A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in Gossypium raimondii

Stabilization of transposable element (TE) copy number involves the biosynthesis of short silencing RNAs (siRNAs) and further initialization of siRNA-mediated TE silencing. To gain insight into the relationship between the biosynthesis of siRNAs and their source TEs, we examined the co-evolutionary dynamics and expression of these two entities by characterizing the siRNA distribution across the genome of Gossypium raimondii Ulbr. We identified an unusual region at the 3’ end of chromosome 1 with significantly enriched siRNA coverage. Analysis of the correlation pattern between uniquely mapped siRNAs and those mapping to multiple regions implicated active biogenesis of siRNAs from these potential young TEs. Furthermore, divergence estimates of TEs within this region confirmed that the majority of TEs are young. Active transcription of the source TEs and their positive correlation with expressed siRNAs indicates that sufficient expression of TEs may be necessary to generate siRNAs and maintain the silenced state of recently transposed TEs. T ransposable elements are ubiquitous components in plant genomes and are the major determinant of genome size differences among angiosperms. Based on structure, encoded proteins and mechanism of transposition, TEs are subcategorized into Class I retroelements (retro-TEs, including long terminal repeat (LTR) and non-LTR TEs) and Class II DNA transposons (DNA TEs, including CACTA, hAT, mutation family etc.), which are amplified via “copy-and-paste” and “cut-and-paste” mechanisms, respectively. Although active transposition of TEs has frequently been reported under special conditions (Eun et al., 2012; Hancock et al., 2011; Liu et al., 2004), TEs often are silenced to prevent their unbridled and presumably deleterious transposition. One of the major TE silencing mechanisms in plants is the biogenesis of 24-nucleotide (nt) siRNAs, generated from RNA polymerase (Pol) IV-synthesized TE transcripts (single-strand RNAs), which are then processed by RNAdependent RNA Pol II (RDR2) for double-stranded RNA synthesis and Dicer-like (DCL) 3 enzymes (cleavage of double-stranded RNA into 24-nt siRNA). These siRNAs further target TEs (via argonaute 4 protein binding) establishing DNA and histone hypermethylation at the TE site of origin and block the transcription of targeted TEs (Chapman and Carrington, 2007; Chen, 2010; Slotkin and Martienssen, 2007). Another noncanonical Published in The Plant Genome 8 doi: 10.3835/plantgenome2014.11.0088 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. L. Gong, R.E. Masonbrink, C.E. Grover, S. Renny-Byfield, and J.F. Wendel, Dep. of Ecology, Evolution and Organismal Biology, Iowa State Univ., Ames, IA 50011, USA. L. Gong, current address: Key Lab. of Molecular Epigenetics of the Ministry of Education, Northeast Normal Univ., Changchun, Jilin 130024, China. Received 25 Nov. 2014. Accepted 6 Feb. 2015. *Corresponding author ([email protected]). Abbreviations: DCL, Dicer-like; LTR, long terminal repeat; MM, multiple mapping; nt, nucleotide; Pol II/IV, DNA-dependent RNA polymerase II/IV; RDR2/6, RNA-dependent RNA polymerase II/VI; siRNA, short silencing RNAs; TE, transposable element; UM, unique mapping..