Characterization, genomic organization and chromosomal distribution of Ty1-copia retrotransposons in species of Hypochaeris (Asteraceae).

This study aims to analyze the diversity of Ty1-copia retrotransposons in 18 taxa of Hypochaeris, including two Old World species H. maculata (2n=2x=10) and H. angustifolia (2n=2x=8), and representatives of the South American species (16 accessions of 15 species; all 2n=2x=8). Analysis of 380 PCR-amplified sequences, corresponding to a conserved domain of the subset of Ty1-copia reverse transcriptase (rt) gene amplifiable with degenerate standard primers, showed high levels of intra- and interspecific heterogeneity. Nucleotide diversity (Pi) of the copia fragments was high in all species and varied from 0.229 (H. angustifolia) to 0.412 (H. chillensis). Higher sequence heterogeneity correlates positively with larger genome size among analyzed species. Phylogenetic analyses of amplified fragments revealed different patterns of intraspecific heterogeneity within species, with most sequences forming one well-supported main clade while a few sequences fall into small clades or are left ungrouped. The combined analysis of all sequences revealed the presence of three main clades and showed that highly diverged species contain closely related Tyl-copia group retrotransposons. One of the main clades includes rt sequences of all South American species and three sequences of their putative ancestor, H. angustifolia, but no sequence of the Old World H. maculata. FISH with copia retrotransposons in four Hypochaeris species, including H. maculata and H. angustifolia and New World H. apargioides and H. spathulata, revealed differences in the chromosomal distribution between the two groups. In Old World species copia retroelements are distributed over the whole length of the chromosomes, excluding rDNA sites and some centromeres. In the South American species the two largest chromosome pairs are enriched in copia, while most of the long arms of the two small pairs of chromosomes are devoid of these elements. The patterns of heterogeneity and chromosomal distribution of Ty1-copia retrotransposons in Hypochaeris are discussed in the context of the origin, genome evolution and organization of the South American species.