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Ancient genomes can inform our understanding of the history of human adaptation through the direct tracking of changes in genetic variant frequency across different geographical locations and time periods. The authors review recent ancient DNA analyses of human, archaic hominin, pathogen, and domesticated animal and plant genomes, as well as the insights gained regarding past human evolution and behaviour.
Advances in genome sequencing, editing and synthetic biology have enhanced the feasibility of large-scale genome engineering, termed genome writing. In this Opinion article, Chari and Church discuss the strengths and limitations of diverse strategies for genome writing, including extensively modifying existing genomes versus synthesizing genomesde novo, and they provide future visions for writing large genomes.
Recent microbiome genome-wide association studies have identified numerous associations between human genetic variants and the gut microbiome. Here, the authors review how genetic variation in the host can alter the composition of the gut microbiome towards a disease state, with a focus on disorders of immunity and metabolism.
Cell state transitions during embryonic development are associated with epigenetic changes that alter chromatin structure and gene expression. Interplay between epigenetic regulatory layers can be studied using genomic technologies and embryonic stem cell cultures that reflectin vivocell states.
For clinical cases of Mendelian disease that lack a genetic diagnosis, genome and exome sequencing are increasingly used for seeking the genetic cause. This Review discusses the strategies and computational tools for prioritizing the many genetic variants identified in each genome into those that are most likely to be causal for disease. The authors discuss how diverse types of biochemical, evolutionary, pedigree and clinical-phenotype information are used, and they highlight common pitfalls to be aware of for responsible variant prioritization.
The differentiation of an organism into a male or female phenotype is a critical developmental process, but the mechanisms that control this decision are remarkably evolutionarily labile. This Review discusses the wide diversity of vertebrate sex-determination mechanisms, their rapid evolution under different forms of genetic and environmental control and the over-arching principles that are shared despite this mechanistic diversity.
The last 25 years has seen a revolution in sequencing, with more than 100 vertebrate genome sequences now available. In this Review, Meadows and Lindblad-Toh discuss how the genomics of non-human organisms can provide insights into vertebrate biology and conservation, and how they can contribute to the understanding of human health and disease.
Recent studies have provided insights into the sources of endogenous replication stress, which can result in DNA damage, checkpoint activation and genome-wide replication fork slowing. The authors review established mechanisms involved in the replication stress response, and propose a new model that reconciles data gained from different cellular models.
Saccharomyces cerevisiaehas become an important model organism in the field of evolutionary genomics. Comparative genomic analysis of laboratory, wild and domesticated yeast populations is generating insights into how new species form and how populations adapt to their environments.
