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. 2021 Apr 16;44(2):e20200384.
doi: 10.1590/1678-4685-GMB-2020-0384. eCollection 2021.

Identification and characterization of repetitive DNA in the genus Didelphis Linnaeus, 1758 (Didelphimorphia, Didelphidae) and the use of satellite DNAs as phylogenetic markers

Cayo Augusto Rocha Dias  1 , Gustavo C S Kuhn  2 , Marta Svartman  2 , José Eustáquio Dos Santos Júnior  3 , Fabrício Rodrigues Santos  3 , Christian Miguel Pinto  4 , Fernando Araújo Perini  1
Affiliations

Identification and characterization of repetitive DNA in the genus Didelphis Linnaeus, 1758 (Didelphimorphia, Didelphidae) and the use of satellite DNAs as phylogenetic markers

Cayo Augusto Rocha Dias et al. Genet Mol Biol. .

Abstract

Didelphis species have been shown to exhibit very conservative karyotypes, which mainly differ in their constitutive heterochromatin, known to be mostly composed by repetitive DNAs. In this study, we used genome skimming data combined with computational pipelines to identify the most abundant repetitive DNA families of Lutreolina crassicaudata and all six Didelphis species. We found that transposable elements (TEs), particularly LINE-1, endogenous retroviruses, and SINEs, are the most abundant mobile elements in the studied species. Despite overall similar TE proportions, we report that species of the D. albiventris group consistently present a less diverse TE composition and smaller proportions of LINEs and LTRs in their genomes than other studied species. We also identified four new putative satDNAs (sat206, sat907, sat1430 and sat2324) in the genomes of Didelphis species, which show differences in abundance and nucleotide composition. Phylogenies based on satDNA sequences showed well supported relationships at the species (sat1430) and groups of species (sat206) level, recovering topologies congruent with previous studies. Our study is one of the first attempts to present a characterization of the most abundant families of repetitive DNAs of Lutreolina and Didelphis species providing insights into the repetitive DNA composition in the genome landscape of American marsupials.

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Conflict of interest statement

Conflict of Interest: The authors declare that there is no conflict of interest that could be perceived as prejudicial to the impartiality of the reported research.

Figures

Figure 1 -
Figure 1 -. Bar-plot depicting the genome proportion of the transposable elements (TE) identified by the RepeatExplorer 2 pipeline (A) with LINE-L1 elements and (B) without LINE-L1 elements.
Figure 2 -
Figure 2 -. Stacked bar-plot depicting the genome proportion of the satellite DNAs identified by the TAREAN pipeline for Didelphis species and Lutreolina crassicaudata.
Figure 3 -
Figure 3 -. Maximum likelihood trees inferred from putative satellite DNA sequences from (A) sat206 and (B) sat1430. “*” indicates bootstrap values ≥ 95.
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