Biology subjects

Burt, D. W.

Publications and source records attributed to Burt, D. W..

9 recordsLinked to original sources

bioRxiv2025

Is it chaotic? Chicken Linkage Disequilibrium and quantitative trait loci

Linkage disequilibrium (LD) underpins genome-wide association studies (GWAS) to map Quantitative Trait Loci Regions (QTLRs). A common yet misled assumption is that the closest sites to a significant marker are the prime candidates as the causative mutation. However, LD blocks are typically fragmented and intermingled. We studied chicken LD of mapped QTLRs for Mareks Disease in numerous chicken populations. We estimated background LD by random sampling of non-syntenic or syntenic marker pairs from different or same chromosomes. We defined LD blocks as a group of markers located on the same chromosome having significant moderate (0.15 [≥] r2 < 0.7) or high (r2 [≥] 0.7) LD, regardless of distance and the number of mixed markers with no LD. Next, we studied QTLR LD by all SNP markers within the QTLRs. We found very complex, nearly chaotic, LD patterns, with fragmented and interdigitated LD blocks. Exceptional LD was found between QTLRs 4-5. LD blocks and protein networks shared by the two QTLRs suggest possible functional relationships. Thus, potential causative candidates could be found beyond non-LD sites, occasionally at a very large distance from a significant marker, and even in another QTLR. Multiple effects might make LD intrinsically chaotic, thus limiting GWAS informativity and repeatability. Chaotic complexity challenges the practical use of LD across populations, and must be accounted for while interpreting genetic mapping studies.

genetics↗

bioRxiv2022

The swan genome and transcriptome: its not all black and white

The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related Northern Hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious disease, notably infectious diseases from which Australia has been largely shielded. Indeed, unlike Mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to severe highly pathogenic avian influenza (HPAI). Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Here, we generate the first chromosome-length annotated black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We used these genomes and transcriptomes, to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to HPAI. We also implicate genetic differences in SLC45A2 in the iconic plumage of the Australian black swan. Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat the survival of the black swan would be in significant peril.

genomics↗

bioRxiv2021

Concurrent invasions by European starlings (Sturnus vulgaris) suggest selection on shared genomic regions even after genetic bottlenecks

A species success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings (Sturnus vulgaris) established populations in Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.

evolutionary biology↗

bioRxiv2021

Transcript- and annotation-guided genome assembly of the European starling

The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second North American genome (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present BO_SCPLOWUSCOMPC_SCPLOW, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.

genomics↗

bioRxiv2020

Mapping QTL associated with resistance to avian oncogenic Mareks Disease Virus (MDV) reveals major candidate genes and variants

Mareks Disease (MD) represents a significant global economic and animal welfare issue. Mareks Disease Virus (MDV) is a highly contagious oncogenic and highly immune-suppressive alpha-herpes virus, which infects chickens, causing neurological effects and tumour formation. Though partially controlled by vaccination, MD continues to have a profound impact on animal health and on the poultry industry. Genetic selection provides an alternative and complementary method to vaccination. However, even after years of study, the genetic mechanisms underlying resistance to MDV remain poorly understood. The MHC is known to play a role in disease resistance, along with a handful of other. In this study, one of the largest to date, we used a multi-facetted approach to identify QTL regions (QTLR) influencing resistance to MDV, including an F6 population from a full-sib advanced intercross line (FSIL) between two elite commercial layer lines differing in resistance to MDV, RNA-seq information from virus challenged chicks, and genome wide association study (GWAS) from multiple commercial lines. Candidate genomic elements residing in the QTLR were further tested for association with offspring mortality in the face of MDV challenge in 8 pure lines of elite egg-layer birds. Thirty-eight QTLR were found on 19 chicken chromosomes. Candidate genes, miRNAs, lncRNAs and potentially functional mutations were identified in these regions. Association tests were carried out in 26 of the QTLR, using 8 pure lines of elite egg-layer birds. Numerous candidate genomic elements were strongly associated with MD resistance. Genomic regions significantly associated with resistance to MDV were mapped, and candidate genes identified. Various QTLR elements were shown to have strong genetic association with resistance. These results provide a large number of significant targets for mitigating the effects of MDV infection on both poultry health and the economy - whether by means of selective breeding, improved vaccine design or gene-editing technologies. Author summaryMareks Disease has a huge impact on the global poultry industry in terms of both animal welfare and economic cost. For many years, researchers have sought to identify the genes underlying resistance to Mareks Disease Virus (MDV). However, this is a complex trait with each genetic locus having a small effect, so identifying causal genes and variants is no easy task. To date, it is known that the MHC confers differing susceptibility/resistance. A few other non-MHC genes have also been implicated in disease resistance, although based on experimental inbred lines and not representing real world commercial poultry. Using an F6 intercross population of birds with differences in MDV survival, we have identified many regions of the genome involved in resistance and highlighted candidate genes, miRNAs and lncRNA. Access to DNA from phenotyped birds spanning 15 generations of 8 elite commercial lines has provided a unique opportunity for us to show genetic association of markers in these transcripts with MDV survival. This genetic study, the largest to date, provides novel targets for mitigation of Mareks Disease within the poultry industry. This could be through selective breeding strategies, improved vaccine design or future gene editing technologies.

genomics↗

bioRxiv2020

Circadian clock mechanism driving mammalian photoperiodism

The annual photoperiod cycle provides the critical environmental cue synchronizing rhythms of life in seasonal habitats. In 1936, Bunning proposed a circadian-based coincidence timer for photoperiodic synchronization in plants. Formal studies support the universality of this so-called coincidence timer, but we lack understanding of the mechanisms involved. Here we show in mammals that long photoperiods induce the circadian transcription factor BMAL2, in the pars tuberalis of the pituitary, and triggers summer biology through the eyes absent / thyrotrophin (EYA3 / TSH) pathway. Conversely, long-duration melatonin signals on short photoperiods induce circadian repressors including DEC1, suppressing BMAL2 and the EYA3/TSH pathway, triggering winter biology. These actions are associated with progressive genome-wide changes in chromatin state, elaborating the effect of the circadian coincidence timer. Hence, circadian clock-pituitary epigenetic pathway interactions form the basis of the mammalian coincidence timer mechanism. Our results constitute a blueprint for circadian-based seasonal timekeeping in vertebrates.

molecular biology↗

bioRxiv2019

Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

Symbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies for the symbiotic Symbiodinium tridacnidorum CCMP2592 (genome size 1.3 Gbp) and the free-living Symbiodinium natans CCMP2548 (genome size 0.74 Gbp). These genomes display extensive sequence divergence, sharing only ~1.5% conserved regions ([≥]90% identity). We predicted 45,474 and 35,270 genes for S. tridacnidorum and S. natans, respectively; of the 58,541 homologous gene families, 28.5% are common to both genomes. We recovered a greater extent of gene duplication and higher abundance of repeats, transposable elements and pseudogenes in the genome of S. tridacnidorum than in that of S. natans. These findings demonstrate that genome structural rearrangements are pertinent to distinct lifestyles in Symbiodinium, and may contribute to the vast genetic diversity within the genus, and more broadly in Symbiodiniaceae. Moreover, the results from our whole-genome comparisons against a free-living outgroup support the notion that the symbiotic lifestyle is a derived trait in, and that the free-living lifestyle is ancestral to, Symbiodinium.

genomics↗

bioRxiv2019

Illuminating the dark side of the human transcriptome with TAMA Iso-Seq analysis

The human transcriptome is one of the most well-annotated of the eukaryotic species. However, limitations in technology biased discovery toward protein coding spliced genes. Accurate high throughput long read RNA sequencing now has the potential to investigate genes that were previously undetectable. Using our Transcriptome Annotation by Modular Algorithms (TAMA) tool kit to analyze the Pacific Bioscience Universal Human Reference RNA Sequel II Iso-Seq dataset, we discovered thousands of potential novel genes and identified challenges in both RNA preparation and long read data processing that have major implications for transcriptome annotation.

genomics↗

bioRxiv2019

The quail as an avian model system: its genome provides insights into social behaviour, seasonal biology and infectious disease response

The Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research. We have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organization, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and pathways were downregulated, and this may be key to the susceptibility of quail to H5N1. This genome will facilitate further research into diverse research questions using the quail as a model avian species.

genomics↗