A5091615215- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Insect symbiosis and bacterial influences
- Insect Resistance and Genetics
- Ichthyology and Marine Biology
- RNA and protein synthesis mechanisms
- Identification and Quantification in Food
- Genetic Mapping and Diversity in Plants and Animals
- Animal Behavior and Reproduction
- Amphibian and Reptile Biology
- Aquaculture disease management and microbiota
- Marine animal studies overview
- Turtle Biology and Conservation
- Marine Biology and Environmental Chemistry
- Marine and coastal plant biology
- Insect Utilization and Effects
- Subterranean biodiversity and taxonomy
- Bat Biology and Ecology Studies
- Bacteriophages and microbial interactions
- Insect and Arachnid Ecology and Behavior
- Marine Sponges and Natural Products
- Marine Biology and Ecology Research
- Environmental DNA in Biodiversity Studies
- Invertebrate Immune Response Mechanisms
Wellcome Sanger Institute
2020-2025
Rockefeller University
2023-2024
Shepherd University
2023
University of Edinburgh
2020
Aarhus University
2020
St. Jude Children's Research Hospital
2004
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate...
Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free is therefore ultimate, but sadly still unachieved goal a multitude research projects. Despite ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near genome eukaryotes. Whilst working towards improved datasets fully evaluation curation actively used to bridge this shortcoming significantly reduce...
Abstract Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) provide key insights into evolution 1,2 . Here we generate analyse reference genomes of platypus ( Ornithorhynchus anatinus ) echidna Tachyglossus aculeatus ), which represent two monotreme lineages. The nearly complete genome assembly has anchored almost entire onto chromosomes, markedly improving continuity gene annotation. Together with our sequence, species allow...
Abstract Numerous novel adaptations characterise the radiation of notothenioids, dominant fish group in freezing seas Southern Ocean. To improve understanding evolution this iconic group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups radiation, including five long-read assemblies. We present a estimate onset at 10.7 million years ago, based on time-calibrated phylogeny derived from genome-wide sequence data. identify two-fold variation size,...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such only available a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling most accurate genomes date. Here we summarize these developments, introduce set quality standards, present lessons...
Abstract Background The king scallop, Pecten maximus, is distributed in shallow waters along the Atlantic coast of Europe. It forms basis a valuable commercial fishery and plays key role coastal ecosystems food webs. Like other filter feeding bivalves it can accumulate potent phytotoxins, to which has evolved some immunity. molecular origins this immunity are interest evolutionary biologists, pharmaceutical companies, fisheries management. Findings Here we report genome assembly species,...
Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding final with Hi-C data produced highly contiguous 1.01 Gb 99.75% scaffolds assembled pseudochromosomes representing seven...
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis the unique physiological and ecological traits enabling these species to thrive in diverse habitats remains largely unknown. Additionally, many populations have drastically declined due anthropogenic activities past two centuries, their recovery is a high global conservation priority. We generated analyzed high-quality reference genomes for leatherback (...
Programmed DNA loss is a gene silencing mechanism that employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to high content repeats duplications corresponding lack highly accurate contiguous assemblies for regions. Here, we present an improved assembly sea lamprey (Petromyzon marinus) genome was generated...
Abstract Neutrophils play fundamental roles in innate immune response, shape adaptive immunity, and are a potentially causal cell type underpinning genetic associations with system traits diseases. Here, we profile the binding of myeloid master regulator PU.1 primary neutrophils across nearly hundred volunteers. We show that variants associated differential underlie genetically-driven differences count susceptibility to autoimmune inflammatory integrate these results other multi-individual...
Sex-limited polymorphism has evolved in many species including our own. Yet, we lack a detailed understanding of the underlying genetic variation and evolutionary processes at work. The brood parasitic common cuckoo (
Abstract We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, unique putatively chemosensory tentacles. More than 69% both genomes are composed repeats, retrotransposons being most abundant. identify 1,150 orthogroups that to enriched functions in olfaction detection chemical signals. There 379 signatures positive selection on caecilian lineages...
Abstract The dugong (Dugong dugon) is a marine mammal widely distributed throughout the Indo-Pacific and Red Sea, with Vulnerable conservation status, little known about many of more peripheral populations, some which are thought to be close extinction. We present de novo high-quality genome assembly for from an individual belonging well-monitored Moreton Bay population in Queensland, Australia. Our uses long-read PacBio HiFi sequencing Omni-C data following Vertebrate Genome Project...
<ns4:p>We present a genome assembly from clonal population of <ns4:italic>Eimeria tenella</ns4:italic> Houghton parasites<ns4:italic> </ns4:italic>(Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The sequence is 53.25 megabases in span. entire scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.</ns4:p>
We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The sequence is 2.44 gigabases in span. majority of the scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This assembly, mRatBN7.2, represents new reference for R. has been adopted by Genome Reference Consortium.
The taxonomic classification of a falcon population found in the Mongolian Altai region Asia has been heavily debated for two centuries and previous studies have inconclusive, hindering more informed conservation approach. Here, we generated chromosome-level gyrfalcon reference genome using Vertebrate Genomes Project (VGP) assembly pipeline. Using whole sequences 49 falcons from different species populations, including "Altai" falcons, analyzed their structure, admixture patterns,...
The safety, quality and supply of donor-derived platelet units intended for transfusion have improved over the past decades but significant problems still remain. In vitroderived platelets offer a possible alternative up-scaling production is hindered by our limited understanding thrombopoiesis (the release their mother cell, megakaryocyte [MK]). Here, we developed an integrated strategy aiming to mimic ex vivo bone marrow physiological niche that promotes mature MKs. screening panel 259...
Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, remain relatively enigmatic, many aspects of their biology evolution unexplored. Key questions include whether undergo sexual reproduction, the nature relationship between tetraploid diploid lineages. While few high-quality microsporidian genomes currently exist to help answer such questions, large-scale biodiversity genomics initiatives, as...
We present a genome assembly from an individual female Salmo trutta (the brown trout; Chordata; Actinopteri; Salmoniformes; Salmonidae). The sequence is 2.37 gigabases in span. majority of the scaffolded into 40 chromosomal pseudomolecules. Gene annotation this on Ensembl has identified 43,935 protein coding genes.
Abstract Numerous novel adaptations characterise the radiation of notothenioids, dominant fish group in freezing seas Southern Ocean. To improve understanding evolution this iconic group, we generated and analysed new genome assemblies for 24 species covering all major subgroups radiation. We present a estimate onset at 10.7 million years ago, based on time-calibrated phylogeny derived from genome-wide sequence data. identify two-fold variation size, driven by expansion multiple transposable...
Abstract Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates rays) hold a key phylogenetic position to explore the origin diversifications of jawed vertebrates. Here, we report integrate reference genomic, transcriptomic morphological data in small-spotted catshark Scyliorhinus canicula shed light on evolution sensory organs. We first characterise general aspects genome, confirming high conservation genome organisation across cartilaginous fishes, investigate population genomic...
Abstract Cartilaginous fishes (chondrichthyans: chimaeras and elasmobranchs -sharks, skates rays) hold a key phylogenetic position to explore the origin diversifications of jawed vertebrates. Here, we report integrate reference genomic, transcriptomic morphological data in small-spotted catshark Scyliorhinus canicula shed light on evolution sensory organs. We first characterise general aspects genome, confirming high conservation genome organisation across cartilaginous fishes, investigate...
With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for wide range organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale an emerging wild animal model carcinogenesis, California sea lion (Zalophus californianus). Short-read were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), long-read three types (Hi-C, optical maps 10X linked...