LTR retrotransposons in plants

Abstract

Ty1/copia and Ty3/gypsy LTR retrotransposons represent a significant part of plant genomes and play an important role in their structure, functioning, and evolution. The majority of information about this group of transposable elements is related to agricultural plant species and model objects, such as Arabidopsis thaliana. The most investigated groups of LTR retrotransposons are those present in angiosperms, including the Ty1/copia (Sire, Oryco, Retrofit, and Tork families) and Ty3/gypsy (CRM, Galadriel, Reina, Del, REM, Athila, and Tat) superfamilies. The genomes of gymnosperms can include both common (CRM, Galadriel, Reina, and Del), and specific Ty3/gypsy (PpRT1, IFG7, PtGypsyX1, PGGYPSYX1) and Ty1/copia (TPE1, Tpa, PtCopiaX1, PGCOPIAX1, and Tgb) LTR retrotransposons. There is little information about the diversity and distribution of LTR retrotransposons in nonseed plants (mosses, ferns, etc.). Fern genomes contain some Ty3/gypsy retroelements, closely related to the CRM family, as well as some specific retroelements from the Galahad and Mordred families. Club moss genomes contain Ty3/gypsy elements from the Tcn1 family, orig inally described only in fungal genomes, and from the Galahad and Mordred families. Retroelements, described in moss genomes, belong to the Galahad and Tcn1 families. Ty1/copia retroelements have been revealed in the genomes of certain nonseed plants, but they have not been described in detail, and the question of their belonging to any phylogenetic group of LTR retrotransposons still remains unclear. There are no data on the diversity of LTR retrotransposons in the genomes of green algae and charophytes, except for informa tion about the REM (Ty3/gypsy) element from the genome of green alga Chlamydomonas reinhardtii and the Osser (Ty1/copia) element from the genome of colonial green alga Volvox carteri.

Sequence Evolution, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in the <b><i>Saccharum spontaneum</i></b> Genome

“…In plants, the copy number of retrotransposons is generally high, and they typically account for more than half of the nuclear genome [SanMiguel et al, 1996;Baucom et al, 2009]. Moreover, it has been reported that amplification of retrotransposons makes a strong contribution to genome evolution [Sormacheva and Blinov, 2011;Kawahara et al, 2013]. For example, through recent bursts of the LTR-RT family, the Oryza granulata genome size increased by 50% [El Baidouri et al, 2014].…”

In situ gene expression profiling of the thermoacidophilic alga Cyanidioschyzon in relation to visible and ultraviolet irradiance

“…And while previous studies have suggested LTR, retrotransposons were absent from the nuclear genome of C. merolae strain 10D (Zhang et al ., ; Nozaki et al ., ), sequence similarity searches in this study annotated a significant number of the Yellowstone Cyanidioschyzon repetitive elements as containing Gypsy ‐type LTR retrotransposon sequences (Table ). The importance of LTR retrotransposons has become increasingly appreciated (Zhang et al ., ; Peddigari et al ., ), as these elements can represent a large proportion of total plant genomes (Sormacheva and Blinov, ). In the context of function, we draw attention to a previous study linking altered LTR‐retroelement transcription in response to UV irradiance stress response in plants (Ramallo et al ., ).…”

Retro-Element Gypsy-163 Is Differentially Methylated in Reproductive Tissues of Apomictic and Sexual Plants of Cenchrus ciliaris

“…While Gag is responsible for the packaging of retroelements (REs), Pol encodes for protease (PR), reverse transcriptase (RT), integrase (INT), and RNase H, which are essential for amplification and integration of the RE in plant genome ( Suoniemi et al, 1998 ). REs are categorized into two groups (i) long terminal repeats REs (LTRs), and (ii) non-LTR REs based on their flanking terminal repeats ( Sormacheva and Blinov, 2011 ). LTR REs are further sub-classified into Ty1- Copia ( Pseudoviridae) and Ty3- Gypsy ( Metaviridae) based on the order of RT and INT domains present in Pol , and the extent of similarity in their sequences ( Kumar and Bennetzen, 1999 ).…”