这里，我们报告了豌豆蚜虫的CNV，这是一个强大的系统，用于研究寄主-植物适应和物种形成的遗传结构，这要归功于多个寄主小种形成的遗传分化连续体。最近的研究强调了化学感觉基因的潜在重要性，包括味觉和嗅觉受体基因家族(分别为Gr和或)，在宿主种族形成过程中。我们使用有针对性的重测序来实现非常高的覆盖深度，从而揭示了分布在豌豆蚜8个寄主小种的104个个体中434个基因的CNV范围，其中包括150个化学感受基因。我们发现CNV在我们的全球样本中广泛存在，在多基因家族中的发生率明显更高，尤其是在Ors中。我们还观察到，随着编码序列长度的增加，基因被完全复制或缺失(CDD)的概率降低。带有CDD变异体的基因通常拷贝数更多，特别是在P450基因家族中，其毒素抗性可能与基因剂量有关。我们发现，在区分寄主小种的基因中，GR过表达，CDD基因和假基因也是如此。我们的观察为CNV的动态提供了新的线索，并与CNV在局部适应和物种形成中发挥的作用一致。
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
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影响因子：
3.2
作者：
Dempsey, Michael P.;Nietfeldt, Joseph;Benson, Andrew K.
通讯作者：
Benson, Andrew K.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
3.3
作者：
Ferrari, Julia;Godfray, H. Charles J.;Via, Sara
通讯作者：
Via, Sara
影响因子：
4.5
作者：
Briscoe AD;Macias-Muñoz A;Kozak KM;Walters JR;Yuan F;Jamie GA;Martin SH;Dasmahapatra KK;Ferguson LC;Mallet J;Jacquin-Joly E;Jiggins CD
通讯作者：
Jiggins CD
影响因子：
30.8
作者：
Cooper, Gregory M.;Nickerson, Deborah A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.