TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
by
Maria Waldl 1,†, Bernhard C. Thiel 1,†, Roman Ochsenreiter 1, Alexander Holzenleiter 2,3, João Victor De Araujo Oliveira 4, Maria Emília M. T. Walter 4, Michael T. Wolfinger 1,5,*
and Peter F. Stadler 1,6,7,8,*
Maria Waldl 1,†, Bernhard C. Thiel 1,†, Roman Ochsenreiter 1, Alexander Holzenleiter 2,3, João Victor De Araujo Oliveira 4, Maria Emília M. T. Walter 4, Michael T. Wolfinger 1,5,* and Peter F. Stadler 1,6,7,8,*
1
Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
2
BioInformatics Group, Fakultät CB Hochschule Mittweida, Technikumplatz 17, D-09648 Mittweida, Germany
3
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
4
Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário–Asa Norte, Brasília, DF CEP: 70910-900, Brazil
5
Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
6
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Universität Leipzig, D-04107 Leipzig, Germany
7
Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
8
Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2018, 9(8), 372; https://doi.org/10.3390/genes9080372
Received: 15 May 2018 / Revised: 17 July 2018 / Accepted: 18 July 2018 / Published: 26 July 2018
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.
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Keywords:
non-coding RNA; telomerase RNA; secondary structure; synteny; homology search; yeast
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MDPI and ACS Style
Waldl, M.; Thiel, B.C.; Ochsenreiter, R.; Holzenleiter, A.; De Araujo Oliveira, J.V.; Walter, M.E.M.T.; Wolfinger, M.T.; Stadler, P.F. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes 2018, 9, 372.
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