Analysis of mammalian rDNA internal transcribed spacers.
Analysis of mammalian rDNA internal transcribed spacers.
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DOI：
10.1371/journal.pone.0079122
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Coleman AW
中科院分区：
文献类型：
--
作者：
Coleman AW
核rDNA内转录间隔区（ITS 1和ITS 2）被广泛用于真核生物从序数水平到种水平的系统发育研究，甚至有一个ITS 2序列数据库。然而，ITS区在哺乳动物系统发育研究中一直被忽视，只有少数啮齿类和猿类的序列在GenBank中有代表性。这种缺乏的原因，以及补救措施，在这里描述。我们已经从36种哺乳动物中恢复了这些序列，大多数长度>1 kb。序列比对和转录本折叠比较揭示了rRNA转录本的二级结构。哺乳动物的ITS区虽然很长，但仍然折叠成其他真核生物的可识别的二级结构。ITS 2特别具有四个标准的螺旋环，环II和III具有真核生物通用的标志性特征。转录本二级结构螺旋的序列和插入/缺失支持胎盘的四个总目分类。在家庭层面上，主要的独特的插入缺失，整齐地切除整个螺旋，将是有用的，当额外的物种代表，从而显着进一步了解哺乳动物进化史的细节。此外，ITS 1的一个高度保守的元素，常见的温血脊椎动物的鉴定可能有助于破译RNA转录加工的复杂机制。这是最后一个主要的陆生脊椎动物类群，其rRNA ITS二级结构已被解析。
Nuclear rDNA Internal Transcribed Spacers, ITS1 and ITS2, are widely used for eukaryote phylogenetic studies from the ordinal level to the species level, and there is even a database for ITS2 sequences. However, ITS regions have been ignored in mammalian phylogenetic studies, and only a few rodent and ape sequences are represented in GenBank. The reasons for this dearth, and the remedies, are described here. We have recovered these sequences, mostly >1 kb in length, for 36 mammalian species. Sequence alignment and transcript folding comparisons reveal the rRNA transcript secondary structure. Mammalian ITS regions, though quite long, still fold into the recognizable secondary structure of other eukaryotes. The ITS2 in particular bears the four standard helix loops, and loops II and III have the hallmark characters universal to eukaryotes. Both sequence and insertions/deletions of transcript secondary structure helices observed here support the four superorder taxonomy of Placentalia. On the family level, major unique indels, neatly excising entire helices, will be useful when additional species are represented, resulting in significant further understanding of the details of mammalian evolutionary history. Furthermore, the identification of a highly conserved element of ITS1 common to warm-blooded vertebrates may aid in deciphering the complex mechanism of RNA transcript processing. This is the last major group of terrestrial vertebrates for which rRNA ITS secondary structure has been resolved.
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影响因子：
3.5
作者：
MICHOT, B;BACHELLERIE, JP;RENALIER, MH
通讯作者：
RENALIER, MH
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通讯作者：
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