Abstract
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.
Highlights
In 1956, Romer [1] recognized 15 orders of Eutheria, placental mammals, and this has grown to 18, 17 of which include living species (Placentalia) (e.g. [2,3])
Both sequence comparisons and the structural indels found in ITS1 and ITS2 emphasize the basal position of these two insectivores of the Laurasiatheria
Mammalian ITS sequences are nearly the last major eukaryote group to be assessed for sequence and secondary structure
Summary
In 1956, Romer [1] recognized 15 orders of Eutheria, placental mammals, and this has grown to 18, 17 of which include living species (Placentalia) (e.g. [2,3]). In 1956, Romer [1] recognized 15 orders of Eutheria, placental mammals, and this has grown to 18, 17 of which include living species (Placentalia) Molecular phylogenetic analyses have primarily utilized total mitochondrial sequences [6] and sequences from >3,000 nuclear genes [5,7]. In addition to these sequence comparison methods, there are several striking examples of multicodon indels supporting the monophyly of the Afrotheria and/or Afrotheria + Xenarthra [8,9,10]. The most widely used nucleotide sequences for eukaryote phylogenetic reconstructions [11,12], the two Internal Transcribed Spacer regions of the nuclear ribosomal repeats, remain unexamined from this perspective in mammals
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