Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

Abstract

Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

msechBari, a new MITE-like element inDrosophila sechelliarelated to theBaritransposon

“…Accordingly, the groupings of sequences in the network, represented by large circles, indicate that the sequences are identical ; therefore, these sequences are very recent and have not had sufficient time to diverge. Similar events have been reported for other transposable elements (Yang et Konovalov et al, 2010 ;Lerat, 2010) and MITE-like sequences in different organisms (Jiang et al, 2003 ;Chen et al, 2008;Zhou et al, 2008 ;Han et al, 2010 ;Hikosaka et al, 2011). This recent origin is also supported by the average time of origin of the insertions of each subfamily, 155 000 years (msechBari1) and 127 000 years (msechBari2).…”

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

“…SSAP analysis was carried out by the method used in the study of wheat varieties (Konovalov et al, 2010): 40 ng of genomic DNA was treated with 10 U of Taq α I restriction enzyme for 3 h at 65 °С. Ligation was performed by adding 2.5 Weiss units of T4 DNA-ligase, 5 mM ATP, and 50 pmol of double-strand adapter [5'-ACTCGATTCTCAACCCGAAAGTATAGATCCCA; 5'-PO4-CGTGGGATCTATACTT-(C6linker)-NH2] and incubation for 7 h at 37°С (Konovalov et al, 2010).…”

“…Ligation was performed by adding 2.5 Weiss units of T4 DNA-ligase, 5 mM ATP, and 50 pmol of double-strand adapter [5'-ACTCGATTCTCAACCCGAAAGTATAGATCCCA; 5'-PO4-CGTGGGATCTATACTT-(C6linker)-NH2] and incubation for 7 h at 37°С (Konovalov et al, 2010). The product was diluted twofold with deionized water (mQ).…”

“…The following LTR primers were used: At the second stage of amplification, the adapter primer 5'-GTTTACTCGATTCTCAACCCGA-3' (Konovalov et al, 2010) and one of the primers fitted to the LTR region of FaRE1 retrotransposon were used. The PCR mix contained 15 µl of the first-stage PCR product, 1 U of Taq polymerase, Taq polymerase buffer, 1.5 mM MgCl 2 , …”

“…et al, 2011. Molecular markers based on polymorphism of retrotransposon integration sites are widely used in assessment of retrotransposon activity, phylogenetic studies, gene mapping, studies of somaclonal variation, and estimation of genetic diversity of cereals (Waugh et al, 1997;Queen et al, 2004;Konovalov et al, 2010), legumes Pearce et al, 2000;Vershinin et al, 2003;Sanz et al, 2007), potato (Lightbourn et al, 2007), vine (Labra et al, 2004), sunflower (Tang et al, 2004), flax (Smykal et al, 2011), and many other plants (Feschotte et al, 2002;Kalendar et al, 2011).…”