Biology subjects

Faulk, C.

Publications and source records attributed to Faulk, C..

16 recordsLinked to original sources

bioRxiv2026

A Telomere-to-telomere genome of the hibernating fat-tailed dwarf lemur (Cheirogaleus medius)

Madagascars dwarf lemurs (genus Cheirogaleus) are the only obligate-hibernating primates and closest relative to humans capable of hibernation. Endemic to the increasingly fragmented dry forests of Madagascar, the fat tailed dwarf lemur (Cheirogaleus medius) represents a unique model for understanding primate physiology and tropical hibernation. Here we present FatTail1, a highly contiguous diploid genome assembly generated from a male C. medius at the Duke Lemur Center using Oxford Nanopore Technologies PromethION sequencing. The assembly spans 2.3 Gb, with an N50 of 103Mb, L50 of 10, and a BUSCO completeness score of over 99%. In addition to a complete mitogenome, we generated allele-specific DNA methylation profiles and annotated 23,925 genes using NCBIs EGAPX. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes, representing the first telomere-to-telomere genome of a Strepsirrhine primate, and providing a foundation for future studies of primate hibernation, epigenetic regulation, and conservation genomics. ARTICLE SUMMARYDwarf lemurs are the only primates and closest relative to humans capable of months-long hibernation, making them an important model for understanding metabolic adaptations with relevance to human physiology. Here we present FatTail1, the first telomere-to-telomere genome assembly of a strepsirrhine primate, generated from a fat-tailed dwarf lemur (Cheirogaleus medius) using Oxford Nanopore Technologies PromethION sequencing. In addition to a highly complete nuclear genome, we assembled the mitogenome, identified allele-specific DNA methylation profiles and annotated 23,925 genes. FatTail1 exceeds the gap-free contiguity of previously published strepsirrhine genomes and provides an improved genomic resource for studies of hibernation, comparative genomics, epigenetic regulation, evolutionary biology, and conservation of this threatened primate.

genomics↗

bioRxiv2026

Hierarchical Transcriptomic and Epigenetic Recovery and Remodeling in the Developing Hippocampus Following Early-life Environmental Insults: An Iron Deficiency Rat Model

BackgroundsEarly-life environmental insults cause persistent neurodevelopmental abnormalities accompanied by transcriptional and epigenetic dysregulation despite removal of the original insult or postnatal intervention. However, transcriptomic and epigenomic responses to developmental insults and subsequent treatment during active neurodevelopment remain insufficiently characterized. Developmental iron deficiency (ID) provides a unique model for investigating this question because iron is an essential cofactor for TET DNA dioxygenases and developmental ID causes persistent behavioral and molecular alterations despite iron repletion. ResultsWe integrated the hippocampal transcriptome, DNA methylome (5mC), and hydroxymethylome (5hmC) in male rats at postnatal day 15 following developmental ID and postnatal iron treatment, using Oxford Nanopore sequencing for native DNA modification profiling. Developmental ID induced substantial transcriptional and epigenetic alterations associated with synaptic function, neurodevelopment, and neuroinflammation. Postnatal iron treatment induced a hierarchical response across molecular layers: while transcriptomic alterations largely normalized, 5mC showed only partial recovery, and 5hmC showed extensive de novo modifications. Recovered, persistent, and newly emerged epigenetic marks were associated with increasingly specialized biological functions, from broad neurodevelopmental processes to specific pathways. Furthermore, while 5mC enrichment was associated with transcriptionally suppressed pathways, 5hmC enrichment showed weaker coupling with concurrent transcriptomic activity, suggesting epigenetic poising rather than immediate transcriptional output. MergeOmics integration identified key driver genes showing post-treatment epigenetic regulation despite transcriptional recovery. ConclusionsMolecular recovery following developmental ID extends beyond transcriptomic normalization, involving persistent and extensive epigenetic remodeling. This study provides a framework for understanding molecular responses following early-life environmental insults and highlights the importance of delineating persistent regulatory reprogramming.

genomics↗

bioRxiv2026

Diet-dependent effects of kombucha on the gut microbiome and its neuroactive potential: Associations with reduced anxiety and depressive-like behaviors in mice

Fermented foods are increasingly recognized for their health-boosting potential, yet the mechanisms involved are not fully resolved. Here, we tested whether kombucha reshapes the gastrointestinal microbiome and whether these changes are associated with stress-related behaviors under contrasting dietary backgrounds. Male C57BL/6 mice were fed either a total Western diet (TWD) or a control diet (CTRL) supplemented with kombucha or water three times weekly for seven weeks. Depressive-like and anxiety-related behaviors were evaluated using the forced swimming (FST) and marble burying tests (MBT). Ileum, cecum, and colon microbiomes were profiled via 16S rRNA, ITS2, and shotgun metagenomics, while feces and whole brains were profiled by LC-MS metabolomics. Serum cytokines were measured by ELISA. Results highlight diet-dependent effects of Kombucha on behavioral, microbial and metabolic outcomes. Kombucha reduced immobility in the FST under both diets, whereas fewer marbles buried were observed only under TWD. Kombucha intake enriched Bifidobacterium pseudolongum in the ileum under CTRL and TWD diets, while cecal microbial functions related to amino acid metabolism were stimulated mainly under CTRL. Only CTRL mice receiving kombucha showed higher fecal acetate and butyrate together with lower fecal levels of neurochemically relevant amino acids, including glutamine, phenylalanine, tryptophan, and tyrosine. Under TWD, kombucha was associated with lower spleen weight and altered brain tryptophan/kynurenine profiles. These findings identify kombucha as a food intervention that can remodel gastrointestinal microbial and neuroactive metabolism in a diet depending manner. Associations with reduced depressive and anxiety-related behaviors are promising but warrant further exploration. Key HighlightsO_LIKombucha supplementation reshaped the mice gastrointestinal microbiome and its neuroactive potential C_LIO_LIKombucha intake was associated reduced depressive and anxious like behaviors C_LIO_LIThe potential of kombucha to modulate microbial, metabolic and behavioral outcomes may be dependent on subject dietary background C_LI

microbiology↗

bioRxiv2025

Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish

Heritable epigenetic adaptation to environmental stressors is a compelling but highly contested possibility. Previously, we showed evidence of a generationally heritable epigenetic memory at the cytochrome P450 1a (cyp1a) gene in wild Atlantic killifish (Fundulus heteroclitus) with acquired tolerance to polycyclic aromatic hydrocarbons (PAHs). This memory leads to blunted induction of cyp1a by PAHs; this blunted response protects against PAH-induced cancer. Here, using Oxford Nanopore long-read sequencing in PAH-tolerant and -sensitive F. heteroclitus embryos, we show that PAH-tolerant embryos displayed reduced plasticity in DNA methylation response to PAH, as compared to PAH-sensitive embryos, that was not due to mutational loss of CpG sites. Notably, we observed population differences in DNA methylation of genes in pathways linked to the PAH tolerance phenotype, including aryl hydrocarbon receptor (ahr) and voltage-gated potassium channel signaling, as well as developmental processes and energy metabolism. Specifically, we observed PAH-induced loss of cyp1a gene body methylation in PAH-sensitive but not-tolerant embryos. We observed similar patterns at cyp1b1, cyp1c1, and the aryl hydrocarbon receptor repressor, ahrr, which show similarly blunted expression in response to PAH challenge. The reduced loss in genic methylation in tolerant embryos was correlated with greater induction of natural anti-sense RNA transcripts in cis (cis-NATs), which may regulate transcription of these genes. Our data support the existence of stable epigenetic responses to chronic environmental stressors in a natural experimental setting, with broad implications for natural or directed adaptation strategies for other populations.

genomics↗

bioRxiv2025

Genomics and reproductive biology of Leptopilina malgretoutensis Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae): An asexual parasitoid of Caribbean Drosophila

Drosophila and parasitic wasps in the genus Leptopilina have long been a model for understanding host-parasite interactions. Indeed, parasitic wasps are important drivers of ecological and evolutionary processes broadly, but we are generally lacking information about the diversity, natural history, and evolution of these relationships. We collected insects from the Caribbean Island of Saint Lucia, home to the eastern Caribbean dunni subgroup of Drosophila: a clade long appreciated for its recent patterns of speciation and adaptation. Here we present an integrative approach that incorporates natural history, taxonomy, physiology, and genomics to describe Leptopilina n. sp. Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of dunni group flies, especially Drosophila antillea. Leptopilina n. sp. is nested within an early-branching clade of Leptopilina, offering insights into the evolution of this important genus of Drosophila parasitoids. We present a high-quality assembly for this wasps 1Gbp genome, and for its bacterial endosymbiont: Wolbachia strain "wLmal". Furthermore, we show that wLmal induces parthenogenesis in the wasp, and that these wasps are reliant upon their Wolbachia infections to produce female offspring. Finally, comparison to historical museum specimens indicate that Leptopilina n. sp. had been collected approximately 40 years prior from the nearby island of Guadeloupe and were also asexually reproducing. This work represents one of only a handful of studies in which field biology, taxonomy, systematics, genomics, and experimental biology are integrated into a species description: showcasing the possibilities for biodiversity research in the genomic era.

evolutionary biology↗

bioRxiv2025

The Genome of the American Dog Tick (Dermacentor variabilis)

The American dog tick (Dermacentor variabilis) is a vector of zoonotic pathogens in North America that poses emerging threats to public health. Despite its medical importance, genomic resources for D. variabilis remain scarce. Leveraging long-read nanopore sequencing, we generated a high-quality genome assembly for D. variabilis with a final size of 2.15 Gb, an N50 of 445 kb, and a BUSCO completeness score of 95.2%. Comparative BUSCO analyses revealed fewer duplicate genes in our assembly than in other Dermacentor genomes, indicating improved haplotype resolution. The mitochondrial genome, assembled as a single circular contig, clustered monophyletically with D. variabilis isolates from the Upper Midwest, corroborating regional phylogenetic relationships. Repetitive element analysis identified 61% of the genome as repetitive, dominated by LINEs and LTR elements, with 24% remaining unclassified, underscoring the need for further exploration of transposable elements in tick genomes. Gene annotation predicted 21,722 putative genes, achieving a protein BUSCO completeness of 80.88%. Additionally, genome-wide methylation analysis revealed 9.9% global 5mC methylation, providing the first insights into epigenetic modifications in D. variabilis. Further, nanopore sequencing detected Rickettsia montanensis and a non-pathogenic Francisella-like endosymbiont. These findings expand our understanding of tick genomics and epigenetics, offering valuable resources for comparative studies and evolutionary analyses.

genomics↗

bioRxiv2025

Epigenomic insights into extreme longevity in the world's oldest terrestrial animal, Jonathan

Giant tortoises exhibit exceptional longevity, often exceeding the human lifespan. To understand the genomic and epigenomic basis of their longevity, awe analyzed the DNA sequence and methylome of Jonathan, an Aldabra giant tortoise (Aldabrachelys gigantea), estimated to be 192 years old. Relative to other giant tortoises (Aldabrachelys gigantea and Chelonoidis abingdonii), we found Jonathan has gene variants in pathways associated with aging, including DNA repair and telomere regulation. Consistent with his advanced age, Jonathan has significant age-related changes in DNA methylation and methylation entropy, compared with a 5-year-old Aldabra individual. Notably, we found that low entropy regions in Jonathans methylome were enriched for genes involved in the electron transport chain. This suggests that high-fidelity transcription of these genes may be crucial for extreme longevity. With this data, we propose a model for aging, that links efficient mitochondrial energy production with nuclear maintenance of low methylation entropy.

genomics↗

bioRxiv2024

The genome of Przewalski's horse (Equus ferus przewalskii)

The Przewalskis horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalskis mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalskis horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalskis horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.

genomics↗

bioRxiv2023

Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling

AO_SCPLOWBSTRACTC_SCPLOWAccurate species identification is essential to mammalogy. Despite this necessity, rapid and accurate identification of cryptic, understudied, and elusive mammals remains challenging. Traditional barcoding of mitochondrial genes is standard for molecular identification but requires time-consuming wet-lab methodologies. Recent bioinformatic advancements for nanopore sequencing data offer exciting opportunities for non-invasive and field-based identification of mammals. Nanopore adaptive sampling (NAS), a PCR-free method, selectively sequences regions of DNA according to user-specified reference databases. Here, we utilized NAS to enrich mammalian mitochondrial genome sequencing to identify species. Fecal DNA extractions were sequenced from nine mammals, several collected in collaboration with Minnesota Tribal Nations, to demonstrate utility for NAS-barcoding of non-invasive samples. By mapping to the entire National Center for Biotechnology Information (NCBI) mammalian mitochondrial reference genome database and bioinformatically analyzing highly similar matches, we successfully produced species identifications for all of our fecal samples. Eight of nine species identifications matched previous PCR or animal/fecal morphological identifications. For the ninth species, our genetic data indicate a misidentification stemming from the original study. Our approach has a range of applications, particularly field-based wildlife research, conservation, disease surveillance, and monitoring of wildlife trade. Of importance to Minnesota tribes is invasive species monitoring, detections, and confirmation as climate impacts causes changes in biodiversity and shifts in species distributions. The rapid assessment techniques described here will be useful as new introductions and range expansions of native and invasive species may first be detected by the presence of signs such as scat rather than direct observations and will be helpful for chronically understaffed tribal natural resources agencies.

genomics↗

bioRxiv2023

The Genome of the Soybean Gall Midge (Resseliella maxima)

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagne, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae (Wood-Mason). The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

genomics↗

bioRxiv2023

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

Genome skimming is defined as low-pass sequencing below 0.05X coverage and is typically used for mitochondrial genome recovery and species identification. Long read nanopore sequencers enable simultaneous reading of both DNA sequence and methylation and can multiplex samples for low-cost genome skimming. Here I present nanopore sequencing as a highly precise platform for global DNA methylation and transposon assessment. At coverage of just 0.001X, or 30 Mb of reads, accuracy is sub-1%. Biological and technical replicates validate high precision. Skimming 40 vertebrate species reveals conserved patterns of global methylation consistent with whole genome bisulfite sequencing and an average mapping rate above 97%. Genome size directly correlates to global DNA methylation, explaining 44% of its variance. Accurate SINE and LINE transposon methylation in both mouse and primates can be obtained with just 0.0001X coverage, or 3 Mb of reads. Sample multiplexing, field portability, and the low price of this instrument combine to make genome skimming for DNA methylation an accessible method for epigenetic assessment from ecology to epidemiology, and by low resource groups.

genomics↗

bioRxiv2022

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

Pallass cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manuls zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17,097 bp mitogenome for O. manul. The primary nuclear assembly had 56x sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; sixty-one differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.

genomics↗

bioRxiv2022

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.

The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America east of the Rocky Mountains. Its frequent infestation in human buildings justifies close genetic examination and its large size and small genome make it ideal for individual sequencing. From a single individual I used long-read nanopore sequencing to assemble a genome of 306 Mb, with an N50 of 565 Kb, and 60X coverage, with quality assessed by a 97.0% BUSCO score, improving upon related ant assemblies. The reads provided secondary information in the form of parasitic and symbiont genomes, as well as epigenetic information. I assembled a complete Wolbachia bacterial isolate with a genome size of 1.2 Mb and 76X coverage, as well as a commensal bacterium of the carpenter ant tribe, the species-specific symbiont Blochmannia pennsylvanicus, at 791 Kb, 2400X coverage, which matched to within 200 bp of its previously published reference. I also produced a complete mitochondrial genome with over 5000X coverage, revealing minor rearrangements and the first assembly for this species. DNA methylation and hydroxymethylation was measured simultaneously at whole genome, base-pair resolution level from the same nanopore reads and confirmed extremely low levels seen in the Formicidae family of Hymenoptera. A phased diploid assembly was built, revealing a moderate level of heterozygosity, with 0.16% of bases having biallelic SNPs from the two parental haplotypes. Protein prediction yielded 20,209 putative amino acid sequences and annotation identified 86% matched to previously known proteins. All assemblies were derived from a single Minion flow cell generating 20 Gb of sequence for a cost of $1047 including all consumable reagents. Adding fixed costs for required equipment and batch costs for reagents brings the cost to assemble an ant-sized genome to less than $5000. Complete analysis was performed in under 1 week on a commodity computer desktop with 64 Gb memory.

genomics↗

bioRxiv2021

Nanopore adaptive sampling for mitogenome sequencing and bloodmeal identification in hematophagous insects

Blood-feeding insects are important vectors for an array of zoonotic pathogens. Despite significant research focused on well-documented insect vectors of One Health importance, resources for molecular species identification of a large number of hematophagous arthropods are limited. Advancements in next-generation sequencing technologies provide opportunities for targeting mitochondrial genomes of blood-feeding insects, as well as their bloodmeal hosts. This dual approach holds great promise for elucidating complex disease transmission pathways and enhancing the molecular resources for the identification of cryptic insect species. To this end, we leveraged the newly developed Oxford Nanopore Adaptive Sampling (NAS) pipeline to dually sequence the mitogenomes of hematophagous insects and their bloodmeals. Using NAS, we sequenced the entire mitogenomes of Aedes vexans, Culex restuans, Culex territans, and Chrysops niger and successfully identified bloodmeal hosts of Chrysops niger, Culex restuans, and Aedes trivittatus. We show that NAS has the utility to simultaneously molecularly identify blood-feeding insects and characterize disease transmission pathways through bloodmeal host identification. Moreover, our data indicate NAS can facilitate a wide array of molecular systematic studies through novel phylogenetic capture methods. We conclude the NAS approach has great potential for informing global One Health initiatives centered on the mitigation of vector-borne disease through dual vector and bloodmeal identification.

genomics↗

bioRxiv2021

Enabling metagenomic surveillance for bacterial tick-borne pathogens using nanopore sequencing with adaptive sampling

Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) pipeline facilitates immediate mapping of individual nucleotide molecules (i.e., DNA, cDNA, and RNA) to a given reference as each molecule is sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence entire genomes of bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis. The NAS method provided a two-fold increase in targeted pathogen sequences, successfully enriching for Borrelia (Borreliella) burgdorferi s.s.; Borrelia (Borrelia) miyamotoi; Anaplasma phagocytophilum; and Ehrlichia muris eauclairensis genomic DNA within our I. scapularis samples. Our results indicate that NAS has strong potential for real-time sequence-based pathogen surveillance.

microbiology↗

bioRxiv2021

The Mitochondrial Genome and Epigenome of the Golden Lion Tamarin from Fecal DNA using Nanopore Adaptive Sequencing

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. 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. Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.

genomics↗