ArticleBMC genomics2021
The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 40 citations in OpenAlex.
- Complete mitochondrial genome characterization and exploratory mitochondrial DNA modification signals in square-head catfish Chaca chaca.Scientific reports · 2026Article
- Going Mobile: Using Portable Genomic Technologies for PCR-Free In Situ Species Identification and Real-Time Molecular Systematics.Ecology and evolution · 2025Article
- Sequencing and assembling the genome of Przewalski's horse in the classroom.Journal of equine veterinary science · 2025Review
- Evaluation of long-read sequencing for Ostreid herpesvirus type 1 genome characterization fromMicrobiology spectrum · 2025Article
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling.Journal of mammalogy · 2024Article
- Selective whole-genome sequencing ofmBio · 2024Article
- Real-time genomics for One Health.Molecular systems biology · 2023Review
- Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling.Scientific reports · 2023Article
- Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates.Genome research · 2023Article
- Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat,NAR genomics and bioinformatics · 2023Article
- Nanopore adaptive sampling for targeted mitochondrial genome sequencing and bloodmeal identification in hematophagous insects.Parasites & vectors · 2023Article
- Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates.bioRxiv : the preprint server for biology · 2023Article
- De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing.Nucleic acids research · 2023Article
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes.Genome biology and evolution · 2022Article
- Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum.Scientific reports · 2022Article
- Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.Scientific reports · 2022Article
- Rapid PCR-Based Nanopore Adaptive Sequencing Improves Sensitivity and Timeliness of Viral Clinical Detection and Genome Surveillance.Frontiers in microbiology · 2022Article
- Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era.Innovation (Cambridge (Mass.)) · 2021Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsAdaptive 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.
conclusionsOverall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.