Patterns of Transposable Element Variations in the Human Pangenome Reference Consortium v.1 Dataset
Single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes
Non-canonical (non-B) DNA secondary structures, e.g., G-quadruplexes and triplex DNA, are mutation hotspots and genome regulators contributing to disease and evolution. Yet they …
Protocol for Duplex Sequencing of Mitochondrial DNA in Single Human Oocytes
Oocytes are densely packed with mitochondria, the energy-producing organelles that contain their own genome, mitochondrial DNA (mtDNA). Each cell contains multiple copies of mtDNA, …
Nuclear Mitochondrial Sequences in Great Ape Telomere-to-Telomere Genomes
Mitochondrial sequences have integrated into the nuclear genome since the origin of eukaryotes. Recent insertions that retain homology to extant mitochondrial DNA (mtDNA), termed …
The complete genome of a songbird
Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, …
A Complete Genome for the Common Marmoset
The common marmoset is a New World monkey (NWM) commonly used as a model organism to investigate questions in primate evolution and human disease, including Alzheimers and other …
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation
A pangenome reference overcomes the inherent limitation of any individual reference genome by integrating the variation present in a population. We present the Human Pangenome …
Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches
Progress has been made in identifying G-quadruplexes (G4s) and other non-canonical (non-B) DNA structures in live cells. However, these experiments have been limited by …
The Vertebrate Genomes Project Phase I: A global reference genome resource
The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species1. Organized in four phases, it …
Variation and selection at predicted G-quadruplexes across the human pangenome
G-quadruplexes (G4s), non-canonical DNA structures whose sequence motifs occupy approximately 1% of the human genome, are important for myriad cellular functions, including …
