Danielle E. Khost
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View article: Combining population genomics with ancient DNA to understand island colonization history of the Madagascar turtle dove
Combining population genomics with ancient DNA to understand island colonization history of the Madagascar turtle dove Open
The Mascarene archipelago (Mauritius, Reunion and Rodrigues), characterized by first human arrival being recent, offers a unique setting to study species colonization. Here we use a combination of modern and ancient DNA data as a case stud…
View article: Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants Open
Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species…
View article: Expanding on Our Knowledge of Ecdysozoan Genomes: A Contiguous Assembly of the Meiofaunal Priapulan <i>Tubiluchus corallicola</i>
Expanding on Our Knowledge of Ecdysozoan Genomes: A Contiguous Assembly of the Meiofaunal Priapulan <i>Tubiluchus corallicola</i> Open
Genomic data for priapulans are limited to a single species, restricting broad comparative analyses and thorough interrogation of questions spanning phylogenomics, ecdysozoan physiology, and development. To help fill this void, we present …
View article: Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in<i>Epiperipatus broadwayi</i>
Sizing Up the Onychophoran Genome: Repeats, Introns, and Gene Family Expansion Contribute to Genome Gigantism in<i>Epiperipatus broadwayi</i> Open
Genome assemblies are growing at an exponential rate and have proved indispensable for studying evolution but the effort has been biased toward vertebrates and arthropods with a particular focus on insects. Onychophora or velvet worms are …
View article: Epiperipatus broadwayi Genome
Epiperipatus broadwayi Genome Open
Supplementary materials for Sato et al. 2022
View article: Evolution of genome structure in the <i>Drosophila simulans</i> species complex
Evolution of genome structure in the <i>Drosophila simulans</i> species complex Open
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genom…
View article: Tetrastigma voinierianum genome assembly and annotation
Tetrastigma voinierianum genome assembly and annotation Open
Genome assembly and annotation of Tetrastigma voinierianum. Citation: Cai, Liming, et al. "Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff.(Rafflesiaceae)." Current Biology 31.5 (2021): 1002-…
View article: Genome assembly and annotation of Sapria himalayana
Genome assembly and annotation of Sapria himalayana Open
Genome assembly and annotation of Sapria himalayana. Annotations are based on MAKER ab initio gene predictions combined with transciptome evidence. Pfam annotation are also provided.
View article: Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade
Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade Open
Satellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know littl…
View article: Evolution of genome structure in the<i>Drosophila simulans</i>species complex
Evolution of genome structure in the<i>Drosophila simulans</i>species complex Open
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genom…
View article: Dynamic evolution of euchromatic satellites on the X chromosome in<i>Drosophila melanogaster</i>and the<i>simulans</i>clade
Dynamic evolution of euchromatic satellites on the X chromosome in<i>Drosophila melanogaster</i>and the<i>simulans</i>clade Open
Satellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know littl…
View article: Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in <i>Drosophila melanogaster</i>
Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in <i>Drosophila melanogaster</i> Open
Highly repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembl…
View article: Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in<i>Drosophila melanogaster</i>
Single molecule long read sequencing resolves the detailed structure of complex satellite DNA loci in<i>Drosophila melanogaster</i> Open
Satellite DNA (satDNA) repeats can make up a large fraction of eukaryotic genomes. These blocks of tandem repeats are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses genome asse…