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, …
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, …
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 …
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 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 …
Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures
The human Y chromosome is among the most structurally dynamic chromosomes in the human genome, yet much of its diversity remains unresolved because of extensive palindromes, …
Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes
Telomere-to-telomere (T2T) genome assemblies now provide a complete representation of genomic sequences, enabling unprecedented exploration of non-B DNA structures—secondary …
How and why ampliconic genes survive on the human Y chromosome
The mammalian Y chromosome presents an evolutionary paradox: despite its lack of recombination and propensity for degeneration, it retains multi-copy genes essential for male …
