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

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.

Satellite DNAs—From Localized to Highly Dispersed Genome Components

“…Not only a substantial number of (even low-copy) repetitive sequences can be detected by satellitome analysis, as exampled by 164 satDNAs of Megaleporinus macrocephalus [ 106 ], but such studies can also help in elucidating evolutionary relations among repetitive sequences in related species [ 94 , 119 , 121 , 124 , 126 , 133 , 134 , 135 , 136 , 137 , 138 , 139 ]. The use of NGS data has also been employed for the studies of evolution of B and sex chromosomes, e.g., to characterize the composition and putative ancestry of B chromosomes in grasshopper species Rhammatocerus brasiliensis , Schistocerca rubiginosa, Xyleus discoideus angulatus, Abracris flavolineata, Eumigus monticola [ 93 , 102 , 112 ] or in characid fish Characidium gomesi [ 96 ].…”