Abstract
The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.
Highlights
Transposable elements (TEs) are DNA sequences that are able to change their position in the chromosomes
The abundance of each of the 123 long terminal repeats (LTR)-RE families contained in the reference library [23] in each accession was measured by counting the total number of reads that mapped onto the contigs belonging to such families
In order to evaluate how such gene products might be involved in biochemical processes such that LTR-REs insertion could induce phenotypic variation between wild and cultivated genotypes, we identified the Kyoto encyclopedia of genes and genomes (KEGG) biochemical pathways of the genes lying near these LTR-REs (Figure 5)
Summary
Transposable elements (TEs) are DNA sequences that are able to change their position in the chromosomes. They are classified into two classes depending on whether the transposition intermediate is RNA (Class I transposons or retrotransposons) or DNA The most abundant retrotransposon order is that with long terminal repeats (LTRs), two direct repeats containing promoter and RNA processing signals, flanking a region encoding a polyprotein that includes the enzymes necessary for its transposition [1]. Plant LTR-retrotransposons (LTR-REs) are classified into two main superfamilies—Copia and Gypsy [1]—which differ in the order of the enzymes within the polyprotein [2]. LTR-RE length ranges from a few hundred base pairs to over 10 kbp [2]
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