Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions

Improved knowledge of genome composition, especially of its repetitive component, generates important informations in both theoretical and applied research. In this study, we provide the Wrst insight into the local organization of the sunXower genome by sequencing and annotating 349,380 bp from 3 BAC clones, each including one single-copy gene. These analyses resulted in the identiWcation of 11 putative gene sequences, 18 full-length LTR retrotransposons, 6 incomplete LTR retrotransposons, 2 nonautonomous LTR-retroelements (LINEs), 2 putative DNA transposons fragments and one putative helitron. Among LTR-retrotransposons, non-autonomous elements (the socalled LARDs), which do not carry any protein-encoding sequence, were discovered for the Wrst time in the sun- Xower. The insertion time of intact retroelements was measured, based on sister LTRs divergence. All isolated elements were inserted relatively recently, especially those belonging to the Gypsy superfamily. Retrotransposon families related to those identiWed in the BAC clones are present also in other species of Helianthus, both annual and perennial, and even in other Asteraceae. In one of the three BAC clones, we found Wve copies of a lipid transfer protein (LTP) encoding gene within less than 100,000 bp, four of which are potentially functional. Two of these are interrupted by LTR retrotransposons, in the intron and in the coding sequence, respectively. The divergence between sister LTRs of the retrotransposons inserted within the genes indicates that LTP gene duplication started earlier than 1.749 MYRS ago. On the whole, the results reported in this study conWrm that the sunXower is an excellent system to study transposons dynamics and evolution