Transposable elements and plant genome evolution

Abstract

Transposable elements (TEs) were first discovered in maize by Barbara McClintock more than half a cen tury ago. Since then, a good amount of information has been generated about existing types of transpos able elements, including information about both transposable elements and their interactions with the genome of the host organism. Progress in genome sequencing during the last decade provided availability of large data sets for plant nucleotide sequences. It allowed the initiation of research on the families of transposable elements and their populations within genomes, which is exceptionally interesting for studies of evolutionary dynamics not only transposable ele ments but also plant genome evolution.Transposable elements in a genome can be sepa rated into two classes: class I elements (retrotrans posons), which transpose through the mechanism of "copy and paste" using an RNA intermediate, and class II elements (DNA transposable elements) that employ a "cut and paste" mechanism forming either single or double DNA strand breaks (Wicker et al., 2007).Class I transposable elements are arranged into LTR retrotransposons, which are characterized by the presence of long terminal repeats at both ends of the element; DIRS elements; and Penelope, LINE , and SINE elements, as well as nonautonomous variants of LTR retrotransposons such as TRIM (terminal repeat retrotransposons in miniature) and LARD (large retrotransposon derivatives)elements. Plant LTR retrotransposons are divided into two major sub classes called gypsy and copia elements, which differ in the relative position of the domains that encode inte grase and reverse transcriptase within the gene encod ing polyprotein (Wicker et al., 2007).Class II transposable elements in plant genomes are represented by two subclasses. The first subclass combines elements that transpose using the classic "cut and paste" mechanism to form a double DNA strand break, while the second class is comprised of elements that utilize the "rolling circle" mechanism for their transposition. Subclass I is represented by TIRs (terminal inverted repeats), which is characterized by the pres ence of TIRs at both ends of the element. The ele ments of the subclass I transpose with the help of enzyme transposase. Plant TIRs are represented by the superfamilies Tc Mariner, hAT, Mutator (MULU), P, PIF Harbinger, and CACTA (Wicker et al., 2007). The most extensively studied hAT families are Ac Ds ele ments of maize and Tam3 of snapdragon (Rubin et al., 2001). The CACTA elements are characterized by a specific structural feature such as the conserved CACTA motif at the terminal ends of the TIR. The best studied is the CACTA transposable element of the Spm (Suppressor-Mutator) family (Frey et al., 1990). Moreover, a large and heterogeneous group of nonau tonomous MITE elements (miniature invertedrepeat transposable element) belongs to subclass I. These elements vary in size, from several dozen to sev eral hundred nucleotides. Depending on the nucle otide sequence of TIRs, the MITE elements are divi...

Repetitive DNA sequences in plant genomes

“…Subclass 1 also includes the numerous and hetero geneous group of nonautonous MITE elements (Min iature Inverted Repeat Transposable Element) (Ser geeva and Salina, 2011). These elements are tens to hundreds of base pairs in length.…”

“…To date, there is a lack of precise information on the contents of LINEs in plant genomes, because their identification is difficult. It appears that they consti tute a much smaller portion of the genome than LTR retrotransposons (Sergeeva and Salina, 2011). Auton omous LINEs encode at least RT and endonuclease (EN) domains in the POL ORF, required for transposi tion, (Ostertag and Kazazian, 2005) (Fig.…”

“…2). Additional groups of non LTR retrotransposons are DIRS like elements, Penelope like elements, and nonautonomous elements: TRIM (Terminal Repeat Retrotransposons in Miniature) and LARD (Large Retrotransposon Derivatives), reviewed in (Sergeeva and Salina, 2011).…”

“…Subclass I includes ele ments migrating by the common cut and paste mech anism via a double stranded DNA break. Subclass II migrates by means of the rolling circle mechanism (Sergeeva and Salina, 2011).…”

Why did theTc1-like elements of mollusks acquired the spliceosomal introns?

“…They represent the DNA fragments capable of transpositions within the genome and, thus, of increasing their copy number. The proportion of TEs in different genomes varies from 3% to 90% (Guo et al 2010;de Koning et al 2011;Sergeeva and Salina 2011). TEs play an important role in structure and function of the genomes and serve as a source of new genes (Bourque et al 2018).…”