A5060637041- Nematode management and characterization studies
- Parasite Biology and Host Interactions
- Genomics and Phylogenetic Studies
- Insect symbiosis and bacterial influences
- Genetics, Aging, and Longevity in Model Organisms
- Genetic diversity and population structure
- Parasitic Diseases Research and Treatment
- Protist diversity and phylogeny
- Chromosomal and Genetic Variations
- Environmental DNA in Biodiversity Studies
- Parasites and Host Interactions
- Plant and animal studies
- Lepidoptera: Biology and Taxonomy
- Helminth infection and control
- Microbial Community Ecology and Physiology
- Insect and Arachnid Ecology and Behavior
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Legume Nitrogen Fixing Symbiosis
- Tardigrade Biology and Ecology
- Gene expression and cancer classification
- Insect-Plant Interactions and Control
- Parasitic Infections and Diagnostics
- Mollusks and Parasites Studies
- Species Distribution and Climate Change
Wellcome Sanger Institute
2019-2025
Institut de Biologia Evolutiva
2008-2024
Institució Catalana de Recerca i Estudis Avançats
2024
Centre for Genomic Regulation
2024
Universitat Pompeu Fabra
2024
Smithsonian Institution
2024
Norwich Research Park
2023
John Innes Centre
2023
University of Edinburgh
2013-2022
Aarhus University
2020
Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded contaminant DNA. Whether introduced during sample processing or through co-extraction alongside DNA, if insufficient care is taken assembly process, final assembled genome a mixture several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, included downstream analyses users unaware...
The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare unfit, but even infrequent can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate in Heliconius, a rapidly radiating genus neotropical butterflies widely used studies ecology, behaviour, mimicry speciation. We sequenced the genome Heliconius melpomene compared it with other taxa chromosomal evolution Lepidoptera gene flow among...
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them sorely needed. We report the draft genome sequence of root-knot nematode Meloidogyne incognita, a biotrophic parasite many crops, including tomato, cotton coffee. Most assembled this asexually reproducing nematode, totaling 86 Mb, exists in pairs homologous but divergent segments. This suggests that ancient allelic regions M. incognita evolving toward effective haploidy, permitting new...
Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more contiguous genomes. In eukaryotes the mitochondrial is sequenced alongside nuclear often at very coverage. A dedicated tool for using HiFi still missing. Results MitoHiFi was developed within Darwin Tree Life Project assemble genomes from generated target species. The input either raw or...
The scale of diversity life on this planet is a significant challenge for any scientific programme hoping to produce complete catalogue, whatever means used. For DNA barcoding studies, difficulty compounded by the realization that chosen barcode sequence not gene 'for' speciation and taxa have evolutionary histories. How are we disentangle confounding effects reticulate population genetic processes? Using data from meiofaunal surveys, here discuss benefits treating defined barcodes without...
<ns4:p>The goal of many genome sequencing projects is to provide a complete representation target (or genomes) as underpinning data for further analyses. However, it can be problematic identify which sequences in an assembly truly derive from the genome(s) and are derived associated microbiome or contaminant organisms. </ns4:p><ns4:p> We present BlobTools, modular command-line solution visualisation, quality control taxonomic partitioning datasets. Using guanine+cytosine content sequences,...
RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it not clear how many biological replicates are needed to ensure valid interpretation results or which statistical tools best analyzing data. An experiment with 48 in each two conditions was performed answer these questions and provide guidelines experimental design. With three replicates, nine 11 evaluated found only 20%-40% significantly differentially expressed (SDE) genes identified full...
Using a molecular barcode, derived from single-specimen polymerase chain reaction (PCR) and sequencing of the 5' segment small subunit ribosomal RNA (SSU) gene, we have developed operational taxonomic unit (MOTU) scheme for soil nematodes. Individual specimens were considered to belong same MOTU when sequenced 450 bases was > 99.5% identical. A Scottish upland Agrostis-Festuca grassland sampled, using both culture-based random selection methods. One hundred sixty-six cultured isolates...
Abstract In mammalian systems RNA can move between cells via vesicles. Here we demonstrate that the gastrointestinal nematode Heligmosomoides polygyrus , which infects mice, secretes vesicles containing microRNAs (miRNAs) and Y RNAs as well a Argonaute protein. These are of intestinal origin enriched for homologues exosome proteins. Administration exosomes to mice suppresses Type 2 innate responses eosinophilia induced by allergen Alternaria. Microarray analysis mouse incubated with in vitro...
Next-generation sequencing technologies are making a substantial impact on many areas of biology, including the analysis genetic diversity in populations. However, genome-scale population studies have been accessible only to well-funded model systems. Restriction-site associated DNA sequencing, method that samples at reduced complexity across target genomes, promises deliver high resolution genomic data-thousands sequenced markers individuals-for any organism reasonable costs. It has found...
Most speciation events probably occur gradually, without complete and immediate reproductive isolation, but the full extent of gene flow between diverging species has rarely been characterized on a genome-wide scale. Documenting timing admixture can clarify role geographic isolation in speciation. Here we use new methodology to quantify at different stages divergence Heliconius butterflies, based whole-genome sequences 31 individuals. Comparisons sympatric allopatric populations H. melpomene...
Parasitic nematodes that cause elephantiasis and river blindness threaten hundreds of millions people in the developing world. We have sequenced approximately 90 megabase (Mb) genome human filarial parasite Brugia malayi predict 11,500 protein coding genes 71 Mb robustly assembled sequence. Comparative analysis with free-living, model nematode Caenorhabditis elegans revealed that, despite these having maintained little conservation local synteny during 350 million years evolution, they...
Intracellular bacteria have been observed in various species of filarial nematodes (family Onchocercidae). The intracellular bacterium the canine filaria Dirofilaria immitis has shown to be closely related Wolbachia, a rickettsia-like micro–organism that is widespread among arthropods. However, relationships between endosymbionts different filariae, and these arthropod wolbachiae, appear not studied. To address issues we examined ten for presence Wolbachia. For nine species, all samples were...
Not only is the number of described species a very small proportion estimated extant taxa, but it also appears that all concepts extent and boundaries 'species' fail in many cases. Using conserved molecular sequences possible to define diagnose operational taxonomic units (MOTU) have similar traditional 'species'. Use MOTU system not allows rapid effective identification most including those encountered before, investigation evolution patterns diversity. A approach without problems,...
Terry Burke, Mark Blaxter, David Lank and colleagues report a reference genome sequence of the ruff analysis three distinct male morphs this bird species. They identify 'supergene' consisting fixed inversion in two candidate reproductive trait genes region. Three strikingly different alternative mating (aggressive 'independents', semicooperative 'satellites' female-mimic 'faeders') coexist as balanced polymorphism ruff, Philomachus pugnax, lek-breeding wading bird1,2,3. Major differences...
We used 20 de novo genome assemblies to probe the speciation history and architecture of gene flow in rapidly radiating Heliconius butterflies. Our tests distinguish incomplete lineage sorting from introgression indicate that has obscured several ancient phylogenetic relationships this group over large swathes genome. Introgressed loci are underrepresented low-recombination gene-rich regions, consistent with purging foreign alleles more tightly linked incompatibility loci. Here, we identify...
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans animals, decimate crop production are a major impediment to socioeconomic development. Here we report broad comparative study 81 genomes parasitic non-parasitic worms. We have identified gene family births hundreds expanded families at key nodes in the phylogeny that relevant parasitism. Examples include modulate host immune responses, enable parasite migration though tissues or...
We inferred the rate and properties of new spontaneous mutations in Drosophila melanogaster by carrying out whole-genome shotgun sequencing-by-synthesis three mutation accumulation (MA) lines that had been maintained close inbreeding for an average 262 generations. tested presence generating alignments each MA line to D. reference genome sequence then compared these base base. determined empirically at least five reads a site within are required accurate single nucleotide calling. mapped...
Generating expressed sequence tags is a simple, cheap, and efficient way to sample the genome of target organism. An tag (EST) single-pass derived from single complementary DNA (cDNA) clone, serves identify gene which it derives. We present set tested laboratory protocols for setting up performing an EST analysis any chosen species. These medium-throughput do not require dedicated genomics equipment, such as robots, focus on use microtiter plates multichannels. Using these protocols,...
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed illuminate evolution highly insect societies. Bumblebees also invaluable natural and agricultural pollinators, there widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects bumblebee biology, including susceptibility implicated viability threats.We report high quality draft genome sequences...
Biodiversity is of crucial importance for ecosystem functioning, sustainability and resilience, but the magnitude organization marine diversity at a range spatial taxonomic scales are undefined. In this paper, we use second-generation sequencing to unmask putatively diverse metazoan biodiversity in Scottish temperate benthic ecosystem. We show that remarkable differences occurred microgeographical refute currently accepted ecological paradigms meiofaunal identity, rank abundance concomitant...