Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants.
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DOI：
10.1186/1471-2148-7-135
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发表时间：
2007-08-09
影响因子：
3.4
通讯作者：
Palmer JD
中科院分区：
文献类型：
--
作者：
Mower JP;Touzet P;Gummow JS;Delph LF;Palmer JD
人们早就知道，开花植物和其他陆地植物的线粒体基因同义替换率异常低。尽管最近报道了这一模式的两个戏剧性的例外，但目前尚不清楚在植物线粒体进化过程中替代率的主要增加发生的频率，以及植物间替代率变化的总体幅度。对被子植物和裸子植物线粒体基因的同义取代率进行了广泛的研究。尽管大多数分类群符合植物线粒体序列进化缓慢的一般规律，但也发现了一些高度加速的情况。我们详细探讨这些新的情况之一，属内的沉默。据估计，在过去的500万年里，同义词替换率大约增加了100倍，而且只涉及本研究中取样的10种Silene中的一种。序列进化异常缓慢的例子也被发现。比较最快和最慢的世系表明，同义代代率在种子植物中相差4个数量级。换句话说，一些植物线粒体谱系在1万年中积累的同义变化比其他植物在1亿年中积累的同义变化要多。几个令人困惑的情况下，基因变异的序列分歧在植物内被发现。其中一些可能反映了有趣的生物学现象，如水平基因转移、线粒体到细胞核转移和线粒体替代率的基因组内变异，而其他可能是各种错误的结果。这里测量的同义取代率的极端构成了迄今为止已知的任何一组生物的速率变化的最大范围。这些结果强调了在系统发育背景下检查绝对替代率的效用，而不是通过传统的两两方法。为什么植物线粒体基因组的替代率通常很低，但偶尔又会急剧增加，这仍然是个谜。
It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants. A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genus Silene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species of Silene sampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors. The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious.
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影响因子：
3.3
作者：
Magallón, SA;Sanderson, MJ
通讯作者：
Sanderson, MJ
影响因子：
10.7
作者：
Laroche, J;Bousquet, J
通讯作者：
Bousquet, J
影响因子：
3.9
作者：
PALMER, JD;HERBON, LA
通讯作者：
HERBON, LA
DOI：
10.1073/pnas.94.11.5722
发表时间：
1997-05-27
影响因子：
11.1
作者：
Laroche, J;Li, P;Bousquet, J
通讯作者：
Bousquet, J
DOI：
10.1073/pnas.042694899
发表时间：
2002-07-23
影响因子：
11.1
作者：
Adams, KL;Qiu, YL;Palmer, JD
通讯作者：
Palmer, JD