Isolation and characterization of genomic retrotransposon sequences from octoploid strawberry (Fragaria × ananassa Duch.)

Abstract

Strawberry (Fragaria spp.) is a kind of herbaceous perennial plant that propagates vegetatively. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of LTR retrotransposons were amplified from the cultivated strawberry (Fragaria x ananassa Duch.). Sequence analysis of clones demonstrated that 5 of 19 Ty1-copia group unique sequences and 2 of 10 Ty3-gypsy unique sequences in F. x ananassa genome possessed either stop codon or frameshift. Ty1-copia group sequences are highly heterogeneous (divergence ranged from 1 to 69.8%), but the Ty3-gypsy group sequences are less (divergence ranged from 1 to 10%). Southern dot blot hybridization result suggested that both of the LTR retrotransposons are present in the genome of cultivated strawberry with high copy number (Ty1-copia group 2,875 Ty3-gypsy group 348). RT-PCR amplification from total RNA, which was extracted from leaves of micropropagated strawberry plants, did not yield either of the RT fragments. This is the first report on the presence of RT sequences of Ty1-copia and Ty3-gypsy group retrotransposons in F. x ananassa genome.

Characterization and chromosomal distribution of Ty3-gypsy-like retrotransposons in wax gourd (Benincasa hispida)

“…The Ty3-gypsy-like RT sequences exhibited significant levels of heterogeneity. The similarity at the amino acid level ranged from 65% to 100%, which is in agreement with previous observations reported in other plant species, such as strawberry 13 and mungbean 12 . The classification of these sequences into four groups further illustrated the divergence of Ty3-gypsy retrotransposons in wax gourd (Fig.…”

“…One particular effective strategy to detect LTR retrotransposons is to amplify the relevant sequences using degenerate primers for the reverse transcriptase domain [7][8][9] . This strategy has been employed to study the distribution of retrotransposons in many plant species, such as cereals 10 , Olea 11 , mung bean 12 , strawberry 13 , and Cucumis hystrix 14 . This approach is especially useful when genomic sequences for the species in question are not available.…”

Identification and characterization of jute LTR retrotransposons

“…In this regard we relied on the approach followed out by other groups. 1,18 LTR retrotransposons copy number in jute. To determine the copy numbers of Ty1-copia and Ty3-gypsy elements of jute genome two heterogenous populations of 280 bp Ty1-copia and 290 bp Ty3-gypsy whole PCR products were used as probes for of the reverse transcriptase, 31 (2) mixture of active and defective populations of retrotransposons, 2 (3) pressure of copy number since the divergence of a retrotransposon in any population is proportional to their copy number, 22,32 (4) homologous recombination, 33,34 (5) horizontal and (6) vertical transmission.…”

“…Among the transposable elements, retrotransposons are the largest group. 1 They are ubiquitous in plants, though their abundance varies widely. For example, retrotransposons constitutes only 5.5% of the genomic content of Arabidopsis thaliana but more than 50% of Zea mays.…”

The FaRE1 LTR-retrotransposon Based SSAP Markers Reveal Genetic Polymorphism of Strawberry (Fragaria x ananassa) Cultivars

“…Other LTR retrotransposons of F. x ananassa (Ma et al, 2008) have been characterized; the transposon families of F. vesca have been identified, of which LTR retrotransposons proved to be the most abundant (Pontaroli et al, 2009;Davis et al, 2010). The sequenced genome of F. vesca has revealed 576 transposons (Shulaev et al, 2011), among which, according to the cited authors, LTR retrotransposons are the most abundant and comprise about 16% of the nuclear genome.…”