PT - JOURNAL ARTICLE AU - Maria Waldl AU - Bernhard C. Thiel AU - Roman Ochsenreiter AU - Alexander Holzenleiter AU - João Victor de Araujo Oliveira AU - Maria Emília M. T. Walter AU - Michael T. Wolfinger AU - Peter F. Stadler TI - TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes AID - 10.1101/323675 DP - 2018 Jan 01 TA - bioRxiv PG - 323675 4099 - http://biorxiv.org/content/early/2018/05/16/323675.short 4100 - http://biorxiv.org/content/early/2018/05/16/323675.full AB - The telomerase RNA in yeasts is large, usually > 1,000 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 still remain without annotated telomerase RNA.