Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat

Abstract

In this paper we describe a pair of novel Ty3/gypsy retrotransposons isolated from the dioecious plant Silene latifolia, consisting of a non-autonomous element Retand-1 (3.7 kb) and its autonomous partner Retand-2 (11.1 kb). These two elements have highly similar long terminal repeat (LTR) sequences but differ in the presence of the typical retroelement coding regions (gag-pol genes), most of which are missing in Retand-1. Moreover, Retand-2 contains two additional open reading frames in antisense orientation localized between the pol gene and right LTR. Retand transcripts were detected in all organs tested (leaves, flower buds and roots) which, together with the high sequence similarity of LTRs in individual elements, indicates their recent transpositional activity. The autonomous elements are similarly abundant (2,700 copies) as non-autonomous ones (2,100 copies) in S. latifolia genome. Retand elements are also present in other Silene species, mostly in subtelomeric heterochromatin regions of all chromosomes. The only exception is the subtelomere of the short arm of the Y chromosome in S. latifolia which is known to lack the terminal heterochromatin. An interesting feature of the Retand elements is the presence of a tandem repeat sequence, which is more amplified in the non-autonomous Retand-1.

The role of repetitive DNA in structure and evolution of sex chromosomes in plants

“…Most TEs are distributed uniformly along both the X and Y chromosomes. Two exceptions are Retand elements, which are localized at subtelomeres (Kejnovsky et al, 2006b) and Ogre-like elements, which are present on whole X chromosome but restricted to the PAR region of the Y chromosome (Cermak et al, 2008). Tandem repeats colonize the centromeres (STAR-C) and subtelomeres (X-43.1) of X chromosome, whereas in the Y chromosome STAR-C and STAR-Y are located in the middle of both arms and X-43.1 is at the subtelomere of the q-arm.…”

Co-evolution of plant LTR-retrotransposons and their host genomes

“…Different from many truncated LTR-RTs, which seem to have lost capability of amplifi cation, these nonautonomous elements are thought to be able to utilize the retrotransposition machinery provided by their autonomous partners to proliferate, and in some cases, to very high copy numbers ( Fig. 1) (Jiang et al, 2002a, b;Kalendar et al, 2004;Kejnovsky et al, 2006;Du et al, 2010b) (Fig. 1).…”

“…While no direct evidence for the autonomous and nonautonomous LTR-RT partnerships have been found, indirect evidence derived from sequence comparison suggests the existence of such partnerships, e.g., between autonomous element RIRE2 and nonautonomous element Dasheng in rice (Jiang et al, 2002a, b); between autonomous element Retand-1 and nonautonomous element Retand-2 in Silene latifolia (Kalendar et al, 2004;Kejnovsky et al, 2006); and between autonomous element SARE and nonautonomous element SNRE in soybean (Du et al, 2010b). Some nonautonomous elements are large retrotransposon derivatives (LARDs) with several kilo-base pairs of internal sequences between two LTRs of individual elements (Kalendar et al, 2004), while others are terminal-repeat retrotransposons in miniature (TRIMs) with a few hundred base pairs of internal sequences ( Fig.…”

“…1) (Witte et al, 2001;Yang et al, 2007;Gao et al, 2012). Despite the lack of direct evidence for the origin of non-autonomous elements, it is believed that they were derived from their respective autonomous partners (Jiang et al, 2002b;Kejnovsky et al, 2006;Du et al, 2010b). A recent study suggests that such partnerships can be enhanced and maintained by homogenization of LTR sequences between autonomous and nonautonomous partners by LTR swapping, perhaps through RNA template switch (Sabot and Schulman, 2007), during the reverse transcription process (Du et al, 2010b).…”

Preferential Epigenetic Suppression of the Autonomous MusD over the Nonautonomous ETn Mouse Retrotransposons

“…For example, both the copy number and transcript levels of the barley nonautonomous BARE-2 elements are higher than those of the autonomous BARE-1 elements (61). For other yet-unconfirmed, but highly plausible, pairs of nonautonomous/autonomous plant LTR retrotransposons, the nonautonomous members have comparable or higher copy numbers than their likely autonomous counterparts (25,29,63). ERV families in mammals show similar characteristics.…”