ORCID Profile
0000-0001-8843-3596
Current Organisations
Eidgenössische Technische Hochschule Zürich
,
EMBL-EBI
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Publisher: Oxford University Press (OUP)
Date: 06-2017
DOI: 10.1093/GBE/EVX115
Publisher: Cold Spring Harbor Laboratory
Date: 11-06-2019
DOI: 10.1101/668384
Abstract: The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been h ered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo PacBio assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb. The development of a high-resolution linkage map confirmed the global chromosome organization and the linear order of genomic segments along the chromosomes. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few interchromosomal but frequent intrachromosomal rearrangements. The improved assembly makes the analysis of previously intractable large-scale structural variation more feasible allowing, for ex le, the detection of a 7.8 Mb inversion on chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations from the northern and southern parts of the species distribution. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation in the Atlantic herring.
Publisher: American Society for Microbiology
Date: 19-01-2017
Abstract: Providencia rettgeri is an opportunistic bacterial pathogen of clinical significance due to its association with urinary tract infections and multidrug resistance. Here, we report the first complete genome sequence of P. rettgeri . The genome of strain RB151 consists of a 4.8-Mbp chromosome and a 108-kbp bla NDM-1 -positive plasmid.
Publisher: Cold Spring Harbor Laboratory
Date: 23-05-2020
DOI: 10.1101/2020.05.22.110833
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and bio ersity conservation. However, such assemblies are only available for a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, hibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2019
Abstract: The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been h ered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for ex le, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation.
Publisher: Oxford University Press (OUP)
Date: 08-11-2018
DOI: 10.1093/NAR/GKY1113
Publisher: Informa UK Limited
Date: 11-2011
DOI: 10.4161/MGE.19153
Publisher: eLife Sciences Publications, Ltd
Date: 23-03-2017
DOI: 10.7554/ELIFE.22510
Abstract: The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.
Publisher: Cold Spring Harbor Laboratory
Date: 09-06-2022
DOI: 10.1101/2022.06.08.494096
Abstract: Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use long-read sequencing data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Finally, we show that both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.
Publisher: Oxford University Press (OUP)
Date: 11-2022
DOI: 10.1093/NAR/GKAC958
Abstract: Ensembl (www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global bio ersity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.
Publisher: Cold Spring Harbor Laboratory
Date: 12-2022
DOI: 10.1101/2022.12.01.518724
Abstract: The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications 1–3 . As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished 4, 5 . Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029 base pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, revealing the complete liconic structures of TSPY , DAZ , and RBMY gene families 41 additional protein-coding genes, mostly from the TSPY family and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a prior assembly of the CHM13 genome 4 and mapped available population variation, clinical variants, and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
Publisher: F1000 Research Ltd
Date: 13-05-2021
DOI: 10.12688/WELLCOMEOPENRES.16838.1
Abstract: We present a genome assembly from an in idual female Salmo trutta (the brown trout Chordata Actinopteri Salmoniformes Salmonidae). The genome sequence is 2.37 gigabases in span. The majority of the assembly is scaffolded into 40 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 43,935 protein coding genes.
Publisher: Oxford University Press (OUP)
Date: 02-11-2020
DOI: 10.1093/NAR/GKAA942
Abstract: The Ensembl project (www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download files and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large bio ersity sequencing projects. Our SARS-CoV-2 genome browser (covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
Publisher: The Royal Society
Date: 12-08-2009
Abstract: Horizontal gene transfer (HGT) plays a significant role in microbial evolution. It can accelerate the adaptation of an organism, it can generate new metabolic pathways and it can completely remodel an organism's genome. We examine 27 closely related genomes from the YESS group of gamma proteobacteria and a variety of four-taxon datasets from a erse range of prokaryotes in order to explore the kinds of effects HGT has had on these organisms.
Publisher: Springer Science and Business Media LLC
Date: 28-04-2021
DOI: 10.1038/S41586-021-03451-0
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and bio ersity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Publisher: Oxford University Press (OUP)
Date: 22-11-2013
Location: United States of America
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Leanne Haggerty.