Abstract
Much has been said about sunflower (Helianthus annuus L.) retrotransposons, representing the majority of the sunflower’s repetitive component. By contrast, class II transposons remained poorly described within this species, as they present low sequence conservation and are mostly lacking coding domains, making the identification and characterization of these transposable elements difficult. The transposable element Tetu1, is a non-autonomous CACTA-like element that has been detected in the coding region of a CYCLOIDEA (CYC) gene of a sunflower mutant, tubular ray flower (turf). Based on our knowledge of Tetu1, the publicly available genome of sunflower was fully scanned. A combination of bioinformatics analyses led to the discovery of 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements. A detailed characterization of the identified elements allowed further classification into three subgroups of 347 elements on the base of their terminal repeat sequences. Only 39 encode a protein similar to known transposases (TPase), with 10 TPase sequences showing signals of activation. Finally, an analysis of the proximity of CACTA transposons to sunflower genes showed that the majority of CACTA elements are close to the nearest gene, whereas a relevant fraction resides within gene-encoding sequences, likely interfering with sunflower genome functionality and organization.
Highlights
Transposable elements (TEs) are dynamic genomic sequences capable of moving within the host genome by specific transposition mechanisms
For each CACTA sequence, the genomic abundance was first assessed by mapping DNA reads of the sunflower genome, downloaded from NCBI (SRR5004633), according to the strategy already used for repetitive sequences in Mascagni et al [41,42]
A number of elements were fully characterized, identifying three clades of sunflower-specific CACTAs that include complete and incomplete elements among which we found two copies of transposable element of turf1 (Tetu1)
Summary
Transposable elements (TEs) are dynamic genomic sequences capable of moving within the host genome by specific transposition mechanisms. RE elements transpose using a copy-and-paste mechanism, resulting in an identical copy of the starting element, whereas DNA transposons exploit a cut-and-paste mechanism, resulting in the excision of the sequence from the original locus [4]. In both cases, the TEs may integrate into new genomic loci, possibly affecting gene expression and function with consequent effects on phenotype, representing a crucial source of genetic variation [5,6,7,8]. Starting from our knowledge of the Tetu element, we performed a genome-wide analysis of CACTA elements into the sunflower reference genome, i.e., the HanXRQ inbred line [24], to estimate their abundance, gene proximity, and related expression patterns
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