title: Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize.
abstract: We report a whole-genome comparison of gene content in allelic BAC contigs from two maize inbred lines. Genic content polymorphisms involve as many as 10,000 sequences and are mainly generated by DNA insertions. The termini of eight of the nine genic insertions that we analyzed shared the structural hallmarks of helitron rolling-circle transposons. DNA segments defined by helitron termini contained multiple gene-derived fragments and had a structure typical of nonautonomous helitron-like transposons. Closely related insertions were found in multiple genomic locations. Some of these produced transcripts containing segments of different genes, supporting the idea that these transposition events have a role in exon shuffling and the evolution of new proteins. We identified putative autonomous helitron elements and found evidence for their transcription. Helitrons in maize seem to continually produce new nonautonomous elements responsible for the duplicative insertion of gene segments into new locations and for the unprecedented genic diversity. The maize genome is in constant flux, as transposable elements continue to change both the genic and nongenic fractions of the genome, profoundly affecting genetic diversity.
authors.affiliation: Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, 33100 Udine, Italy. michele.morgante@uniud.it
authors.forename: Michele
authors.initials: M
authors.lastname: Morgante
authors.forename: Stephan
authors.initials: S
authors.lastname: Brunner
authors.forename: Giorgio
authors.initials: G
authors.lastname: Pea
authors.forename: Kevin
authors.initials: K
authors.lastname: Fengler
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Antoni
authors.initials: A
authors.lastname: Rafalski
mesh_terms: D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry; D005091:Exons / Q000235:genetics*; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant; D008969:Molecular Sequence Data; D013045:Species Specificity; D003313:Zea mays / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant