Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. Issue 2 (23rd January 2014)

• Record Type: Journal Article
• Authors: Kubat, Zdenek; Zluvova, Jitka; Vogel, Ivan; Kovacova, Viera; Cermak, Tomas; Cegan, Radim; Hobza, Roman; Vyskot, Boris; Kejnovsky, Eduard
• Is Part Of: New phytologist. Volume 202:Issue 2(2014)
• Page Start: 662
• Page End: 678
• Publication Date: 2014-01-23
• Subjects: Botany -- Periodicals; 580
• DOI: 10.1111/nph.12669
• Languages: English
• ISSNs: 0028-646X

Abstract

<abstract abstract-type="main" id="nph12669-abs-0001"> <title>Summary</title> <p> <list id="nph12669-list-0001" list-type="bullet"> <list-item> <p>Some transposable elements (TEs) show extraordinary variance in abundance along sex chromosomes but the mechanisms responsible for this variance are unknown. Here, we studied <italic>Ogre</italic> long terminal repeat (LTR) retrotransposons in <italic>Silene latifolia</italic>, a dioecious plant with evolutionarily young heteromorphic sex chromosomes. <italic>Ogre</italic> elements are ubiquitous in the <italic>S. latifolia</italic> genome but surprisingly absent on the Y chromosome.</p> </list-item> <list-item> <p>Bacterial artificial chromosome (BAC) library analysis and fluorescence <italic>in situ</italic> hybridization (FISH) were used to determine <italic>Ogre</italic> structure and chromosomal localization. Next generation sequencing (NGS) data were analysed to assess the transcription level and abundance of small RNAs. Methylation of <italic>Ogres</italic> was determined by bisulphite sequencing. Phylogenetic analysis was used to determine mobilization time and selection forces acting on <italic>Ogre</italic> elements.</p> </list-item> <list-item> <p>We characterized three <italic>Ogre</italic> families ubiquitous in the <italic>S. latifolia</italic> genome. One family is nearly absent on the Y chromosome despite all the families having similar structures and spreading mechanisms. We showed that <italic>Ogre</italic> retrotransposons evolved before sex chromosomes appeared but were mobilized after formation of the Y chromosome. Our data suggest that the absence of one <italic>Ogre</italic> family on the Y chromosome may be caused by 24‐nucleotide (24‐nt) small RNA‐mediated silencing leading to female‐specific spreading.</p> </list-item> <list-item> <p>Our findings highlight epigenetic silencing mechanisms as potentially crucial factors in sex‐specific spreading of some TEs, but other possible mechanisms are also discussed.</p> </list-item> </list> </p> </abstract>