Bernard Kim
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View article: Predicting the functional impact of single nucleotide variants in <i>Drosophila melanogaster</i> with FlyCADD
Predicting the functional impact of single nucleotide variants in <i>Drosophila melanogaster</i> with FlyCADD Open
Understanding how genetic variants drive phenotypic differences is a major challenge in molecular biology. Single nucleotide polymorphisms form the vast majority of genetic variation and play critical roles in complex, polygenic phenotypes…
View article: Highly contiguous assemblies of 101 drosophilid genomes
Highly contiguous assemblies of 101 drosophilid genomes Open
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for severa…
View article: Strong bias in long-read sequencing prevents assembly of <i>Drosophila melanogaster</i> Y-linked genes
Strong bias in long-read sequencing prevents assembly of <i>Drosophila melanogaster</i> Y-linked genes Open
Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio) are generally considered free from sequence composition bias, a key factor - alongside read length - that explains their success in producing high quality genome assemblie…
View article: Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in <i>Drosophila melanogaster</i> euchromatin
Manual validation finds only ultra-long long-read sequencing enables faithful, population-level structural variant calling in <i>Drosophila melanogaster</i> euchromatin Open
The increasing accessibility of long-read sequencing and the rapid development of automated variant callers are promoting the generation of population-level structural variation data. However, the effect of the length of long-reads on auto…
View article: Comparative gene annotation of 304 species of Drosophilidae
Comparative gene annotation of 304 species of Drosophilidae Open
High-quality genome annotations are essential if we are to address central questions in comparative genomics, such as the origin of new genes, the drivers of genome size variation, and the evolutionary forces shaping gene content and struc…
View article: Predicting the functional impact of single nucleotide variants in <i>Drosophila melanogaster</i> with FlyCADD
Predicting the functional impact of single nucleotide variants in <i>Drosophila melanogaster</i> with FlyCADD Open
Understanding how genetic variants drive phenotypic differences is a major challenge in molecular biology. Single nucleotide polymorphisms form the vast majority of genetic variation and play critical roles in complex, polygenic phenotypes…
View article: Strong sequencing bias in Nanopore and PacBio prevents assembly of <i>Drosophila melanogaster</i> Y-linked genes
Strong sequencing bias in Nanopore and PacBio prevents assembly of <i>Drosophila melanogaster</i> Y-linked genes Open
Nanopore and PacBio are generally considered free from sequence composition bias, a key factor – alongside read length – that explains their success in producing high quality genome assemblies. However, our study reveals a systematic failu…
View article: Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years
Double trouble: two retrotransposons triggered a cascade of invasions in Drosophila species within the last 50 years Open
View article: Evolutionary adaptation under climate change: <i>Aedes</i> sp. demonstrates potential to adapt to warming
Evolutionary adaptation under climate change: <i>Aedes</i> sp. demonstrates potential to adapt to warming Open
Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, promoting expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their war…
View article: Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids
Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids Open
Metazoan parasites have played a major role in shaping innate immunity in animals. Insect hosts and parasitoid wasps are excellent models for illuminating how animal innate immune systems have evolved to neutralize these enemies. One such …
View article: Genomics of a sexually selected sperm ornament and female preference in Drosophila
Genomics of a sexually selected sperm ornament and female preference in Drosophila Open
View article: Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids
Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids Open
The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on…
View article: DNA extraction and Nanopore library prep for ultralong-reads v1
DNA extraction and Nanopore library prep for ultralong-reads v1 Open
This protocol is optimized for rapid and cost-effective (about $150) genome assembly of Drosophila species from laboratory lines using ONT PromethION sequencers. Following this protocol, a typical Drosophila Nanopore sequencing run should …
View article: Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
Structural genomic variation and behavioral interactions underpin a balanced sexual mimicry polymorphism Open
View article: Unraveling the genomic diversity and admixture history of captive tigers in the United States
Unraveling the genomic diversity and admixture history of captive tigers in the United States Open
Genomic studies of endangered species have primarily focused on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investigated gen…
View article: Evolutionary adaptation under climate change:<i>Aedes</i>sp. demonstrates potential to adapt to warming
Evolutionary adaptation under climate change:<i>Aedes</i>sp. demonstrates potential to adapt to warming Open
Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their …
View article: Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life Open
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost…
View article: Retracing the horizontal transfer of a novel innate immune factor in<i>Drosophila</i>
Retracing the horizontal transfer of a novel innate immune factor in<i>Drosophila</i> Open
Summary Immune systems are among the most dynamically evolving traits across the tree of life, and long-lived macroparasites play an outsized role in shaping animal immunity. Even without adaptive immunity, insects have evolved potent inna…
View article: Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism
Complex structural variation and behavioral interactions underpin a balanced sexual mimicry polymorphism Open
Summary How phenotypic diversity originates and persists within populations are classic puzzles in evolutionary biology. While polymorphisms hypothesized to be under balancing selection segregate within many species, it remains rare for th…
View article: Enrichment of hard sweeps on the X chromosome compared to autosomes in six <i>Drosophila</i> species
Enrichment of hard sweeps on the X chromosome compared to autosomes in six <i>Drosophila</i> species Open
The X chromosome, being hemizygous in males, is exposed one-third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enr…
View article: Decoupled evolution of the <i>Sex Peptide</i> gene family and <i>Sex Peptide Receptor</i> in Drosophilidae
Decoupled evolution of the <i>Sex Peptide</i> gene family and <i>Sex Peptide Receptor</i> in Drosophilidae Open
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accele…
View article: Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life
Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life Open
Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost…
View article: DNA extraction and Nanopore library prep from single flies v1
DNA extraction and Nanopore library prep from single flies v1 Open
This protocol is optimized for rapid and cost-effective (about $150) genome assembly of Drosophila species from single flies using ONT PromethION sequencers. Following this protocol, a typical Drosophila Nanopore sequencing run should have…
View article: DNA extraction and Nanopore library prep from 15-30 whole flies- V.3.2 v1
DNA extraction and Nanopore library prep from 15-30 whole flies- V.3.2 v1 Open
This protocol is optimized for rapid and cost-effective (about $150) genome assembly of Drosophila species from laboratory lines using ONT PromethION sequencers. Following this protocol, a typical Drosophila Nanopore sequencing run should …
View article: Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species
Rapid evolutionary diversification of the flamenco locus across simulans clade Drosophila species Open
Suppression of transposable elements (TEs) is paramount to maintain genomic integrity and organismal fitness. In D . melanogaster , the flamenco locus is a master suppressor of TEs, preventing the mobilization of certain endogenous retrovi…
View article: Genome Report: chromosome-scale genome assembly of the African spiny mouse (<i>Acomys cahirinus</i>)
Genome Report: chromosome-scale genome assembly of the African spiny mouse (<i>Acomys cahirinus</i>) Open
There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality referenc…
View article: Decoupled evolution of the<i>Sex Peptide</i>gene family and<i>Sex Peptide Receptor</i>in<i>Drosophilidae</i>
Decoupled evolution of the<i>Sex Peptide</i>gene family and<i>Sex Peptide Receptor</i>in<i>Drosophilidae</i> Open
Across internally fertilising species, males transfer ejaculate proteins that trigger wide-ranging changes in female behaviour and physiology. Much theory has been developed to explore the drivers of ejaculate protein evolution. The accele…
View article: Enrichment of hard sweeps on the X chromosome compared to autosomes in six<i>Drosophila</i>species
Enrichment of hard sweeps on the X chromosome compared to autosomes in six<i>Drosophila</i>species Open
The X chromosome, being hemizygous in males, is exposed one third of the time increasing the visibility of new mutations to natural selection, potentially leading to different evolutionary dynamics than autosomes. Recently, we found an enr…
View article: Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States
Unraveling the Genomic Diversity and Admixture History of Captive Tigers in the United States Open
Genomic studies of rare and endangered species have focused broadly on describing diversity patterns and resolving phylogenetic relationships, with the overarching goal of informing conservation efforts. However, few studies have investiga…
View article: Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae
Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae Open
Herbivorous insects are exceptionally diverse, accounting for a quarter of all known eukaryotic species, but the genomic basis of adaptations that enabled this dietary transition remains poorly understood. Many studies have suggested that …