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

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Abstract

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.

Original languageEnglish (US)
Article number726
JournalBMC Genomics
Volume22
Issue number1
DOIs
StatePublished - Dec 2021

Bibliographical note

Funding Information:
This work was supported by USDA AES Project. No. MIN-16-129, the UM Informatics Institute, and the SUNY Polytechnic Institute Research Foundation.

Funding Information:
We thank Executive Director Andria Heath, Director of Administrative Operations Nikki Sheehan and the keeper and animal care staff of the Utica Zoo as well as their tamarins Arie and Kane for generous donation of fecal material. We also thank A. Barks for experimental suggestions with DNA methylation analysis. We thank Sydney McGraw (sydneyruthart@gmail.com) for the tamarin drawing. The authors have no conflicts of interest and declare no competing financial interests. The mitogenome sequence has been deposited into NCBI GenBank with accession number MZ262294 and is available as supplementary file?3. Reads used to generate this assembly are available as supplementary file?4.

Publisher Copyright:
© 2021, The Author(s).

Keywords

  • DNA hydroxymethylation
  • DNA methylation
  • Lion Tamarin
  • Mitochondria
  • Poop
  • Primates

PubMed: MeSH publication types

  • Journal Article

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