The discovery of multiple active mys-related LTR-retroelements within the Neotominae subfamily of cricetid rodents

Abstract

Abstract Retrotransposon families in the rodent family Cricetidae have been understudied in contrast to Muridae, both taxa classified within the superfamily Muroidea. Therefore, we pursued advancing our knowledge of the unique mys-1 LTR-retroelement identified in Peromyscus leucopus by utilizing intra-ORF PCR, quantitative dot bots, DNA and protein library screens, the generation of molecular phylogenies, and analyses of orthologous LTR-retroelement loci. This led to the discovery of three additional related families of LTR-retroelements. These include a 2900 bp full-length element of mys-related sequences (mysRS), an 8,000 bp element containing the mys ORF1 sequence (mORF1) with ERV-related sequences downstream in the reverse orientation, as well as an 1800 bp element primarily consisting of mys ORF2 (mORF2) related sequences flanked by LTRs. Our data revealed a very limited number of full-length mys elements among genera of the Neotominae subfamily of cricetid rodents. Additionally, although we estimated roughly 5,000–10,000 genomic copies of the mysRS element among Neotominae, most exist as partial copies. The mORF1 elements are also limited to the genomes of the Neotominae subfamily of cricetid rodents, whereas mORF2 appears limited to the Peromyscus genus. Molecular phylogenies demonstrating concerted evolution, along with an assessment of orthologous loci in Peromyscus for the presence or absence of elements, are consistent with recent activity of these novel LTR-retroelement families. Together with known activity of various families of non-LTR retroelements in Peromyscus species, we propose that retrotransposons have been continually contributing to the dynamics of Peromyscus genomes and are plausibly associated with the evolution of the over 50 identified species.