The rise and fall of the CR1 subfamily in the lineage leading to penguins.
The rise and fall of the CR1 subfamily in the lineage leading to penguins.
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DOI：
10.1016/j.gene.2005.09.042
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发表时间：
2006-01
期刊：
影响因子：
3.5
通讯作者：
M. Watanabe;M. Nikaido;T. Tsuda;H. Inoko;D. Mindell;K. Murata;N. Okada
中科院分区：
文献类型：
--
作者：
M. Watanabe;M. Nikaido;T. Tsuda;H. Inoko;D. Mindell;K. Murata;N. Okada
企鹅的进化已经被形态学家、生物学家和分子生物遗传学家广泛研究过，尽管没有定论。我们调查了这个问题，使用逆转录酶分析插入CR 1，这是一个成员的线（长散置元件）家庭，在企鹅和企鹅亲属的基因组。逆转录酶方法是鉴定单系类群的有力工具。由于逆转座子在进化过程中经常表现出不同的相对频率，因此首先有必要确定在所讨论的物种分化期间特别活跃的某个亚组。因此，我们系统地分析了从企鹅和企鹅相关基因组中分离的许多CR 1成员。这些CR 1被分为至少三个不同的亚组，它们共享诊断性核苷酸插入和/或缺失，即企鹅CR 1 Sph I、Sph II A型和Sph II B型。对插入的逆转录子进行PCR分析，发现在企鹅进化的不同时期，不同的CR 1亚家族或类型以不同的速率扩增。也就是说，企鹅CR 1 SphI亚科在本研究中检查的所有目的共同祖先中或至少在所有现存企鹅的共同祖先中具有较高的后移率，并且亚科SphII A型也具有相同的趋势。因此，这些CR 1成员可以用来阐明楔鼻形目（企鹅）在不同鸟类目之间的系统发育关系。与此相反，企鹅CR 1 SphII型B亚科有较高的后移率之前和之后出现的现存的属在Sphenisplaceae，这表明他们是有用的阐明现存的企鹅之间的内部关系。这是第一次报道的禽基因组中的CR 1家族成员之间的特征，鸡除外。因此，这项工作将是一个基石，阐明在企鹅进化的系统发育关系，使用逆转录酶的方法。
The evolution of penguins has been investigated extensively, although inconclusively, by morphologists, biogeographers and molecular phylogeneticists. We investigated this issue using retroposon analysis of insertions of CR1, which is a member of the LINE (long interspersed element) family, in the genomes of penguins and penguin relatives. The retroposon method is a powerful tool for identifying monophyletic groups. Because retroposons often show different relative frequencies of retroposition during evolution, it is first necessary to identify a certain subgroup that was specifically active during the period when the species in question diverged. Hence, we systematically analyzed many CR1 members isolated from penguin and penguin-related genomes. These CR1s are divided into at least three distinct subgroups that share diagnostic nucleotide insertions and/or deletions, namely, penguin CR1 Sph I, Sph II type A and Sph II type B. The analysis of the inserted retroposons by PCR revealed that different CR1 subfamilies or types had amplified at different rates among different periods during penguin evolution. Namely, the penguin CR1 Sph I subfamily had higher rates of retroposition in a common ancestor of all orders examined in this study or at least in a common ancestor of all extant penguins, and the subfamily Sph II type A also had the same tendency. Therefore, these CR1 members can be used to elucidate the phylogenetic relationships of Sphenisciformes (penguins) among different avian orders. In contrast, the penguin CR1 Sph II type B subfamily had higher rates of retroposition just before and after the emergence of the extant genera in Spheniscidae, suggesting that they are useful for elucidating the intra-relationships among extant penguins. This is the first report for the characterization among the members of CR1 family in avian genomes excluding those of chickens. Hence, this work will be a cornerstone for elucidating the phylogenetic relationships in penguin evolution using the retroposon method.