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,Fabrício Rodrigues Santos,Gustavo C S Kuhn,José Eustáquio Dos Santos Júnior,Marta Svartman,Christian Miguel Pinto,Fernando Araújo Perini

doi:10.1590/1678-4685-gmb-2020-0384

Cayo Augusto Rocha Dias, Fabrício Rodrigues Santos + Show 5 more

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https://doi.org/10.1590/1678-4685-gmb-2020-0384

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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.

Highlights

The genus Didelphis Linnaeus, 1758 comprises six species of medium-sized American marsupials (Astúa, 2015a; Cerqueira and Tribe, 2008): Didelphis virginiana Kerr, 1792, inhabiting tropical, subtropical, and temperate zones of North America, and two groups of species found in tropical and subtropical zones of Neotropics (Astúa, 2015a; Cerqueira, 1985)
The overall genome proportion of repDNAs detected by these pipelines ranged from 10.85 % in D. marsupialis to 13.63 % in D. imperfecta (Table 1)
long terminal repeats (LTRs) proportions exceed 3 % in D. aurita, D. marsupialis and D. virginiana, individual LTR families proportion did not reach 2 % (Figure 1 and Table S2). Both long interspersed elements (LINEs) and LTRs are less abundant in the genomes of white-eared opossums

Summary

Introduction

The genus Didelphis Linnaeus, 1758 comprises six species of medium-sized American marsupials (Astúa, 2015a; Cerqueira and Tribe, 2008): Didelphis virginiana Kerr, 1792, inhabiting tropical, subtropical, and temperate zones of North America, and two groups of species found in tropical and subtropical zones of Neotropics (Astúa, 2015a; Cerqueira, 1985). The D. marsupialis group (black-eared opossums) is composed of two Neotropical species: D. aurita Wied-Newied, 1826 and D. marsupialis Linnaeus, 1758 (Cerqueira and Tribe, 2008). Most molecular-based phylogenies failed to provide significant support for the relationships among white-eared opossums (Amador and Giannini, 2016; Dias and Perini, 2018), a recent mitogenome-based phylogeny seem to provide support and resolution to the relationships among Didelphis species of this group (Dias et al, 2020)

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