Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.)

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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-4050-6) contains supplementary material, which is available to authorized users.

Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers

“…() and estimates for H. agrestis , H. carnosus and H. porteri were reported previously by Qiu & Ungerer (). All other GS estimates were newly generated for the current study, although independent estimates for some Helianthus species have been reported elsewhere (Sims & Price, ; Tetreault & Ungerer, ; Mascagni et al ., ). Newly reported estimates in the current study are based on an average of 3.57 accessions per species, with between one and 10 biological replicates assayed per accession (Table S1).…”

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

“…TEs, particularly longterminal repeat (LTR) retrotransposons, are also predominantly located in heterochromatic regions of the genome. In plants, LTR retrotransposons tend to be more abundant than non-LTR structural evolution of plant genomes (Flavell et al 1992;Voytas et al 1992;Mascagni et al 2017).…”

“…These observations do not, however, address the extent to which TEs are expressed or mobilised in plant development during germination, much less the possible functional consequences of such activation. Clarifying these issues may afford a new mechanistic view of plant adaptation and evolution (Mascagni et al 2017).…”

High-throughput retrotransposon-based genetic diversity of maize germplasm assessment and analysis

“…Particularly in higher plants, RLXs compose more than half of the repetitive DNA; they not only facilitate homologous recombination, but also can undergo intra-and inter-RLX recombination that is part of their dynamism [4,[8][9][10]. The RLXs are generally dispersed throughout genome, displaying relatively high structural diversity [11][12][13][14][15]. Retroelements have been suggested as an important creative force in genome evolution, driving processes such as mutation, recombination, genome expansion, and adaptation of an organism to changing environmental conditions [3,14,16].…”