Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species.
Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species.
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DOI：
10.1186/s12711-015-0138-0
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发表时间：
2015-07-03
期刊：
影响因子：
--
通讯作者：
de Leaniz CG
中科院分区：
文献类型：
--
作者：
Consuegra S;John E;Verspoor E;de Leaniz CG
线粒体DNA（mitochondrialDNA，mtDNA）是群体遗传学研究中常用的一种中性标记。然而，考虑到线粒体基因组编码的蛋白质的功能重要性，以及线粒体在细胞能量产生中的突出作用，中性的假设越来越受到质疑。我们测试了大西洋鲑鱼的线粒体基因组上的选择证据，大西洋鲑鱼是一种当地适应和广泛养殖的物种，分布在一个大的纬度渐变群中。我们分析了鲑鱼mtDNA的20个独立区域，代表9个基因（ND 1，ND 2，ND 3，COX 1，COX 2，ATP 6，ND 4，ND 5和CYTB）。这20个mtDNA区域使用454方法从该物种的整个欧洲范围内收集的样本中进行测序。我们发现了ND 1，ND 3和ND 4基因的正选择的证据，这是由至少两种不同的基于密码子的方法，也由所涉及的氨基酸的化学性质的差异支持。一些突变的地理分布表明，在选择不是随机的，一些突变是私人的北极地区的人口。我们讨论的可能性，选择大西洋鲑鱼mtDNA基因组可能与需要在低温下提高代谢效率。对代表参与OXPHOS途径的9个线粒体基因的序列的分析揭示了大西洋鲑鱼线粒体基因组中正选择的特征。所涉及的氨基酸的性质表明，一些被鉴定为正选择的突变可能具有功能性影响，可能与代谢效率有关。需要实验证据，更好地了解区域的地理结构，以澄清选择作用于大西洋鲑鱼和其他当地适应鱼类的线粒体基因组的潜在作用。本文的在线版本（doi：10.1186/s12711-015-0138-0）包含补充材料，可供授权用户使用。
Mitochondrial DNA (mtDNA) is frequently used in population genetic studies and is usually considered as a neutral marker. However, given the functional importance of the proteins encoded by the mitochondrial genome, and the prominent role of mitochondria in cellular energy production, the assumption of neutrality is increasingly being questioned. We tested for evidence of selection on the mitochondrial genome of the Atlantic salmon, which is a locally adapted and widely farmed species and is distributed across a large latitudinal cline. We analysed 20 independent regions of the salmon mtDNA that represented nine genes (ND1, ND2, ND3, COX1, COX2, ATP6, ND4, ND5, and CYTB). These 20 mtDNA regions were sequenced using a 454 approach from samples collected across the entire European range of this species. We found evidence of positive selection at the ND1, ND3 and ND4 genes, which is supported by at least two different codon-based methods and also by differences in the chemical properties of the amino acids involved. The geographical distribution of some of the mutations indicated to be under selection was not random, and some mutations were private to artic populations. We discuss the possibility that selection acting on the Atlantic salmon mtDNA genome might be related to the need for increased metabolic efficiency at low temperatures. The analysis of sequences representing nine mitochondrial genes that are involved in the OXPHOS pathway revealed signatures of positive selection in the mitochondrial genome of the Atlantic salmon. The properties of the amino acids involved suggest that some of the mutations that were identified to be under positive selection might have functional implications, possibly in relation to metabolic efficiency. Experimental evidence, and better understanding of regional phylogeographic structuring, are needed to clarify the potential role of selection acting on the mitochondrial genome of Atlantic salmon and other locally adapted fishes. The online version of this article (doi:10.1186/s12711-015-0138-0) contains supplementary material, which is available to authorized users.
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