On the Trail of Tetu1: Genome-Wide Discovery of CACTA Transposable Elements in Sunflower Genome

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.

Genome‐wide identification and characterization of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.)

“…It is to be noted that LTR‐REs and TEs are highly variable in sequence, and that variations occur even within LTR‐RE lineages and TIR superfamilies. However, the transposon coding portions are quite conserved, in fact they are used to assign efficiently an element to one lineage or another (Mascagni, Cavall et al., 2017; Ventimiglia et al., 2020). In this sense, the use of a prototypical sequence for each LTR‐RE lineage or TIR superfamily should ensure to cover most of the intra‐lineage and intra‐superfamily variations, respectively.…”

The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations

“…The En/Spm was the first CACTA system described at molecular level (Pereira, Cuypers, Gierl, Sommer, & Saedler, 1986). The sunflower genome contains 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements (Ventimiglia et al, 2020).…”

“…The En/Spm was the first CACTA system described at molecular level (Pereira, Cuypers, Gierl, Sommer, & Saedler, 1986). The sunflower genome contains 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements (Ventimiglia et al, 2020). Analysis of proximity of CACTA elements to sunflower genes showed that the majority of CACTAs resulted in close proximity to the nearest gene, while a relevant fraction resides within gene‐encoding sequences, possibly interfering with sunflower genome functionality and organization (Ventimiglia et al, 2020).…”

“…The sunflower genome contains 707 putative CACTA sequences: 84 elements with complete ends and 623 truncated elements (Ventimiglia et al, 2020). Analysis of proximity of CACTA elements to sunflower genes showed that the majority of CACTAs resulted in close proximity to the nearest gene, while a relevant fraction resides within gene‐encoding sequences, possibly interfering with sunflower genome functionality and organization (Ventimiglia et al, 2020). Mobilization of CACTA elements usually occurs in both somatic and germ cells (Wicker, Guyot, Yahiaoui, & Keller, 2003).…”