Characterization of a novel panel of polymorphic microsatellite loci and the mitogenome for the Neotropical marsupial Gracilinanus agilis (Didelphimorphia: Didelphidae)

Abstract

Background Microsatellite and mitochondrial markers are important tools for investigating natural populations, enabling the assessment of their diversity, genetic structure, kinship, parentage, and reproductive biology. Although the importance of such markers is widely recognized, their use in Neotropical mammals, especially marsupials, is still limited by the scarcity of species-specific loci characterized for extant species. Methods and results In this study, we describe and characterize 15 polymorphic microsatellite loci and recover part of the mitochondrial genome for the Neotropical marsupial Gracilinanus agilis using massive parallel sequencing with the Illumina platform. DNA sequencing yielded a dataset comprising 2,331,566 paired reads, of which 1,434 were mapped to a previously published mitogenome of the species, resulting in a partial mitogenome of 16,098 base pairs. The microsatellite search identified a total of 4,199 loci, of which 26 pairs were tested on 30 individuals. Of these, 15 loci were successfully amplified and exhibited high levels of genetic variation, with an average of 7.73 alleles per locus, a mean observed heterozygosity of 0.63, and a mean expected heterozygosity of 0.72. Furthermore, these loci collectively provide a high paternity exclusion probability and a low identity probability. Conclusions Our results suggest that the described marker set could be very useful for population genetic studies, evaluation of reproductive strategies (such as semelparity), and analysis of the population dynamics of this species.

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