Transposition of mobile elements has been implicated in genome instability, rearrangements and therefore also adaptation to changing environmental conditions. Transposons could influence gene ...activity directly by transposition inside or close to coding regions by their disruption or by addition of regulative sequences. Further, class I transposable elements, which are the most abundant in plant genomes, utilize a RNA intermediate in their life cycle, therefore retrotransposons could act by producing non-coding RNAs that could affect other transcripts by RNA interference. Transposition activity is suppressed by chromatin modifications, and both classes of transposons have been shown to be activated in plants under various stress conditions and developmental stages. Using a nonspecific amplification approach, we demonstrate the differential transcriptional activation of sequences with homology to transposable elements and other associated sequences in the complex genome of Scots pine (Pinus sylvestris L.) after exposure to heat stress, infestation with pine woolly aphids, and salicylic acid and abscisic acid treatment. Sequences with homology to several retrotransposon classes and families were identified, as well as several chimeric transcript types. Some of them represent chloroplast sequence insertions into the pine nuclear genome and these sequences are highly represented in EST databases of a wide range of species. In this study, we identified several retrotransposon classes and families with differing levels of similarity with known transposable elements from other plant species, and which are differentially expressed under various stress conditions in Scots pine.
Retrotransposable elements (REs) and related sequences form a large proportion of conifer genomes. During genome evolution, some RE sequences are degraded or eliminated, but some are evolutionarily ...stable, and can be identified even in distantly related species. Use of genome sequence information from loblolly pine (
Pinus taeda
) enables investigation of divergent non-coding RE sequences in other pine and conifer species, including Scots pine (
Pinus sylvestris
). Non-specific inter-retrotransposon amplified polymorphism technique (IRAP) as well as the amplification polymorphism of 12 RE families were investigated in 80 gymnosperm species. The obtained results were compared with phylogenetic relationships among gymnosperms. Investigation of distantly related gymnosperm species reveals persistent RE sequences, such as
IFG
and
Pineywoods
, distributed among a wide range of plant lineages
.
RE sequence divergence was observed, reflecting periods of inactivity and degradation during speciation of pine lineages, as demonstrated by the delineation of the main pine subgenera. Intraspecific variation of 10 RE copy numbers (CN) between Scots pine individuals ranged from 8.9 to 26.6% of the overall mean estimates. CN analyses were performed in 16 additional gymnosperm species. The analysed pine species contained a similar complement of RE families; however, CN and genome occupation proportions differ. A decrease in RE CN estimates can reflect sequence divergence, associated with independent transposition events. Transposition of some REs can be induced by stress conditions; therefore, even distantly related species inhabiting extreme environments could have similar patterns or distribution of these elements.
•The clonal composition after two root sucker regenerations of hybrid aspen plantations changed considerably.•Genotypic diversity was significantly reduced where eight clones were planted ...originally.•Root suckers had, on average, spread 15 m from the parent stumps, with a maximum distance of 49 m.
Two hybrid aspen (Populus tremula L. × P. tremuloides Michx.) trials in southern Sweden were used for studies of clonal composition in the second of two root sucker regenerations. Trial 1 was established in 1998 and originally included eight clones randomly distributed in four plots, each having 10 × 10 positions. Trial 2 was planted in 1957, with 150 seedlings from each of 25 full sib families randomly planted. Genotyping, using six SSR markers, was performed on wood samples collected from the second root sucker generation in each trial.
Results from trial 1 clearly indicated a reduction in the genotypic diversity of the second sucker generation. All eight clones were still present, but at significantly different frequencies, with some close to zero. In trial 2, a total of 210 clones were found, genetically matched to 21 families, implying a rather marginal reduction in genetic variation. The clonal structure was mostly aggregated, but at the same time intermixing of ramets from different clones was quite common. The root suckers had, on average, spread 15 m from the stumps of the previous sucker generation of the same clone and the maximum distance was 49 m.
The results indicate a change in clone frequencies over generations in root sucker stands of hybrid aspen. Hybrid aspen reforestation with seedlings originating from several unrelated families will retain genetic variation better in future sucker generations compared to clonal reforestations in which few clones are used. It is appropriate to use a higher number of clones than the normal five to eight used in Sweden today, in order to prevent future clone-specific damage as a result of reduction of clone diversity after several root sucker generations.
