The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms

Abstract

Background CACTA transposable elements (TEs) comprise one of the most abundant superfamilies of Class 2 (cut-and-paste) transposons. Over recent decades, CACTA elements were widely identified in species from the plant, fungi, and animal kingdoms, but sufficiently studied in the genomes of only a few model species although non-model genomes can bring additional and valuable information. It primarily concerned the genomes of species belonging to clades in the base of large taxonomic groups whose genomes, to a certain extent, can preserve relict and/or possesses specific traits. Thus, we sought to investigate the genomes of Chenopodium (Amaranthaceae, Caryophyllales) species to unravel the structural variability of CACTA elements. Caryophyllales is a separate branch of Angiosperms and until recently the diversity of CACTA elements in this clade was unknown. Results Application of the short-read genome assembly algorithm followed by analysis of detected complete CACTA elements allowed for the determination of their structural diversity in the genomes of 22 Chenopodium album aggregate species. This approach yielded knowledge regarding: (i) the coexistence of two CACTA transposons subtypes in single genome; (ii) gaining of additional protein conserved domains within the coding sequence; (iii) the presence of captured gene fragments, including key genes for flower development; and (iv)) identification of captured satDNA arrays. Wide comparative database analysis revealed that identified events are scattered through Angiosperms in different proportions. Conclusions Our study demonstrated that while preserving the basic element structure a wide range of coding and non-coding additions to CACTA transposons occur in the genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with the proposed novel functional features of structural-different CACTA elements can impact evolutionary trajectory of the host genome.

A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce

“…CACTA transposons are one of the most abundant superfamilies of DNA transposons (Tian, 2006;Wicker et al, 2007;Sergeeva et al, 2010;Lisch, 2013;Belyayev et al, 2022). It has been reported that CACTA transposons constitute c. 2-15% of plant genomes (Paterson et al, 2009;Vogel et al, 2010;Gurdon et al, 2021;Z.…”

Identification and Evaluation of Regulatory Role of miR164b in Malaysian Rice Variety (MR303) under Drought Stress

“…Suppressor-mutator (Spm) is the first CACTA element identified in the Zea mays (Poaceae, Poales) genome. The key role of CACTA elements and other transposable elements is their capability to affect the evolution of the host genome [25].…”