About

Chris Faulk is an Associate Professor in the Department of Animal Science at the University of Minnesota Twin Cities. His research focuses on functional genomics, with particular interest in epigenetics, DNA methylation, and genome sequencing. Faulk has contributed to the sequencing and assembly of various genomes, including those of Przewalski's horse, the southern muriqui, and the soybean tentiform leafminer, among others. His work often involves the application of nanopore sequencing technology to study genome structure and epigenetic modifications. He has authored numerous publications on topics such as genome skimming, epigenotoxicity, and the genetic diversity of different species. Faulk's research also explores the effects of environmental exposures, such as lead and illicit drugs, on the epigenome and physiological outcomes. His contributions extend to developing genomic resources and advancing understanding of the genetic and epigenetic mechanisms underlying health, aging, and species conservation.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Computational biology
• Zoology

Selected publications

• Hypomorphic Protein Expression of DNA Polymerase Beta in PolβL301R-V303R/L301R-V303R Knock-In Transgenic Mice Does Not Impact Global DNA Methylation Levels in the Midbrain

  Biomolecules · 2026-03-11

  articleOpen access

  DNA polymerase beta (Polβ) is a 39 kDa, single polypeptide enzyme that possesses both gap tailoring and nucleotidyl transferase activity and is the key polymerase involved in base excision repair (BER) and the final steps of active gene demethylation. We demonstrated that residues in the mouse Polβ protein, L301 and V303, are critical for Polβ’s interaction with the BER scaffolding protein X-ray repair cross-complementing 1 (XRCC1), and mutation of these residues impairs Polβ’s ability to bind to XRCC1, negatively impacting BER complex assembly. We developed PolβL301R-V303R/L301R-V303R knock-in mice to explore how defects with this essential protein complex impact genome stability in the mouse. We found these mice to be viable and fertile yet exhibited a modest reduction in body weight. Here, we examined the protein and mRNA levels in tissues from wild-type (WT), heterozygous (HET), and homozygous (HOM) PolβL301R-V303R/L301R-V303R mice and the derived fibroblast cell lines. We show that HOM mice have significantly diminished Polβ protein levels, as compared to WT mice, in several tissues, yet Polβ mRNA levels were not significantly different, suggesting the decreased levels of Polβ protein could not be attributed to lower gene expression. Upon examination of Polβ stability in mouse ear fibroblasts derived from WT and HOM mice, results are consistent with human cell studies that the PolβL301R-V303R protein is unstable and undergoes proteasome-mediated degradation. Finally, we evaluated WT, and HOM, liver and brain genomic DNA samples for 5-methylcytosine/5-hydroxymethylcytosine (5mC/5hmC) levels by nanopore sequencing to investigate the impact of suppressed Polβ protein levels on active gene demethylation. As expected, we found tissue-specific trends in methylation, when comparing the brain and liver. However, we were unable to discern substantial differences in methylation levels between WT and HOM mice, suggesting that in the absence of external stressors, low Polβ levels do not impact methylation patterns.

  PublisherOA PDFDOI

• Genomics and reproductive biology of <i>Leptopilina malgretoutensis</i> ( <i>sp. nov.</i> ): an asexual parasitoid of Caribbean <i>Drosophila</i>

  Genetics · 2026-01-31

  articleOpen access

  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 malgretoutensis Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of dunni group flies, specifically Drosophila antillea. Leptopilina malgretoutensis 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 wasp's 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, comparisons to historical museum specimens indicated that Leptopilina malgretoutensis had been collected approximately 40 years prior from the nearby island of Guadeloupe, and these wasps 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.

  PublisherOA PDFDOI

• Going Mobile: Using Portable Genomic Technologies for <scp>PCR</scp> ‐Free In Situ Species Identification and Real‐Time Molecular Systematics

  Ecology and Evolution · 2025-11-01 · 1 citations

  articleOpen access

  Across the globe, anthropogenic environmental changes are threatening animal biodiversity and contributing to the emergence of vector-borne and zoonotic pathogens through host range shifts. To combat these challenges, accurate and timely biodiversity assessments and molecular species monitoring efforts are critical. Here, we document how the implementation of a portable laboratory in combination with targeted long-read nanopore sequencing can facilitate in situ genomic and systematic analyses across several animal taxa. Working at two ecologically divergent field sites in Guyana, South America, we collected small mammals and blood-feeding insects, including bats, rodents, a marsupial, mosquitoes, and a phlebotomine sand fly. For each specimen sampled, genomic DNA was extracted in the field and used for the preparation of nanopore sequencing libraries. For field sequencing, we utilized a novel software-based targeted sequencing approach-nanopore adaptive sampling (NAS)-that enabled the selective sequencing of mitochondrial reads using mitogenome assemblies of related taxa as enrichment targets. Basecalled reads from our field sequencing experiments were used to assemble complete mitogenomes and to generate mitochondrial biomarker consensus gene sequences for all nine small mammals and four blood-feeding insects sequenced. Confirmatory molecular identifications were made with a combination of local nucleotide BLAST queries and maximum likelihood analyses using biomarker consensus sequences. Importantly, the mitogenome-based targeted sequencing strategies outlined here are amplification-free and allowed us to bypass time-consuming and potentially troublesome PCR-based methods in the field, streamlining library preparation, sequencing experiments, and on-site analyses. Our findings describe targeted sequencing with NAS as an effective tool for implementation into portable laboratories to widely enhance field-based biodiversity monitoring and rapid molecular species assessments across vertebrate and invertebrate hosts of consequential emerging pathogens.

  PublisherOA PDFDOI

• Utilization of Oxford Nanopore Technology for Human Infectious Diseases Detection and Surveillance in Africa: A Scoping Review

  2025-03-17 · 1 citations

  reviewOpen access

  Background: Nanopore‐based sequencing by Oxford Nanopore Technologies (ONT) offers rapid, cost‐effective, and portable sequencing. As an emerging technology, ONT must be evaluated for efficacy and practical application in both high‐ and low‐resource settings. This scoping review (SR) aimed to: 1) describe how nanopore technology is used in Africa for surveillance and diagnosis of human infectious diseases, 2) describe how nanopore technology aids in the real-time detection of infectious pathogens in Africa, and 3) identify challenges and opportunities for utilizing nanopore technology in Africa to study infectious diseases. Methods: This SR followed the Joanna Briggs Institute Reviewer’s Manual framework for SRs. English‐language studies published from January 1, 2008, to April 30, 2024 that used ONT on human specimens collected in Africa and targeted ≥1 microbial agent were included. Searches were performed in Embase, Medline, PubMed, CINAHL, and the Cochrane Library. The protocol was publicly available on the Open Science Framework (1) prior to data collection. Two independent reviewers screened studies using Covidence, and data was extracted using a custom REDCap instrument. Descriptive statistics and data visualization were performed in Microsoft Excel. Results: 1162 studies were identified and 93 (8%) underwent full-text review. The portable MinION Mk1B was the most common ONT device (65% of studies). Eighty-eight studies analyzed specimens from a single African country. Of these, 45% were sequenced in the same country, 7% in a different African Country, 11% in a non-African country, and 32% did not specify location. Specimen types included direct patient specimens (62%) and cultured isolates (35%), or a combination of both. Blood, serum, or plasma was most common (35%), followed by naso- or oropharyngeal specimens (27%). Forty-four studies used ONT during an active infectious diseases outbreak, 25 of which studied SARS-CoV-2. Seventy-two studies used ONT for genomic surveillance of infectious pathogens or antibiotic resistance genes, and one study used ONT for a direct clinical application. African-affiliated authors were included as first, middle, and last authors in 46% of studies, and 15% were published by entirely African-affiliated teams. Ten studies published information on workflow timeline and five studies published the per-specimen cost. Conclusions: ONT can enable timely and affordable sequencing in African countries as demonstrated through a small number of studies that accomplished these goals individually. Improved reporting of ONT-specific methodology is needed, including timelines, cost, barcoding, flow cell model, and the use of negative controls. Publications that provide these details will enhance reproducibility and support the development of new studies using ONT for the diagnosis and surveillance of infectious diseases in low resource settings.

  PublisherOA PDFDOI

• <i>De novo</i> whole-genome assembly of the critically endangered southern muriqui (<i>Brachyteles arachnoides</i>)

  G3 Genes Genomes Genetics · 2025-02-17

  articleOpen access1st authorCorresponding

  The southern muriqui (Brachyteles arachnoides) is one of the 2 species of muriquis (genus Brachyteles), the largest body-sized nonhuman primate from the Neotropics. Deforestation and illegal hunting have led to a continuing decline in the muriqui population, leading to their current classification as critically endangered. The lack of a reference genome for the genus Brachyteles prevents scientists from taking full advantage of genomic tools to improve their conservation status. This study reports the first whole-genome assemblies of the genus Brachyteles, using DNA from 2 zoo-housed southern muriqui females. We performed sequencing with Oxford Nanopore Technologies' PromethION 2 Solo using a native DNA library preparation to preserve DNA modifications. We used Flye to assemble genomes for each individual. The best final assembly was 2.6 Gb, in 319 contigs, with an N50 of 58.8 Mb and an L50 of 17. BUSCO completeness score for this assembly was 99.5%. The assembly of the second individual had similar quality, with a length of 2.6 Gb, 759 contigs, an N50 of 47.9 Mb, an L50 of 18, and a BUSCO completeness score of 99.04%. Both assemblies had <1% duplicates, missing, or fragments. Gene model mapper detected 24,353 protein-coding genes, and repetitive elements accounted for 46% of the genome. We also reported the mitogenome, which had 16,562 bp over 37 genes, and global methylation of CpG sites, which revealed a mean of 80% methylation. Our study provides a high-quality reference genome assembly for the southern muriqui, expanding the tools that can be used to aid in their conservation efforts.

  PublisherOA PDFDOI

• Genomics and reproductive biology of <i>Leptopilina n. sp.</i> Buffington, Lue, Davis &amp; Tracey sp. nov. (Hymenoptera: Figitidae): An asexual parasitoid of Caribbean <i>Drosophila</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-30 · 3 citations

  preprintOpen access

  ABSTRACT 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 &amp; 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 wasp’s 1Gbp genome, and for its bacterial endosymbiont: Wolbachia strain “ w Lmal”. Furthermore, we show that w Lmal 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.

  PublisherOA PDFDOI

• The genome of the American dog tick ( <i>Dermacentor variabilis</i> )

  G3 Genes Genomes Genetics · 2025-06-09 · 1 citations

  articleOpen accessSenior author

  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 benchmarking universal single-copy ortholog (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 long interspersed nuclear elements and long terminal repeat 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 nonpathogenic Francisella-like endosymbiont. These findings expand our understanding of tick genomics and epigenetics, offering valuable resources for comparative studies and evolutionary analyses.

  PublisherOA PDFDOI

• Going mobile: using portable genomic technologies for PCR-free in situ species identification and real-time molecular systematics

  2025-05-13

  preprintOpen access

  Across the globe, anthropogenic environmental changes are threatening animal biodiversity and contributing to the emergence of vector-borne and zoonotic pathogens through host range shifts. To combat these challenges, accurate and timely biodiversity assessments and molecular species monitoring efforts are critical. Here, we document how implementation of a portable laboratory in combination with targeted long-read nanopore sequencing can facilitate in situ genomic and systematic analyses across several animal taxa. Working at two ecologically divergent field sites in Guyana, South America, we collected small mammals and blood-feeding insects, including bats, rodents, a marsupial, mosquitoes, and a phlebotomine sand fly. For each specimen sampled, genomic DNA was extracted in the field and used for preparation of nanopore sequencing libraries. For field sequencing, we utilized a novel software-based targeted sequencing approach—nanopore adaptive sampling (NAS)—that enabled selective sequencing of mitochondrial reads using mitogenome assemblies of related taxa as enrichment targets. Basecalled reads from our field sequencing experiments were used to assemble complete mitogenomes and to generate mitochondrial biomarker consensus gene sequences for all nine small mammals and four blood-feeding insects sequenced. Confirmatory molecular identifications were made with a combination of local nucleotide BLAST queries and maximum likelihood analyses using biomarker consensus sequences. Importantly, the mitogenome-based targeted sequencing strategies outlined here are amplification-free and allowed us to bypass time-consuming and potentially troublesome PCR-based methods in the field, streamlining library preparation, sequencing experiments, and on-site analyses. Our findings describe targeted sequencing with NAS as an effective tool for implementation into portable laboratories to widely enhance field-based biodiversity monitoring and rapid molecular species assessments across vertebrate and invertebrate hosts of consequential emerging pathogens.

  PublisherOA PDFDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-22

  article

  Abstract 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.

  PublisherDOI

• Sequencing and assembling the genome of Przewalski's horse in the classroom

  Journal of Equine Veterinary Science · 2025-02-15

  reviewOpen access1st authorCorresponding

  Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the previous Przewalski's horse assembly and is on par the domestic horse genome, EquCab3.0. Methods were streamlined, simplified, and conveyed in markdown for complete recording and use in the classroom. All students were authors on the resulting manuscript. By bringing genome assembly into the classroom, we provide both new reference genomes and new genomics expertise to the scientific community at the same time.

  PublisherDOI

Recent grants

• The Environment and Epigenome: Interplay of Toxicants and Transposons in Mammals

  NIH · $728k · 2015–2018

• Linking evolution to aging through DNA methylation and CpG density by examining twelve mammalian species

  NIH · $439k · 2022–2024

• NIH Grant K99ES022221

  NIH · $180k · 2015

Frequent coauthors

• Dana C. Dolinoy

  41 shared

• Mathia Colwell

  University of Minnesota

  22 shared

• Adam T. McLain

  SUNY Polytechnic Institute

  19 shared

• Thomas J. Meyer

  Leidos Biomedical Research Inc. (United States)

  17 shared

• Chelsea Drown

  University of Minnesota

  12 shared

• Maureen A. Sartor

  University of Michigan–Ann Arbor

  12 shared

• Camille F. Abshire

  Louisiana State University Health Sciences Center New Orleans

  12 shared

• Nicole M. Wanner

  University of Minnesota

  11 shared

Labs

• Faulk Lab of Meat SciencePI

Education

• Ph.D., Biological Sciences

  Louisiana State University

  2010

Awards & honors

• Breakthrough Status (Top 1-2% of papers) (2022)