title: Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome.
abstract: A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.
authors.affiliation: Genetics Section, Department of Crop Plant Biology, University of Pisa, Pisa, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavallini
authors.forename: Lucia
authors.initials: L
authors.lastname: Natali
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Tommaso
authors.initials: T
authors.lastname: Giordani
authors.forename: Irena
authors.initials: I
authors.lastname: Jurman
authors.forename: Veronica
authors.initials: V
authors.lastname: Ferrillo
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitacolonna
authors.forename: Vania
authors.initials: V
authors.lastname: Sarri
authors.forename: Federica
authors.initials: F
authors.lastname: Cattonaro
authors.forename: Marilena
authors.initials: M
authors.lastname: Ceccarelli
authors.forename: Pier Giorgio
authors.initials: PG
authors.lastname: Cionini
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
mesh_terms: D001482:Base Composition / Q000235:genetics*; D001483:Base Sequence; D015139:Blotting, Southern; D032461:Chromosomes, Plant / Q000235:genetics; D002999:Clone Cells; D016000:Cluster Analysis; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D006368:Helianthus / Q000235:genetics*; D017403:In Situ Hybridization; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D018626:Retroelements / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant; D018626:Retroelements