Diversity, Origin, and Distribution of Retrotransposons (gypsy and copia) in Conifers

Abstract

We examined the diversity, evolution, and genomic organization of retroelements in a wide range of gymnosperms. In total, 165 fragments of the reverse transcriptase (RT) gene domain were sequenced from PCR products using newly designed primers for gypsy-like retrotransposons and well-known primers for copia-like retrotransposons; representatives of long interspersed nuclear element (LINE) retroposons were also found. Gypsy and copia-like retroelements are a major component of the gymnosperm genome, and in situ hybridization showed that individual element families were widespread across the chromosomes, consistent with dispersion and amplification via an RNA intermediate. Most of the retroelement families were widely distributed among the gymnosperms, including species with wide taxonomic separation from the Northern and Southern Hemispheres. When the gymnosperm sequences were analyzed together with retroelements from other species, the monophyletic origin of plant copia, gypsy, and LINE groups was well supported, with an additional clade including badnaviral and other, probably virus-related, plant sequences as well as animal and fungal gypsy elements. Plant retroelements showed high diversity within the phylogenetic trees of both copia and gypsy RT domains, with, for example, retroelement sequences from Arabidopsis thaliana being present in many supported groupings. No primary branches divided major taxonomic clades such as angiosperms, monocotyledons, gymnosperms, or conifers or (based on smaller samples) ferns, Gnetales, or Sphenopsida (Equisetum), suggesting that much of the existing diversity was present early in plant evolution, or perhaps that horizontal transfer of sequences has occurred. Within the phylogenetic trees for both gypsy and copia, two clearly monophyletic gymnosperm/conifer clades were revealed, providing evidence against recent horizontal transfer. The results put the evolution of the large and relatively conserved genome structure of gymnosperms into the context of the diversity of other groups of plants.

Retrotransposon Sequence Variation in Four Asexual Plant Species

“…To amplify Ty3/gypsy elements the primer CyRT1, 5¢-MRNATGTGYGTNGAYTAYMG-3¢ (Friesen et al 2001), was used. The reaction cycle for Ty3/gypsy elements consisted of 15 min at 95°C, followed by 40 cycles of 1 min at 94°C, 1 min at 60°C, 2 min at 72°C, and a final 10 min at 72°C.…”

Distribution of a Ty3/gypsy-like retroelement on the A and B-chromosomes of Cestrum strigilatum Ruiz & Pav. and Cestrum intermedium Sendtn. (Solanaceae)

“…This fragment was isolated, purified and used as in Friesen et al (2001) and then re-isolated, purified and used as a template for a new reaction with the GyRT3 (internal) and GyRT4 primers. This new PCR reaction produced a band of about 320 bp ( Figure 1B), which was isolated, purified and cloned.…”

“…The GyRT1 (5' MRNATGTGYGTNGAYTAYMG) and GyRT4 (5' RCAYTTNSWNARYTTNGCR) degenerate primers (Friesen et al 2001), giving a 450 bp product, were used for the PCR reactions. The band containing the 450 bp fragment was purified with the Concert Rapid Gel Extraction System Kit (Gibco) and then re-amplified with the GyRT3 (5' YKNWSNGGNTAYCAYCARAT) and GyRT4 primers, as described above, to obtain a 320 bp product.…”

Factors that Affect the Horizontal Transfer of Transposable Elements

“…While horizontal transfer remains a viable hypothesis, careful analysis may reveal alternative explanations for inconsistencies in the distribution or phylogeny of a transposable element. Two recent investigations of retrotransposable element evolution in plants discuss the difficulties associated with attempting to distinguish between horizontal transfer and alternative explanations, especially when the transfer events are postulated to have occurred in the distant past (Frissen et al, 2001;StuartRogers and Flavell, 2001). …”