Repetitive DNA and Plant Domestication: Variation in Copy Number and Proximity to Genes of LTR-Retrotransposons among Wild and Cultivated Sunflower (Helianthus annuus) Genotypes

Abstract

The sunflower (Helianthus annuus) genome contains a very large proportion of transposable elements, especially long terminal repeat retrotransposons. However, knowledge on the retrotransposon-related variability within this species is still limited. We used next-generation sequencing (NGS) technologies to perform a quantitative and qualitative survey of intraspecific variation of the retrotransposon fraction of the genome across 15 genotypes—7 wild accessions and 8 cultivars—of H. annuus. By mapping the Illumina reads of the 15 genotypes onto a library of sunflower long terminal repeat retrotransposons, we observed considerable variability in redundancy among genotypes, at both superfamily and family levels. In another analysis, we mapped Illumina paired reads to two sets of sequences, that is, long terminal repeat retrotransposons and protein-encoding sequences, and evaluated the extent of retrotransposon proximity to genes in the sunflower genome by counting the number of paired reads in which one read mapped to a retrotransposon and the other to a gene. Large variability among genotypes was also ascertained for retrotransposon proximity to genes. Both long terminal repeat retrotransposon redundancy and proximity to genes varied among retrotransposon families and also between cultivated and wild genotypes. Such differences are discussed in relation to the possible role of long terminal repeat retrotransposons in the domestication of sunflower.

Different histories of two highly variable LTR retrotransposons in sunflower species

“…The selected Divaricati species included three diploid (H. divaricatus, H. giganteus, and H. smithii), three tetraploid (H. hirsutus, H. californicus, and H. laevigatus), and one hexaploid species (H. tuberosus). Regarding H. annuus, previous studies reported high variability in the repetitive component between wild and cultivated genotypes (Mascagni et al, 2015). In this study, a wild accession from Illinois was chosen to represent H. annuus; this particular accession exhibits average features among wild H. annuus genotypes (Mascagni et al, 2015).…”

“…Regarding H. annuus, previous studies reported high variability in the repetitive component between wild and cultivated genotypes (Mascagni et al, 2015). In this study, a wild accession from Illinois was chosen to represent H. annuus; this particular accession exhibits average features among wild H. annuus genotypes (Mascagni et al, 2015).…”

“…1). First, custom libraries of sunflower repetitive sequences (described by Natali et al (2013) and by Mascagni et al (2015); see Materials and Methods) were scored for the presence of primer sequences used by Vukich et al (2009a). SURE primers were specific to putative LTRs isolated in accordance with the method established by Kalendar et al (2008).…”

“…However, a number of species showed an admixed structure, confirming the importance of interspecific hybridisation in the evolution of this genus. In general, these two retrotransposon families differentially contributed to interspecific variability, emphasising the need to refer to specific families when 5 The goal of this work was to establish a pipeline for characterising the specific families of repeated elements (rather than the whole RE complement as in the study by Natali et al (2013) or LTR-RE lineages as in the study by Mascagni et al (2015)) using high-throughput sequencing methods and applicable bioinformatic procedures, even in species whose genome has not been sequenced. Given the large variability observed in the Helianthus genus in polymorphism studies that focussed on Helicopia and SURE elements (Vukich et al, 2009a), we decided to analyse these two groups of LTR-REs in detail and to detect the putative evolutionary dynamics that produced the large interspecific variability related to these two retrotransposons.…”

Copy Number Variation of Transposable Elements in Thinopyrum intermedium and Its Diploid Relative Species

“…The hypothesis of 'genetic shock' suggests that interspecific hybridization may be accompanied by the proliferation or elimination of TEs leading to dramatic changes in a hybrid genome [32]. The dynamics of TEs, in particular, LTR retrotransposons, is supposed to be the main cause of plant genome size alterations on the evolutionary time scale [12,[33][34][35][36][37]. Recent findings have shown that TEs are population-specific and apparently involved in population divergence and speciation at the diploid level [38][39][40].…”