Rearrangement and evolution of mitochondrial genomes in parrots.
Rearrangement and evolution of mitochondrial genomes in parrots.
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DOI：
10.1016/j.ympev.2015.08.011
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发表时间：
2016-01
影响因子：
4.1
通讯作者：
Wright TF
中科院分区：
文献类型：
--
作者：
Eberhard JR;Wright TF
已经在多种鸟类中描述了导致控制区重复的线粒体基因组重排，但导致其出现和维持的机制仍不清楚，并且尚未探索它们对序列进化的影响。最近对鹦鹉目（鹦鹉）线粒体基因组的一项调查发现，控制区重复在整个目中独立出现了至少六次。我们分析了 20 个鹦鹉物种的完整线粒体基因组序列，包括具有控制区域重复的每个谱系的代表，以记录基因顺序变化并检查基因组重排对序列进化模式的影响。先前报道的亚马逊鹦鹉的基因顺序在六个独立衍生的基因组重排中的四个中被发现，并且在 Prioniturus luconensis 中发现了先前未描述的基因顺序，代表了基因组重排的第五个进化枝；无法确认剩余重排事件产生的基因顺序。在所有重排的基因组中，存在控制区域的两个副本，并且在序列水平上非常相似，而参与重排的其他基因的副本则显示出退化迹象或已完全丢失。我们比较了有和没有控制区域重复的基因组中的序列进化速率，没有发现与重复相关的一致的加速或减速。这可能是由于鹦鹉中的大多数基因组重排事件都是古老的，此外，我们发现体型对线粒体而非核序列的进化速度有影响。碱基组成分析发现，相对于其他鸟类，鹦鹉的编码序列具有异常强烈的组成不对称性（AT 和 GC 偏度），特别是在四重简并位点。此外，我们发现具有控制区域重复的物种具有更高的 AT 偏差。造成这种成分不对称的一个潜在原因是鹦鹉的线粒体 DNA 复制异常缓慢。如果是这种情况，那么通过拥有第二个控制区域提供的任何复制优势都可能导致选择在复制后维护两个控制区域。
Mitochondrial genome rearrangements that result in control region duplication have been described for a variety of birds, but the mechanisms leading to their appearance and maintenance remain unclear, and their effect on sequence evolution has not been explored. A recent survey of mitochondrial genomes in the Psittaciformes (parrots) found that control region duplications have arisen independently at least six times across the order. We analyzed complete mitochondrial genome sequences from 20 parrot species, including representatives of each lineage with control region duplications, to document the gene order changes and to examine effects of genome rearrangements on patterns of sequence evolution. The gene order previously reported for Amazona parrots was found for four of the six independently derived genome rearrangements, and a previously undescribed gene order was found in Prioniturus luconensis, representing a fifth clade with rearranged genomes; the gene order resulting from the remaining rearrangement event could not be confirmed. In all rearranged genomes, two copies of the control region are present and are very similar at the sequence level, while duplicates of the other genes involved in the rearrangement show signs of degeneration or have been lost altogether. We compared rates of sequence evolution in genomes with and without control region duplications and did not find a consistent acceleration or deceleration associated with the duplications. This could be due to the fact that most of the genome rearrangement events in parrots are ancient, and additionally, to an effect of body size on evolutionary rate that we found for mitochondrial but not nuclear sequences. Base composition analyses found that relative to other birds, parrots have unusually strong compositional asymmetry (AT- and GC-skew) in their coding sequences, especially at four-fold degenerate sites. Furthermore, we found higher AT skew in species with control region duplications. One potential cause for this compositional asymmetry is that parrots have unusually slow mtDNA replication. If this is the case, then any replicative advantage provided by having a second control region could result in selection for maintenance of both control regions once duplicated.