Abstract
BackgroundGenome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels.ResultsAfter determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species.ConclusionsThis large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species.
Highlights
Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species
Two species belong to the section Helianthus (H. annuus and H. petiolaris, with two subspecies: H. petiolaris ssp. petiolaris, and H. petiolaris ssp. fallax), one represents the monotypic annual section Agrestis (H. agrestis), another annual species (H. porteri) and six perennial species belong to the section Divaricati
We observed striking differences analysing the relative abundance of long terminal repeat (LTR)-REs, from the superfamily to the sublineage level. These results suggest that the common ancestor of Helianthus contained different LTR-RE sublineages and that, after species separation, such sublineages were subjected to different rates of amplification/ loss, while no new LTR-RE sublineage originated in the genome
Summary
Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Transposable elements (TEs) play a key role in the evolution of species [1]. They can drive rapid genome remodelling by creating chromosomal rearrangements and new regulatory gene networks, acting as an endogenous force that promotes reproductive isolation [2]. Retrotransposons (REs) are the most common class of elements, making up the bulk of many genomes [2, 11]. They can be classified into five taxonomic orders [9], among which long terminal repeat (LTR) REs and nonLTR-REs differ in the mechanism of integration. Pol encodes a polyprotein with protease, reverse transcriptase (RT), RNaseH, and integrase enzyme domains, which are necessary for the replication and the integration of the elements in the host chromosomes [10]
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