Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes
Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes
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DOI：
10.1016/j.ygeno.2005.08.002
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发表时间：
2005-12-01
期刊：
影响因子：
4.4
通讯作者：
Ramos, MJ
中科院分区：
文献类型：
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作者：
Antunes, A;Ramos, MJ
线粒体起源的核插入拷贝(Numts)在真核生物中差异很大，其中人类和植物基因组拥有最大的谱系。Numts以前被认为不存在于鱼类物种中，但最近公布的三种鱼类核基因组序列为更全面地了解鱼类mtDNA转移的程度提供了资源。通过对红鳍东方河豚、黑绿河豚和丹尼欧河豚基因组的序列分析，我们分别鉴定了2、5和10个最近的Numt整合，它们在不到60万年前(Myr)整合到这些基因组中。这些结果与鱼类中没有Numts或Numts稀有的假设相矛盾，因为(I)在Tigroviridis中Numts与核基因组总大小的比率优于几个高等脊椎动物物种(例如鸡、小鼠和大鼠)中观察到的比率，并且只有人类超过；(Ii)在Numts所调查的整个真核基因组范围内，转移到Durio核基因组的mtDNA覆盖率只有人和小鼠超过。此外，在红豆杉、黑绿假单胞菌和轮纹藻中分别检测到335个、336个和471个老数(>；12.5Myr)。令人惊讶的是，旧的数字优先插入到已知或预测的基因中，正如对人类最近的数字所推断的那样。然而，由于在鱼类基因组中这种整合是古老的，它们可能代表着进化的成功，它们可能被认为是基因组编码区增强的潜在的重要进化机制。(C)2005 Elsevier Inc.，保留所有权利。
Nuclear inserted copies of mitochondrial origin (numts) vary widely among eukaryotes, with human and plant genomes harboring the largest repertoires. Numts were previously thought to be absent from fish species, but the recent release of three fish nuclear genome sequences provides the resource to obtain a more comprehensive insight into the extent of mtDNA transfer in fishes. From the sequence analyses of the genomes of Fugu rubripes, Tetraodon nigroviridis, and Danio rerio, we have identified 2, 5, and 10 recent numt integrations, respectively, which integrated into those genomes less than 0.6 million years (Myr) ago. Such results contradict the hypothesis of absence or rarity of numts in fishes, as (i) the ratio of numts to the total size of the nuclear genome in T nigroviridis was superior to the ratio observed in several higher vertebrate species (e.g., chicken, mouse, and rat), and only surpassed by humans, and (ii) the mtDNA coverage transferred to the nuclear genome of D. rerio is exceeded only by human and mouse, within the whole range of eukaryotic genomes surveyed for numts. Additionally, 335, 336, and 471 old numts (> 12.5 Myr) were detected in F rubripes, T nigroviridis, and D. rerio, respectively. Surprisingly, old numts are inserted preferentially into known or predicted genes, as inferred for recent numts in human. However, because in fish genomes such integrations are old, they are likely to represent evolutionary successes and they may be considered a potential important evolutionary mechanism for the enhancement of genomic coding regions. (c) 2005 Elsevier Inc, All rights reserved.