Intron Research Articles

Genome-Wide Assessment of DNA Methylation in Chicken Cardiac Tissue Exposed to Different Incubation Temperatures and CO2 Levels.

Temperature and CO2 concentration during incubation have profound effects on broiler chick development, and numerous studies have identified significant effects on hatch heart weight (HW) as a result of differences in these parameters. Early life environment has also been shown to affect broiler performance later in life; it has thus been suggested that epigenetic mechanisms may mediate long-term physiological changes induced by environmental stimuli. DNA methylation is an epigenetic modification that can confer heritable changes in gene expression. Using reduced-representation bisulfite sequencing (RRBS), we assessed DNA methylation patterns in cardiac tissue of 84 broiler hatchlings incubated at two egg shell temperatures (EST; 37.8°C and 38.9°C) and three CO2 concentrations (0.1%, 0.4%, and 0.8%) from day 8 of incubation onward. We assessed differential methylation between EST treatments and identified 2,175 differentially methylated (DM) CpGs (1,121 hypermethylated, 1,054 hypomethylated at 38.9° vs. 37.8°) in 269 gene promoters and 949 intragenic regions. DM genes (DMGs) were associated with heart developmental processes, including cardiomyocyte proliferation and differentiation. We identified enriched binding motifs among DM loci, including those for transcription factors associated with cell proliferation and heart development among hypomethylated CpGs that suggest increased binding ability at higher EST. We identified 9,823 DM CpGs between at least two CO2 treatments, with the greatest difference observed between 0.8 and 0.1% CO2 that disproportionately impacted genes involved in cardiac muscle development and response to low oxygen levels. Using HW measurements from the same chicks, we performed an epigenome-wide association study (EWAS) for HW, and identified 23 significantly associated CpGs, nine of which were also DM between ESTs. We found corresponding differences in transcript abundance between ESTs in three DMGs (ABLIM2, PITX2, and THRSP). Hypomethylation of an exonic CpG in PITX2 at 38.9°C was associated with increased expression, and suggests increased cell proliferation in broiler hatchlings incubated at higher temperatures. Overall, these results identified numerous epigenetic associations between chick incubation factors and heart development that may manifest in long-term differences in animal performance.

DNA Methylation of Intragenic CpG Islands are Required for Differentiation from iPSC to NPC.

The effects of gene body DNA methylation on gene regulation still remains highly controversial. In this study, we generated whole genome bisulfite sequencing (WGBS) data with high sequencing depth in induced pluripotent stem cell (iPSC) and neuronal progentior cell (NPC), and investigated the relationship between DNA methylation changes in CpG islands (CGIs) and corresponding gene expression during NPC differentiation. Interestingly, differentially methylated CGIs were more abundant in intragenic regions compared to promoters and these methylated intragenic CGIs (iCGIs) were associated with neuronal development-related genes. When we compared gene expression level of methylated and unmethylated CGIs in intragenic regions, DNA methylation of iCGI was positively correlated with gene expression in contrast with promoter CGIs (pCGIs). To gain insight into regulatory mechanism mediated by iCGI DNA methylation, we executed motif searching in hypermethylated iCGIs and found NEUROD1 as a hypermethylated iCGI binding transcription factor. This study highlights give rise to possibility of activating role of hypermethylation in iCGIs and involvement of neuronal development related TFs. Graphical Abstract The relationship between iCGI DNA methylation and expression of associated genes in neuronal developmental process. During iPSC to NPCdifferentiation, iCGI containing neural developmental genes show iCGI's DNA hypermethylation which is accompanied by gene activation and NEUROD1which is one of the core neuronal TFs interacts with hypermethylated iCGI regions.

Short communication: Locus-specific interrelations between gene expression and DNA methylation patterns in bovine mammary gland infected by coagulase-positive and coagulase-negative staphylococci

Pathogens are able to alter the cell cycle program and immune response of the host by changing the transcription and epigenetics of genes responsible for cell cycle control and inflammation. In this regard, we evaluated interrelations between DNA methylation and expression of autophagy, apoptosis, and lipid metabolism-related genes in a sample set of mammary gland secretory tissue sections derived from bovine mammary glands infected with coagulase-negative and coagulase-positive staphylococci. We assessed relative transcript abundance and DNA bisulfite sequencing in loci of the ATG5, IGF1R, TERT, and DGAT1 genes. Lack of DNA methylation in ATG5 and DGAT1 loci might be associated with maintenance of ATG5 and DGAT1 expression regardless of the health status of bovine mammary gland. Complete methylation of intragenic CpG regions in the IGF1R locus was apparently not related to the presence of its transcript in the investigated udder parenchyma samples. Detected hypermethylation of the TERT upstream element was associated with a small amount of TERT mRNA in bovine mammary gland, regardless of the presence, or absence, of the pathogen. A significant decrease in TERT gene expression in tissue sections of mammary gland free of bacteria and in those infected with coagulase-positive staphylococci was observed in parenchyma samples infected with coagulase-negative staphylococci. Two possible explanations are the direct involvement of the TERT gene in the etiology of bovine mastitis or the increase of TERT mRNA due to activation of the MAPK signaling pathway in response to release of exotoxins by coagulase-negative bacteria in the bovine mammary gland.

High genetic diversity and limited spatial structure in an endangered, endemic South African sparid, the red steenbras Petrus rupestris

The red steenbras Petrus rupestris is endemic to South Africa, occurring from False Bay in the Western Cape Province to St Lucia in the province of KwaZulu-Natal. This species, the largest member of the family Sparidae, has undergone a substantial stock decline as a result of overfishing and is considered to be collapsed. Various aspects of its life history, including high residency, predictable migrations, late maturity and longevity, have made it vulnerable to overexploitation. This study analysed the diversity and genetic structure of red steenbras across seven sampling regions, using mitochondrial (control region) and nuclear (S7 intron 1) DNA markers. Mitochondrial DNA haplotype diversity was high (0.976), exceeding that reported for most studied South African fishes. The haplotype network, a low global fixation index (φST = 0.013, p = 0.055) and pairwise comparisons indicated limited genetic differentiation among sampling regions and a general lack of spatial genetic structure, with the possible exception of the Agulhas Offshore and Transkei regions. Genetic diversity indices based on the S7 intron also indicated very low levels of genetic structuring among sampling regions. A Migrate-n analysis revealed highly asymmetrical migration rates and gene flow among the regions, reflecting aspects of the species’ life history. These findings suggest that red steenbras exists as one panmictic population and should be managed as such.

A genome-wide association study for clinical mastitis in the dual-purpose German Black Pied cattle breed

The dual-purpose German Black Pied Cattle (DSN) has become an endangered breed of approximately 2,550 registered cows in Germany. The breed is genetically related to Holstein-Friesian cattle because the old DSN breed contributed to the selection of the modern Holstein dairy cow. In dairy farms, breeders aim to improve animal health and well-being by reducing the number of mastitis cases, which would also reduce milk losses and treatment costs. On the genomic level, no markers associated with clinical mastitis have been reported in DSN. Therefore, we performed a genome-wide association study on 1,062 DSN cows using a univariate linear mixed model that included a relatedness matrix to correct for population stratification. Although the statistical power was limited by the small population size, 3 markers were significantly associated, and 2 additional markers showed a suggestive association with clinical mastitis. Those markers accounted for 1 to 3% of the variance of clinical mastitis in the examined DSN population. One marker was found in the intragenic region of NEURL1 on BTA26, and the other 4 markers in intergenic regions on BTA3, BTA6, and BTA9. Further analyses identified 23 positional candidate genes. Among them is BMPR1B, which has been previously associated with clinical mastitis in other dairy cattle breeds. The markers presented here can be used for selection for mastitis-resistant animals in the endangered DSN population, and can broadly contribute to a better understanding of mastitis determinants in dairy cattle breeds.

Black raspberries attenuate colonic adenoma development in Apc Min mice: Relationship to hypomethylation of promoters and gene bodies.

Recent studies have suggested that in addition to promoter region, DNA methylation in intragenic and intergenic regions also changes during physiological processes and disease. The current study showed that feeding of black raspberries (BRBs) to ApcMin mice suppressed colon and intestinal tumors. MBDCap-seq suggested that dietary BRBs hypomethylated promoter, intragenic, and intergenic regions. Annotation of those regions highlighted genes in pathways involved in immune regulation, inflammatory signaling, production of nitric oxide and reactive oxygen species, and progression of colorectal cancer. BRB phytochemicals (e.g., ellagic acid, anthocyanins, oligosaccharides) and their gut bacterial metabolites (e.g., urolithin, protocatechuic acid, short-chain fatty acids) inhibited DNMT1 and DNMT3B activities in a cell-free assay. Our results suggest that BRBs’ hypomethylating activities result from the combined effects of multiple BRB phytochemicals and their gut bacterial metabolites. Because similar substances are found in many plant products, our results with BRBs might also apply to commonly consumed fruits and vegetables.

Gametophytic self-incompatibility in Andean capuli (Prunus serotina subsp. capuli): allelic diversity at the S-RNase locus influences normal pollen-tube formation during fertilization.

Capuli (Prunus serotina subsp. capuli) is a tree species that is widely distributed in the northern Andes. In Prunus, fruit set and productivity appears to be limited by gametophytic self-incompatibility (GSI) which is controlled by the S-Locus. For the first time, this research reveals the molecular structure of the capuli S-RNase (a proxy for S-Locus diversity) and documents how S-Locus diversity influences GSI in the species. To this end, the capuli S-RNase gene was amplified and sequenced in order to design a CAPS (Cleaved Amplified Polymorphic Sequence) marker system that could unequivocally detect S-alleles by targeting the highly polymorphic C2–C3 S-RNase intra-genic region. The devised system proved highly effective. When used to assess S-Locus diversity in 15 P. serotina accessions, it could identify 18 S-alleles; 7 more than when using standard methodologies for the identification of S-alleles in Prunus species. CAPS marker information was subsequently used to formulate experimental crosses between compatible and incompatible individuals (as defined by their S-allelic identity). Crosses between heterozygote individuals with contrasting S-alleles resulted in normal pollen tube formation and growth. In crosses between individuals with exactly similar S-allele identities, pollen tubes often showed morphological alterations and arrested development, but for some (suspected) incompatible crosses, pollen tubes could reach the ovary. The latter indicates the possibility of a genotype-specific breakdown of GSI in the species. Overall, this supports the notion that S-Locus diversity influences the reproductive patterns of Andean capuli and that it should be considered in the design of orchards and the production of basic propagation materials.

English

MiRNAs are highly conserved class of small (19-25 nucleotides), non-coding RNAs, which regulate post-transcriptional gene expression by binding to target mRNAs and result in gene silencing. In the genome, miRNAs can be found situated in the exons of non-coding genes, introns of coding and non-coding genes and the intragenic regions. Small interfering RNAs are approximately 22 nucleotides in length and mediate RNA interference (RNAi). miRNAs control endothelial cell, vascular smooth muscle cell and macrophage functions, and thereby regulate the progression of atherosclerosis. miRNAs expression is modulated by different stimuli involved in every stage of atherosclerosis and conversely miRNAs modulates several pathways implicated in plaque development such as cholesterol metabolism. miRNAs are involved in the regulation of key processes that contribute to skin fibrosis, including TGF-beta signaling, ECM deposition, fibroblast proliferation and differentiation, and epithelial to mesenchymal transition or transformation. Some miRNAs are profibrotic and their upregulation favors these processes contributing to fibrosis, while anti-fibrotic miRNAs inhibit these processes and may be reduced in fibrosis. Keywords: Micro RNA, Atherosclerosis, Skin fibrosis, Fibroblast, Plaque

A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.).

Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~ 37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized 6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590 markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~ 520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of future genome sequence assemblies.

Estrogen Induces Selective Transcription of Caveolin1 Variants in Human Breast Cancer through Estrogen Responsive Element-Dependent Mechanisms.

The estrogen receptor (ER) signaling regulates numerous physiological processes mainly through activation of gene transcription (genomic pathways). Caveolin1 (CAV1) is a membrane-resident protein that behaves as platform to enable different signaling molecules and receptors for membrane-initiated pathways. CAV1 directly interacts with ERs and allows their localization on membrane with consequent activation of ER-non-genomic pathways. Loss of CAV1 function is a common feature of different types of cancers, including breast cancer. Two protein isoforms, CAV1α and CAV1β, derived from two alternative translation initiation sites, are commonly described for this gene. However, the exact transcriptional regulation underlying CAV1 expression pattern is poorly elucidated. In this study, we dissect the molecular mechanism involved in selective expression of CAV1β isoform, induced by estrogens and downregulated in breast cancer. Luciferase assays and Chromatin immunoprecipitation demonstrate that transcriptional activation is triggered by estrogen-responsive elements embedded in CAV1 intragenic regions and DNA-binding of estrogen-ER complexes. This regulatory control is dynamically established by local chromatin changes, as proved by the occurrence of histone H3 methylation/demethylation events and association of modifier proteins as well as modification of H3 acetylation status. Thus, we demonstrate for the first time, an estrogen-ERs-dependent regulatory circuit sustaining selective CAV1β expression.

Assessing phylogeographic variation in the Rosyside Dace (Teleostei, Leuciscidae), a widespread morphologically variable taxon

AbstractClinostomus (Leuciscidae) is a wide‐ranging freshwater fish genus that occurs throughout eastern North America and southern portions of Canada with two species currently recognized: C. elongatus and C. funduloides. A previous taxonomic study of C. funduloides recognized two subspecies (estor and funduloides) and one diagnosed, but undescribed subspecies based on morphological characteristics and geographic distribution. In this study, we used three molecular markers (cytochrome b, S7 intron 1 and growth hormone intron 4) to test the three lineage hypothesis and evaluate genetic variation of C. funduloides across the range using Bayesian inference. Our results indicate that C. funduloides is not monophyletic, as individuals of C. elongatus nest within C. funduloides in both the mtDNA and nDNA phylogenetic analyses, although the position of C. elongatus varies between data sets. In addition, some of the recovered clades are deeply divergent from one another, further supporting the distinctiveness of many of the populations. Overall, these results suggest that subspecies designations are not warranted and a taxonomic revision is needed as Clinostomus is likely more diverse than is currently recognized.

A Unique Presentation of XY Gonadal Dysgenesis in Frasier Syndrome due to WT1 Mutation and a Literature Review.

Frasier syndrome (FS), a rare disease caused by inherited or de novo mutation in Wilm's Tumor suppressor gene 1 (WT1), is characterized by slow progressive nephropathy, XY gonadal dysgenesis (XY-DSD), and increased risk for gonadal tumors. Early childhood (1-6 years) nephropathy progresses with age to refractory nephrotic syndrome, and end-stage renal failure in late adolescence, when delayed puberty and/or primary amenorrhea are clinically evident. We report a unique case of FS presenting initially with primary amenorrhea at 16 years, without previous or concomitant renal damage. Only subsequently she developed an extremely late-onset nephropathy. Genetic analysis revealed the IVS9 + 5 G>A mutation in intron 9 of the WT1 gene. This clinical presentation and review of WT1 literature highlights the importance of considering FS in the differential diagnosis of patients with 46,XY disorders of Sexual development, even without nephropathy. Furthermore, the identification WT1 gene mutation prior to evident renal dysfunction indicates an immediate and close surveillance of renal function enabling an optimal and timely medical response.

First Come, First Served: Sui Generis Features of the First Intron.

Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.

Evidence of genetic differentiation in cigar wrasse Cheilio inermis (Labridae) within the western Indian Ocean.

Patterns of genetic structure and connectivity of the monotypic cigar wrasse Cheilio inermis within western Indian Ocean (WIO) are poorly understood. Whether the species exists as a single panmictic population across the WIO is unclear. Sequence data were generated from two mitochondrial genes (cytochrome b and ATPase 6) and one nuclear intron (S7 intron I). High levels of haplotype and allelic diversity (h = 0.88-0.98; A = 0.95-0.98), along with low nucleotide diversities were observed across all markers. The pairwise ΦST values indicated differentiation of Tanga from the four WIO localities (Inhaca, Nosy Bé, Gazi, and Shimoni), as well as differentiation between the northernmost WIO localities. AMOVAs indicated high differentiation among defined locality groups, whereas nuclear gene analysis found little differentiation among groups. The observed genetic differentiation in C. inermis could be caused by oceanic barriers, and by limited larval dispersal with the pelagic larvae possibly settling near their parental origin and promoting differentiation.

A novel incompatibility group X3 plasmid carrying bla NDM-1 encodes a small RNA that regulates host fucose metabolism and biofilm formation

ABSTRACT The emergence of New Delhi metallo-beta-lactamase (NDM-1) has become a major health threat to clinical managements of gram-negative bacteria infections. A novel incompatibility group X3 plasmid (IncX3) pNDM-HN380 carrying bla NDM-1 has recently been found to epidemiologically link with multiple geographical areas in China. In this paper, we studied the metabolic responses of host bacteria E. coli J53 upon introduction of pNDM-HN380. A reduction of bacterial motility was observed in J53/pNDM-HN380. We profiled the RNA repertoires of the transconjugants and found a downregulation of genes involved in flagella and chemotaxis metabolic pathways at logarithmic (log) phase. We also identified a novel intragenic region (IGR) small RNA plas2. The plasmid-transcribed sRNA IGR plas2 was further characterized as a regulator of fucRwhich controls the fucose metabolism. By knockdown of IGR plas2 using an antisense decoy, we managed to inhibit the formation of bacterial biofilm of the host. Our study demonstrated a potential way of utilizing plasmid-transcribed sRNA against infectious bacteria.

Intragenic recruitment of NF-\u03baB drives splicing modifications upon activation by the oncogene Tax of HTLV-1

Chronic NF-κB activation in inflammation and cancer has long been linked to persistent activation of NF-κB–responsive gene promoters. However, NF-κB factors also massively bind to gene bodies. Here, we demonstrate that recruitment of the NF-κB factor RELA to intragenic regions regulates alternative splicing upon NF-κB activation by the viral oncogene Tax of HTLV-1. Integrative analyses of RNA splicing and chromatin occupancy, combined with chromatin tethering assays, demonstrate that DNA-bound RELA interacts with and recruits the splicing regulator DDX17, in an NF-κB activation-dependent manner. This leads to alternative splicing of target exons due to the RNA helicase activity of DDX17. Similar results were obtained upon Tax-independent NF-κB activation, indicating that Tax likely exacerbates a physiological process where RELA provides splice target specificity. Collectively, our results demonstrate a physical and direct involvement of NF-κB in alternative splicing regulation, which significantly revisits our knowledge of HTLV-1 pathogenesis and other NF-κB-related diseases.

Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy.

In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10−16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome–environment interaction in DCM besides simple gene expression regulation.

Screening of compatible maizeSNP384 markers and the construction of DNA fingerprints of maize varieties

<p indent=0mm>In order to improve the management of maize varieties and the protection of intellectual property rights, a compatible multiple platform loci combination maizeSNP384 was developed as a means of identifying varieties of maize. SNP-DNA fingerprints of 335 maize hybrids were constructed. All the 384 SNPs were located in the intra-genic region, showing good polymorphism. The average MAF, PIC, and DP of 384 loci were 0.39, 0.36, and 0.60, respectively. MAF in 88% of the 384 loci was most than 0.30, PIC in 98% was most than 0.30, and DP in 98% was most than 0.50. Pairwise comparative analysis of 335 maize hybrids using genetic similarity showed that the range of variation of GD (1–Nei genetic distance) was 0.60–0.99, and the ratios of GD value greater than or equal to 0.98, 0.95, and 0.90 were 0.10%, 0.38%, and 1.40%, respectively. The range of variation of GS (same allele ratio) was 0.50–0.99, and the ratios of GS value greater than or equal to 0.98, 0.95, and 0.90 were 0.03%, 0.11%, and 0.35%, respectively. The optimal locus combination was extracted from 384 SNPs, with the variety discrimination power of 0.99 when 12 SNPs were extracted; the combination of 20 SNPs was able to identify all 335 varieties. In summary, 384 core SNPs reported in this study are compatible with multiple platforms, highly stable, highly repeatable and having high variety discrimination power. SNP-DNA fingerprints of 335 maize hybrids were constructed based on these core SNPs, which provides key data support for molecular identification, fingerprint data construction, and molecular breeding of maize.

Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals

BackgroundThe HIV-1 proviral genome harbors multiple CpG islands (CpGIs), both in the promoter and intragenic regions. DNA methylation in the promoter region has been shown to be heavily involved in HIV-1 latency regulation in cultured cells. However, its exact role in proviral transcriptional regulation in infected individuals is poorly understood or characterized. Moreover, methylation at intragenic CpGIs has never been studied in depth.ResultsA large, well-characterized HIV-1 patient cohort (n = 72), consisting of 17 long-term non-progressors and 8 recent seroconverters (SRCV) without combination antiretroviral therapy (cART), 15 early cART-treated, and 32 late cART-treated patients, was analyzed using a next-generation bisulfite sequencing DNA methylation method. In general, we observed low level of promoter methylation and higher levels of intragenic methylation. Additionally, SRCV showed increased promoter methylation and decreased intragenic methylation compared with the other patient groups. This data indicates that increased intragenic methylation could be involved in proviral transcriptional regulation.ConclusionsContrasting in vitro studies, our results indicate that intragenic hypermethylation of HIV-1 proviral DNA is an underestimated factor in viral control in HIV-1-infected individuals, showing the importance of analyzing the complete proviral genome in future DNA methylation studies.

The Genome of Caenorhabditis bovis.

The free-living nematode Caenorhabditis elegans is akey laboratory model for metazoan biology. C.elegans has also become a model for parasitic nematodes despite being only distantly related to most parasitic species. All of the ∼65 Caenorhabditis species currently in culture are free-living, with most having been isolated from decaying plant or fungal matter. Caenorhabditis bovis is a particularly unusual species that has been isolated several times from the inflamed ears of Zebu cattle in Eastern Africa, where it is associated with thedisease bovine parasitic otitis. C.bovis is therefore of particular interest to researchers interested in the evolution of nematode parasitism. However, as C.bovis is not in laboratory culture, it remains little studied. Here, by sampling livestock markets and slaughterhouses in Western Kenya, we successfully reisolated C.bovis from the ear of adult female Zebu. We sequenced the genome of C.bovis using the Oxford Nanopore MinION platform in a nearby field laboratory and used the data to generate a chromosome-scaledraft genome sequence. We exploited this draft genome sequence to reconstruct the phylogenetic relationships of C.bovis to other Caenorhabditis species and reveal the changes in genome size and content that have occurred during its evolution. We also identified expansions in several gene families that have been implicated in parasitism in other nematode species. The high-quality draft genome and our analyses thereof represent a significant advancement in our understanding of this unusual Caenorhabditis species.