Sunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Despite its economic relevance, a detailed structural analysis of its genome is still missing. We have investigated the repetitive fraction of the sunflower genome, especially transposable elements, which constitute a major driver of genome size increasing, are able to cause lethal mutations, and may also play a role in the epigenetic setting of the genome. We first characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, then extended our studies to 7 wild accessions and 8 cultivars using Illumina reads. Using RepeatExplorer, we obtained 288 clusters representing the most representative repeat families in a random sample of sunflower reads. The annotated clusters were collected in a library, and a phylogenetic analysis of conserved regions of LTR-retroelement protein domains was performed. This library was used as reference to be mapped with reads of all the accessions. We identified 19 clusters belonging to Gypsy and Copia superfamilies showing different redundancy between cultivars and wild accessions, possibly involved in sunflower domestication.

Retrotransposon copy number variation between wild and cultivated sunflowers

MASCAGNI, FLAVIA;GIORDANI, TOMMASO;CAVALLINI, ANDREA;NATALI, LUCIA
2014-01-01

Abstract

Sunflower (Helianthus annuus) is an important crop species of the Asteraceae family. Despite its economic relevance, a detailed structural analysis of its genome is still missing. We have investigated the repetitive fraction of the sunflower genome, especially transposable elements, which constitute a major driver of genome size increasing, are able to cause lethal mutations, and may also play a role in the epigenetic setting of the genome. We first characterized the repetitive component of a sunflower homozygous experimental line, using 454 reads, then extended our studies to 7 wild accessions and 8 cultivars using Illumina reads. Using RepeatExplorer, we obtained 288 clusters representing the most representative repeat families in a random sample of sunflower reads. The annotated clusters were collected in a library, and a phylogenetic analysis of conserved regions of LTR-retroelement protein domains was performed. This library was used as reference to be mapped with reads of all the accessions. We identified 19 clusters belonging to Gypsy and Copia superfamilies showing different redundancy between cultivars and wild accessions, possibly involved in sunflower domestication.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11568/750828
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