Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model

Morgan, J. A. T. and Blair, D. (1998) Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model. Journal of Molecular Evolution, 47 4: 406-419. doi:10.1007/PL00006398

Author Morgan, J. A. T.
Blair, D.
Title Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model
Journal name Journal of Molecular Evolution   Check publisher's open access policy
ISSN 0022-2844
Publication date 1998-10
Sub-type Article (original research)
DOI 10.1007/PL00006398
Volume 47
Issue 4
Start page 406
End page 419
Total pages 14
Place of publication Secaucus, NJ, United States
Publisher Springer
Language eng
Abstract The secondary structure of rRNA internal transcribed spacer 2 is important in the process of ribosomal biogenesis. Trematode ITS sequences are poorly conserved and difficult to align for phylogenetic comparisons above a family level. If a conserved secondary structure can be identified, it can be used to guide primary sequence alignments. ITS2 sequences from 39 species were compared. These species span four orders of trematodes (Echinostomiformes, Plagiorchiformes, Strigeiformes, and Paramphistomiformes) and one monogenean (Gyrodactyliformes). The sequences vary in length from 251 to 431 bases, with an average GC content of 48%. The monogenean sequence could not be aligned with confidence to the trematodes. Above the family level trematode sequences were alignable from the 5′ end for 139 bases. Secondary structure foldings predicted a four-domain model. Three folding patterns were required for the apex of domain B. The folding pattern of domains C and D varies for each family. The structures display a high GC content within stems. Bases A and U are favored in unpaired regions and variable sites cluster. This produces a mosaic of conserved and variable regions with a structural conformation resistant to change. Two conserved strings were identified, one in domain B and the other in domain C. The first site can be aligned to a processing site identified in yeast and rat. The second site has been found in plants, and structural location appears to be important. A phylogenetic tree of the trematode sequences, aligned with the aid of secondary structures, distinguishes the four recognized orders.
Keyword Secondary structure
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
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