Sequence evolution and copy number of Ty1- copia retrotransposons in diverse plant genomes

Abstract

Sequence evolution of the reverse transcriptase (RT) gene in retrotransposons belonging to the Ty1-copia class was studied in 11 plant species. Phylogenetic reconstruction of the evolutionary history of RT sequences indicated a strong pattern of purifying selection, manifested as high ratios of third to first plus second codon position substitutions, and low ratios of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site, especially in internal portions of the element phylogenies. Evidence of purifying selection was most pronounced in plant species with low estimated copy numbers of Ty1-copia elements. This finding is consistent with the hypothesis that high element turnover rates (e.g., caused by high rates of element loss and selection against high element copy number) favors elements capable of transposition. Simulations of RT sequence evolution were conducted to help verify the logical validity of this conclusion. The results argue that it is incorrect to assume that low copy numbers of transposable elements are the product of reduced levels of element activity.

Saci-1, -2, and -3 and Perere, Four Novel Retrotransposons with High Transcriptional Activities from the Human Parasite Schistosoma mansoni

“…Different parasite isolates are known to exhibit sex-specific polymorphisms, resulting from different numbers of copies of repetitive elements, which indicates genomic instability and suggests that replication of repetitive elements is a method of generating variability within schistosomes (18). In contrast, we propose that the low-copy number retrotransposons would have several copies located in euchromatin and would be subject to a stricter process of selection, which has been shown previously to induce the conservation of retrotransposons with active characteristics (46). It is noteworthy that retrotransposons are thought to proliferate in the sexual species, where they would propagate during sexual reproduction, as suggested by the work of Arkhipova and Meselson (2).…”

Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. I. A Simulation Framework

“…The pattern of TE sequence evolution is similar to that of protein-coding genes under purifying selection (McAllister and Werren 1997;Navarro-Quezada and Schoen 2002). That is, the d N /d S ratio is low for active copies, and once the activity is reduced, it increases and exhibits saturation around 1.0.…”

“…However, these models focus only on the copy number dynamics and did not consider the sequences of TEs. To the best of our knowledge, the most notable exception is the retrotransposon model of Navarro-Quezada and Schoen (2002) (but see Ohta 1985, Slatkin 1985, Brookfield 1986, and Hudson and Kaplan 1986 for fundamental numerical approaches and Quesneville andAnxolabéhère 2001 andCerveau et al 2011 for simple models of DNA transposons). Navarro-Quezada and Schoen (2002) modified the simulation model of Charlesworth and Charlesworth (1983) such that each TE has a DNA sequence.…”

Identification and characterization of jute LTR retrotransposons

“…On the other hand, the genome size of jute is quite large; it may harbor in its genome a large number of transposable elements which move through copy-paste method and part of which is reflected by the large copy number of LTR retrotransposons found in this study. It is worth mentioning that, number of retrotransposons is low in small genomes due to the pressure of rapid cell division 40 whereas it is just the opposite where the genome size is large and retrotransposon selection is relaxed 39 for example; jute genome. abundance of retrotransposon is quite high.…”

“…abundance of retrotransposon is quite high. 38 It has been reported that, copy number of Ty1-copia retrotransposons may vary from several hundred to one million 39 as for example, copy number of Tnt1, a tobacco copia like retrotransposon is 100 whereas BARE-1, a copia-like retrotransposons of barley is 100,000. Ty3-gypsy elements have also been reported to be present in high copy number in several plant genomes, in Vicia species Ty3-gypsy elements contribute 18% to 35% of their genome 20 and in apple genome Ty3-gypsy contributes 33.5%.…”