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

Alexander Belyayev, Jirina Josefiová, Michaela Jandová, Ruslan Kalendar, Václav Mahelka, Bohumil Mandák, Karol Krak

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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. As a result: (i) the presence of two CACTA transposons subtypes coexisting 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) presence of captured satDNA arrays were identified. 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 genomes of C. album aggregate species. Ability to relocate additions inside genome in combination with proposed novel functional features of structurally-different CACTA elements can impact evolutionary trajectory of the host genome.
Original languageEnglish
Article number8
JournalMobile DNA
Volume13
DOIs
Publication statusPublished - Apr 4 2022

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