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Background  The golden lion tamarin ( Leontopithecus rosalia ) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the  L. rosalia  mitogenome from feces, a sample which can be collected non-invasively.    Results  Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the  L. rosalia  mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin ( Saguinus imperator ) and the mitogenome of the closely related black lion tamarin ( Leontopithecus chrysopygus ). The  L. rosalia  mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the  L. chrysopygus  mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3′ side of several coding regions.    Conclusions  Overall, we report a robust new mitogenome assembly for  L. rosalia  and direct detection of cytosine base modifications in all contexts .Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08046-7.

The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing