In contrast to the catalytic subunit of telomerase, its RNA subunit (TR) is highly divergent in size, sequence and biogenesis pathways across eukaryotes. Current views on TR evolution assume a common origin of TRs transcribed with RNA polymerase II in Opisthokonta (the supergroup including Animalia and Fungi) and Trypanosomida on one hand, and TRs transcribed with RNA polymerase III under the control of type 3 promoter, found in TSAR and Archaeplastida supergroups (including e.g. ciliates and Viridiplantae taxa, respectively). Here, we focus on unknown TRs in one of the largest Animalia order - Hymenoptera (Arthropoda) with more than 300 available representative genomes. Using a combination of bioinformatic and experimental approaches, we identify their TRs. In contrast to the presumed type of TRs (H/ACA box snoRNAs transcribed with RNA Polymerase II) corresponding to their phylogenetic position, we find here short TRs of the snRNA type, likely transcribed with RNA polymerase III under the control of the type 3 promoter. The newly described insect TRs thus question the hitherto assumed monophyletic origin of TRs across Animalia and point to an evolutionary switch in TR type and biogenesis that was associated with the divergence of Arthropods.

Agricultural Research Ltd Troubsko CZ 664 41 Czech Republic

Biology Centre of the Czech Academy of Sciences Institute of Entomology České Budějovice CZ 37005 Czech Republic

Department of Cell Biology and Radiobiology Institute of Biophysics of the Czech Academy of Sciences Brno CZ 61265 Czech Republic

Laboratory of Functional Genomics and Proteomics NCBR Faculty of Science Masaryk University Brno CZ 61137 Czech Republic

Mendel Centre for Plant Genomics and Proteomics CEITEC Masaryk University Brno CZ 62500 Czech Republic

The Boyce Thompson Institute Cornell University 533 Tower Road Ithaca NY 14850 USA

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Biessmann H., Mason J.M.. Telomerase-independent mechanisms of telomere elongation. Cell. Mol. Life Sci. 2003; 60:2325–2333. PubMed PMC

Podlevsky J.D., Chen J.J.L.. Evolutionary perspectives of telomerase RNA structure and function. RNA Biol. 2016; 13:720–732. PubMed PMC

Fajkus P., Peska V., Zavodnik M., Fojtova M., Fulneckova J., Dobias S., Kilar A., Dvorackova M., Zachova D., Necasova I.et al. .. Telomerase RNAs in land plants. Nucleic Acids Res. 2019; 47:9842–9856. PubMed PMC

Fajkus P., Kilar A., Nelson A.D.L., Hola M., Peska V., Goffova I., Fojtova M., Zachova D., Fulneckova J., Fajkus J.. Evolution of plant telomerase RNAs: farther to the past, deeper to the roots. Nucleic Acids Res. 2021; 49:7680–7694. PubMed PMC

Waldl M., Thiel B.C., Ochsenreiter R., Holzenleiter A., Oliveira J.V.D., Walter M.E.M.T., Wolfinger M.T., Stadler P.F.. TERribly difficult: searching for Telomerase RNAs in Saccharomycetes. Genes. 2018; 9:372. PubMed PMC

Logeswaran D., Li Y., Podlevsky J.D., Chen J.J.L.. Monophyletic origin and divergent evolution of animal telomerase RNA. Mol. Biol. Evol. 2021; 38:215–228. PubMed PMC

Shakirov E.V., Chen J.J., Shippen D.E.. Plant telomere biology: the green solution to the end-replication problem. Plant Cell. 2022; 34:2492–2504. PubMed PMC

Greider C.W., Blackburn E.H.. A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis. Nature. 1989; 337:331–337. PubMed

Hargrove B.W., Bhattacharyya A., Domitrovich A.M., Kapler G.M., Kirk K., Shippen D.E., Kunkel G.R.. Identification of an essential proximal sequence element in the promoter of the telomerase RNA gene of Tetrahymena thermophila. Nucleic Acids Res. 1999; 27:4269–4275. PubMed PMC

Lingner J., Hendrick L.L., Cech T.R.. Telomerase RNAs of different ciliates have a common secondary structure and a permuted template. Genes Dev. 1994; 8:1984–1998. PubMed

Burki F., Roger A.J., Brown M.W., Simpson A.G.B.. The new tree of eukaryotes. Trends Ecol. Evol. 2020; 35:43–55. PubMed

Lukhtanov V.A. Diversity and evolution of telomere and subtelomere DNA sequences in insects. 2022; bioRxiv doi:10 April 2022, preprint: not peer reviewed10.1101/2022.04.08.487650. DOI

Zhou Y.H., Wang Y., Xiong X., Appel A.G., Zhang C., Wang X.. Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans. Life Sci. Alliance. 2022; 5:e202101163. PubMed PMC

Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27:573–580. PubMed PMC

Peska V., Sitova Z., Fajkus P., Fajkus J.. BAL31-NGS approach for identification of telomeres de novo in large genomes. Methods. 2017; 114:16–27. PubMed

Novak P., Neumann P., Macas J.. Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2. Nat. Protoc. 2020; 15:3745–3776. PubMed

Nawrocki E.P., Eddy S.R.. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29:2933–2935. PubMed PMC

Peri S., Roberts S., Kreko I.R., McHan L.B., Naron A., Ram A., Murphy R.L., Lyons E., Gregory B.D., Devisetty U.K.et al. .. Read mapping and transcript assembly: a scalable and high-throughput workflow for the processing and analysis of ribonucleic acid sequencing data. Front Genet. 2020; 10:1361. PubMed PMC

Raden M., Ali S.M., Alkhnbashi O.S., Busch A., Costa F., Davis J.A., Eggenhofer F., Gelhausen R., Georg J., Heyne S.et al. .. Freiburg RNA tools: a central online resource for RNA-focused research and teaching. Nucleic Acids Res. 2018; 46:W25–W29. PubMed PMC

Griffiths-Jones S., Bateman A., Marshall M., Khanna A., Eddy S.R.. Rfam: an RNA family database. Nucleic Acids Res. 2003; 31:439–441. PubMed PMC

Bailey T.L., Johnson J., Grant C.E., Noble W.S.. The MEME Suite. Nucleic Acids Res. 2015; 43:W39–W49. PubMed PMC

Hernandez G., Valafar F., Stumph W.E.. Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity. Nucleic Acids Res. 2007; 35:21–34. PubMed PMC

Mei Y., Jing D., Tang S.Y., Chen X., Chen H., Duanmu H.N., Cong Y.Y., Chen M.Y., Ye X.H., Zhou H.et al. .. InsectBase 2.0: a comprehensive gene resource for insects. Nucleic Acids Res. 2022; 50:D1040–D1045. PubMed PMC

Wickham H. Ggplot2 Elegant Graphics for Data Analysis introduction. Ggplot2: Elegant Graphics for Data Analysis. 2009; 1–7.

Korandova M., Krucek T., Vrbova K., Frydrychova R.C.. Distribution of TTAGG-specific telomerase activity in insects. Chromosome Res. 2014; 22:495–503. PubMed

Frydrychova R., Marec F.. Repeated losses of TTAGG telomere repeats in evolution of beetles (Coleoptera). Genetica. 2002; 115:179–187. PubMed

Fajkus P., Peska V., Sitova Z., Fulneckova J., Dvorackova M., Gogela R., Sykorova E., Hapala J., Fajkus J.. Allium telomeres unmasked: the unusual telomeric sequence (CTCGGTTATGGG)(n) is synthesized by telomerase. Plant J. 2016; 85:337–347. PubMed

Mason J.M., Randall T.A., Frydrychova R.C.. Telomerase lost?. Chromosoma. 2016; 125:65–73. PubMed PMC

Prusakova D., Peska V., Pekar S., Bubenik M., Cizek L., Bezdek A., Frydrychova R.C.. Telomeric DNA sequences in beetle taxa vary with species richness. Sci. Rep. 2021; 11:13319. PubMed PMC

Cervenak F., Sepsiova R., Nosek J., Tomaska L.. Step-by-Step evolution of Telomeres: lessons from yeasts. Genome Biol. Evol. 2021; 13:evaa268. PubMed PMC

Peska V., Garcia S.. Origin, diversity, and evolution of telomere sequences in plants. Front. Plant Sci. 2020; 11:117. PubMed PMC

Peska V., Fajkus P., Bubenik M., Brazda V., Bohalova N., Dvoracek V., Fajkus J., Garcia S.. Extraordinary diversity of telomeres, telomerase RNAs and their template regions in Saccharomycetaceae. Sci. Rep. 2021; 11:12784. PubMed PMC

Peska V., Matl M., Mandakova T., Vitales D., Fajkus P., Fajkus J., Garcia S.. Human-like telomeres in Zostera marina reveal a mode of transition from the plant to the human telomeric sequences. J. Exp. Bot. 2020; 71:5786–5793. PubMed

Koubova J., Jehlik T., Kodrik D., Sabova M., Sima P., Sehadova H., Zavodska R., Frydrychova R.C.. Telomerase activity is upregulated in the fat bodies of pre-diapause bumblebee queens (Bombus terrestris). Insect Biochem. Mol. Biol. 2019; 115:103241. PubMed

Hernandez N. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J. Biol. Chem. 2001; 276:26733–26736. PubMed

Tzfati Y., Fulton T.B., Roy J., Blackburn E.H.. Template boundary in a yeast telomerase specified by RNA structure. Science. 2000; 288:863–867. PubMed

Chen J.L., Greider C.W.. Template boundary definition in mammalian telomerase. Genes Dev. 2003; 17:2747–2752. PubMed PMC

Tzfati Y., Knight Z., Roy R., Blackburn E.H.. A novel pseudoknot element is essential for the action of a yeast telomerase. Genes Dev. 2003; 17:1779–1788. PubMed PMC

Chen J.L., Greider C.W.. Functional analysis of the pseudoknot structure in human telomerase RNA. Proc. Natl. Acad. Sci. U.S.A. 2005; 102:8080–8085. PubMed PMC

Cash D.D., Cohen-Zontag O., Kim N.K., Shefer K., Brown Y., Ulyanov N.B., Tzfati Y., Feigon J.. Pyrimidine motif triple helix in the Kluyveromyces lactis telomerase RNA pseudoknot is essential for function in vivo. Proc. Natl. Acad. Sci. U.S.A. 2013; 110:10970–10975. PubMed PMC

Jansson L.I., Akiyama B.M., Ooms A., Lu C., Rubin S.M., Stone M.D.. Structural basis of template-boundary definition in Tetrahymena telomerase. Nat. Struct. Mol. Biol. 2015; 22:883–888. PubMed PMC

Song J.R., Logeswaran D., Castillo-Gonzalez C., Li Y., Bose S., Aklilu B.B., Ma Z.Y., Polkhovskiy A., Chen J.J.L., Shippen D.E.. The conserved structure of plant telomerase RNA provides the missing link for an evolutionary pathway from ciliates to humans. Proc. Natl. Acad. Sci. U.S.A. 2019; 116:24542–24550. PubMed PMC

Malm T., Johanson K.A., Wahlberg N.. The evolutionary history of Trichoptera (Insecta): a case of successful adaptation to life in freshwater. Proc. Int. Congr. Entomol., 10th. 2013; 38:459–473.

Kawahara A.Y., Plotkin D., Espeland M., Meusemann K., Toussaint E.F.A., Donath A., Gimnich F., Frandsen P.B., Zwick A., dos Reis M.et al. .. Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths. Proc. Natl. Acad. Sci. U.S.A. 2019; 116:22657–22663. PubMed PMC

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