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Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome

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Abstract

Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 103 to 105 copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites’ SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.

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Acknowledgments

This work has been supported by Canziani donation, Fondazione del Monte—Bologna and PRIN-2008 funds to BM. We are particularly grateful to Claudia Husseneder for her encouragement to use the Coptotermes formosanus EST library she produced. We also wish to thank the two anonymous referees whose suggestions substantially improved this work.

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  1. Dip. Biologia Evoluzionistica Sperimentale, Università di Bologna, via Selmi, 3, 40126, Bologna, Italy

    Andrea Luchetti & Barbara Mantovani

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  1. Andrea Luchetti
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  2. Barbara Mantovani
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Correspondence to Andrea Luchetti.

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Communicated by S. Hohmann.

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Luchetti, A., Mantovani, B. Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome. Mol Genet Genomics 285, 175–184 (2011). https://doi.org/10.1007/s00438-010-0595-7

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