Biology subjects

Clark, E. L.

Publications and source records attributed to Clark, E. L..

27 records · Page 2Linked to original sources

bioRxiv2020

A putative genomic map for resistance of Bos indicus cattle in Cameroon to bovine tuberculosis

Bovine Tuberculosis (bTB) caused by Mycobacterium bovis is a livestock disease of global economic and public health importance. There are currently no effective vaccines available for livestock and so control relies on animal level surveillance and pasteurisation of dairy products. A new alternative control approach is to exploit the genetic variability of the host; recent studies have demonstrated that breeding Bos taurus cattle for increased resistance to bTB is feasible. The utility of such an approach is still unknown for the Bos indicus cattle population. This study aims to assess genetic variation in bTB resistance and the underlying genomic architecture in Bos indicus breeds in Cameroon. We conducted a cross-sectional study of slaughter cattle in Cameroon and genotyped a sample of 213 cattle. Their genomic diversity was characterised using PCA, hierarchical clustering and admixture analysis. We assessed genetic variation in bTB resistance using heritability analysis and compared quantitative trait loci. Previous studies had found that breed was an important factor in explaining the epidemiology of bTB, with Fulani cattle appearing to be more susceptible than mixed breeds. However, we show that the apparent phenotypic differences in visual appearance between the breeds was not reflected by clear genomic differences. At the genetic level, cattle belonging to different hierarchical genomic clusters differed in their susceptibility to bTB. There was evidence of a genomic association between M. bovis infection status with specific SNPs. We highlight the need to understand the challenges faced by livestock in specific settings both in terms of pathogens and the environment, in addition to their intended purpose and how they fit into a defined management system. It is only at this point livestock keepers can then make informed breeding choices, not only for resistance to disease but also for increasing production.

genetics↗

bioRxiv2020

Gene expression in the cardiovascular system of the domestic sheep (Ovis aries); a new tool to advance our understanding of cardiovascular disease.

Large animal models are of increasing importance in cardiovascular disease research as they demonstrate more similar cardiovascular features (in terms of anatomy, physiology and size) to humans than do rodent species. The maintenance of a healthy cardiovascular system requires expression of genes that contribute to essential biological activities and repression of those that are associated with functions likely to be detrimental to cardiovascular homeostasis. In this study we have used the transcriptome of the sheep, which has been utilised extensively to model human physiology and disease, to explore genes implicated in the process of vascular calcification. Vascular calcification is a major disruption to cardiovascular homeostasis where tissues of the cardiovascular system undergo ectopic calcification and consequent dysfunction. We investigate the gene expression profiles of genes involved in vascular calcification in a wide array of cardiovascular tissues and across multiple developmental stages, using RT-qPCR. The majority of transcriptomic studies on the mammalian cardiovascular system to date have focused on regional expression of specific genes. Here we also use RNA sequencing results from the sheep heart and cardiac valves to further explore the transcriptome of the cardiovascular system in this large animal. Our results demonstrate that there is a balance between genes that promote and those that suppress mineralisation during development and across cardiovascular tissues. We show extensive expression of genes encoding proteins involved in formation and maintenance of the extracellular matrix in cardiovascular tissues, and high expression of haematopoietic genes in the cardiac valves. Our analysis will support future research into the functions of implicated genes in the development of vascular calcification, and increase the utility of the sheep as a large animal model for understanding cardiovascular disease. This study provides a foundation to explore the transcriptome of the developing cardiovascular system and is a valuable resource for the fields of mammalian genomics and cardiovascular research.

genomics↗

bioRxiv2019

A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

genomics↗

bioRxiv2019

Genomic diversity affects the accuracy of bacterial SNP calling pipelines

BackgroundAccurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained.\n\nThis study evaluates the performance of 41 SNP calling pipelines using simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella.\n\nResultsWe evaluated the performance of 41 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis.\n\nConclusionsThe accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. However, across the full range of (divergent) genomes, among the consistently highest-performing pipelines was Snippy.

bioinformatics↗

bioRxiv2019

The maternal-fetal interface of successful pregnancies and impact of fetal sex using single cell sequencing

The first trimester is a critical window of maternal-fetal communication for pregnancy. Therefore, we characterized crosstalk in ongoing human pregnancies at 11-13 weeks gestation. RNA-sequencing of matched maternal decidua and placenta identified 818 receptors and 3502 ligands, including 126 differentially expressed receptor-ligand pairs. Using single cell RNA-sequencing to further dissect placenta heterogeneity, we identified five major cell types (trophoblasts, stromal cells, hofbauer cells, antigen presenting cells and endothelial cells) with unique crosstalk at the maternal-fetal interface. We identified seven unique trophoblast subclusters, including new subtypes that transition into the terminal cell types, extra-villous trophoblasts and syncytiotrophoblasts. As fetal sex impacts pregnancy, we analyzed sex differences in each cell type and identified differences in immune cell function. TGF{beta}1, {beta}-estradiol, and dihydrotestosterone emerge as upstream regulators of sexually dimorphic genes in a cell type specific manner. Thus, the fetal contribution at the maternal-fetal interface is cell and sex specific.

developmental biology↗

bioRxiv2019

Elimination of reference mapping bias reveals robust immune related allele-specific expression in cross-bred sheep

Pervasive allelic variation at both gene and single nucleotide level (SNV) between individuals is commonly associated with complex traits in humans and animals. Allele-specific expression (ASE) analysis, using RNA-Seq, can provide a detailed annotation of allelic imbalance and infer the existence of cis-acting transcriptional regulation. However, variant detection in RNA-Seq data is compromised by biased mapping of reads to the reference DNA sequence. In this manuscript we describe an unbiased standardised computational pipeline for allele-specific expression analysis using RNA-Seq data, which we have adapted and developed using tools available under open licence. The analysis pipeline we present is designed to minimise reference bias while providing accurate profiling of allele-specific expression across tissues and cell types. Using this methodology, we were able to profile pervasive allelic imbalance across tissues and cell types, at both the gene and SNV level, in Texel x Scottish Blackface sheep, using the sheep gene expression atlas dataset. ASE profiles were pervasive in each sheep and across all tissue types investigated. However, ASE profiles shared across tissues were limited and instead they tended to be highly tissue-specific. These tissue-specific ASE profiles may underlie the expression of economically important traits and could be utilized as weighted SNVs, for example, to improve the accuracy of genomic selection in breeding programmes for sheep. An additional benefit of the pipeline is that it does not require parental genotypes and can therefore be applied to other RNA-Seq datasets for livestock, including those available on the Functional Annotation of Animal Genomes (FAANG) data portal. This study is the first global characterisation of moderate to extreme ASE in tissues and cell types from sheep. We have applied a robust methodology for ASE profiling, to provide both a novel analysis of the multi-dimensional sheep gene expression atlas dataset, and a foundation for identifying the regulatory and expressed elements of the genome that are driving complex traits in livestock.

genomics↗

bioRxiv2018

Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmental stage specific gene expression

One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterisation of transcription of the entire the gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 168 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Using network cluster analysis we illustrate how the complexity of the GI tract is reflected in tissue- and developmental stage-specific differences in gene expression. The most significant transcriptional differences between neonatal and adult sheep were observed in the rumen complex. Differences in transcription between neonatal and adult sheep were particularly evident in macrophage specific signatures indicating they might be driving the observed developmental stage-specific differences. Comparative analysis of gene expression in three GI tract tissues from age-matched sheep and goats revealed species-specific differences in genes involved in immunity and metabolism. This study improves our understanding of the transcriptomic mechanisms involved in the transition from pre-ruminant to ruminant. It highlights key genes involved in immunity, microbe recognition, metabolism and cellular differentiation in the GI tract. The results form a basis for future studies linking gene expression with microbial colonisation of the developing GI tract and will contribute towards identifying genes that underlie immunity in early development, which could be utilised to improve ruminant efficiency and productivity.\n\nReference Numbers for Data in the Public RepositoriesThe raw RNA-Sequencing data are deposited in the European Nucleotide Archive (ENA) under study accessions PRJEB19199 (sheep) and PRJEB23196 (goat). Metadata for all samples is deposited in the EBI BioSamples database under group identifiers SAMEG317052 (sheep) and SAMEG330351 (goat).

genomics↗

bioRxiv2018

Assembly and validation of conserved long non-coding RNAs in the ruminant transcriptome

mRNA-like long non-coding RNAs (lncRNA) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. In many cases, therefore, lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNA, we compared de novo assembled lncRNA derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNA assembled in cattle and human. Few lncRNA could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNA assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNA to identify a consensus set of ruminant lncRNA and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. The majority of lncRNA were encoded by single exons, and expressed at < 1 TPM. In sheep, 20-30% of lncRNA had expression profiles significantly correlated with neighbouring protein-coding genes, suggesting association with enhancers. Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNA in other species.

genomics↗

bioRxiv2017

A High Resolution Atlas Of Gene Expression In The Domestic Sheep (Ovis aries)

Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of guilt by association was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages.\n\nAuthor SummarySheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as disease resiliance. The sheep genome is however missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If for example a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.

genomics↗