The structural diversity of CACTA transposons in genomes of Chenopodium (Amaranthaceae, Caryophyllales) species: specific traits and comparison with the similar elements of angiosperms
Belyayev A. Josefiová J. Jandová M. Kalendar R. Mahelka V. Mandák B. Krak K.
December 2022BioMed Central Ltd
Mobile DNA
2022#13Issue 1
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.
CACTA transposons , Chenopodium , Flowering plants , Genome evolution , Next generation sequencing
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Czech Academy of Sciences, Institute of Botany, Zámek 1, Průhonice, CZ-252 43, Czech Republic
Institute of Biotechnology HiLIFE, University of Helsinki, P.O. Box 65, Helsinki, FI-00014, Finland
National Laboratory Astana, Nazarbayev University, 53 Kabanbay batyr Ave., 010000, Nur-Sultan, Kazakhstan
Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha, Suchdol, 165 00, Czech Republic
Czech Academy of Sciences
Institute of Biotechnology HiLIFE
National Laboratory Astana
Faculty of Environmental Sciences
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