Genomics

  • Article |

    Genetic analyses of teosinte, the wild ancestor of maize, identify a locus (THP9) that is associated with high seed protein content and increased nitrogen-use efficiency, suggesting that THP9 could have applications in crop breeding.

    • Yongcai Huang
    • , Haihai Wang
    •  & Yongrui Wu
  • Article
    | Open Access

    RNA sequencing reveals widespread transcriptomic changes across the cerebral cortex in autism spectrum disorder, including primary sensory regions, in addition to association regions, as well as an attenuation of regional identity.

    • Michael J. Gandal
    • , Jillian R. Haney
    •  & Daniel H. Geschwind
  • Article
    | Open Access

    A study examining DNA transfer from mitochondria to the nucleus using whole-genome sequences from 66,083 people shows that this is an ongoing dynamic process in normal cells with distinct roles in different types of cancer.

    • Wei Wei
    • , Katherine R. Schon
    •  & Patrick F. Chinnery
  • Article
    | Open Access

    Sequencing of individual human lymphocyte clones shows that they are highly prone to mutations, with higher burdens in memory cells than in naive cells arising from mutational processes associated with differentiation and tissue residency.

    • Heather E. Machado
    • , Emily Mitchell
    •  & Peter J. Campbell
  • Article |

    cis-RNA editing quantitative trait loci, which are associated with immunogenic double-stranded RNAs, underlie genome-wide association study variants in common autoimmune and inflammatory diseases.

    • Qin Li
    • , Michael J. Gloudemans
    •  & Jin Billy Li
  • Article
    | Open Access

    High-quality diploid assemblies of potato genomes from 24 wild and 20 cultivated potatoes provide insights into the complex evolution and diversity of potatoes, and could have applications in the breeding of hybrid potatoes.

    • Dié Tang
    • , Yuxin Jia
    •  & Sanwen Huang
  • Article
    | Open Access

    A precise catalogue of more than 19 million variants from 838 tomato genomes, including 32 new reference-level genome assemblies, advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

    • Yao Zhou
    • , Zhiyang Zhang
    •  & Sanwen Huang
  • Article |

    The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.

    • Christoph Neumayr
    • , Vanja Haberle
    •  & Alexander Stark
  • Article
    | Open Access

    Haematopoiesis has high clonal diversity up to about 65 years of age, after which diversity drops precipitously owing to positive selection acting on a handful of clones that expand exponentially throughout adulthood.

    • Emily Mitchell
    • , Michael Spencer Chapman
    •  & Peter J. Campbell
  • Article
    | Open Access

    A study of 21,879 families with rare genetic diseases identifies 12 with 2- to 7-fold excess of germline mutations, most of which are due to DNA repair defects or exposure to mutagenic chemotherapy, although most individuals with a hypermutated genome will not have a genetic disease.

    • Joanna Kaplanis
    • , Benjamin Ide
    •  & Matthew Hurles
  • Article |

    Analyses of single-cell whole-genome sequencing data show that somatic mutations are increased in the brain of individuals with Alzheimer’s disease compared to neurotypical individuals, with a pattern of genomic damage distinct from that of normal ageing.

    • Michael B. Miller
    • , August Yue Huang
    •  & Christopher A. Walsh
  • Article
    | Open Access

    Whole-genome sequencing is used to analyse the landscape of somatic mutation in intestinal crypts from 16 mammalian species, revealing that rates of somatic mutation inversely scale with the lifespan of the animal across species.

    • Alex Cagan
    • , Adrian Baez-Ortega
    •  & Iñigo Martincorena
  • Article |

    A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.

    • Eeshit Dhaval Vaishnav
    • , Carl G. de Boer
    •  & Aviv Regev
  • Article |

    A study describes single-cell characterization of the human cerebrovasculature, revealing human-specific transcriptomic signatures and providing insights into transcriptional changes associated with Huntington’s disease.

    • Francisco J. Garcia
    • , Na Sun
    •  & Myriam Heiman
  • Article
    | Open Access

    Analyses of circulating cell-free RNA (cfRNA) in blood samples from pregnant mothers identify changes in gene expression that could be used in liquid biopsy tests to identify and monitor individuals who are at risk of preeclampsia.

    • Mira N. Moufarrej
    • , Sevahn K. Vorperian
    •  & Stephen R. Quake
  • Article
    | Open Access

    A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.

    • Yucheng Wang
    • , Mikkel Winther Pedersen
    •  & Eske Willerslev
  • Article |

    Whole-genome sequencing analysis of somatic mutations in liver samples from patients with chronic liver disease identifies driver mutations in metabolism-related genes such as FOXO1, and shows that these variants frequently exhibit convergent evolution.

    • Stanley W. K. Ng
    • , Foad J. Rouhani
    •  & Peter J. Campbell
  • Article
    | Open Access

    A comprehensive survey of the epigenome from 45 regions of the mouse cortex, hippocampus, striatum, pallidum and olfactory areas using single-nucleus DNA methylation sequencing enables identification of 161 cell clusters with distinct locations and projection targets and provides insights into the regulatory landscape underlying neuronal diversity and spatial regulation.

    • Hanqing Liu
    • , Jingtian Zhou
    •  & Joseph R. Ecker
  • Article |

    Whole-genome sequencing of haematopoietic colonies from human fetuses reveals the somatic mutations acquired by individual progenitors, which are used as barcodes to construct a phylogenetic tree of blood development.

    • Michael Spencer Chapman
    • , Anna Maria Ranzoni
    •  & Ana Cvejic
  • Article
    | Open Access

    A revised, universal nomenclature for the vertebrate genes that encode the oxytocin and vasopressin–vasotocin ligands and receptors will improve our understanding of gene evolution and facilitate the translation of findings across species.

    • Constantina Theofanopoulou
    • , Gregory Gedman
    •  & Erich D. Jarvis
  • Article |

    NanoSeq is used to detect mutations in single DNA molecules and analyses show that mutational processes that are independent of cell division are important contributors to somatic mutagenesis.

    • Federico Abascal
    • , Luke M. R. Harvey
    •  & Iñigo Martincorena
  • Article
    | Open Access

    The complete assembly of human chromosome 8 resolves previous gaps and reveals hidden complex forms of genetic variation, enabling functional and evolutionary characterization of primate centromeres.

    • Glennis A. Logsdon
    • , Mitchell R. Vollger
    •  & Evan E. Eichler
  • Article |

    Single-cell analysis of genomes from primary human breast tumours and cell lines shows that chromosomal aberrations continue to evolve during primary tumour expansion, resulting in a milieu of subclones within the tumour.

    • Darlan C. Minussi
    • , Michael D. Nicholson
    •  & Nicholas E. Navin
  • Article |

    Phylogenies of human placental cells based on whole-genome sequencing of bulk samples and microdissections reveal extensive mutagenesis in placental tissue, and suggest that mosaicism is a typical part of normal placental development.

    • Tim H. H. Coorens
    • , Thomas R. W. Oliver
    •  & Sam Behjati
  • Article |

    Siberian mammoth genomes from the Early and Middle Pleistocene subepochs reveal adaptive changes and a key hybridization event, highlighting the value of deep-time palaeogenomics for studies of speciation and long-term evolutionary trends.

    • Tom van der Valk
    • , Patrícia Pečnerová
    •  & Love Dalén
  • Article
    | Open Access

    The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

    • John T. Lovell
    • , Alice H. MacQueen
    •  & Jeremy Schmutz
  • Article
    | Open Access

    A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

    • Axel Meyer
    • , Siegfried Schloissnig
    •  & Manfred Schartl
  • Article
    | Open Access

    New reference genomes of the two extant monotreme lineages (platypus and echidna) reveal the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution.

    • Yang Zhou
    • , Linda Shearwin-Whyatt
    •  & Guojie Zhang
  • Article |

    Ancient DNA reveals genetic differences between stone-tool users and people associated with ceramic technology in the Caribbean and provides substantially lower estimates of population sizes in the region before European contact.

    • Daniel M. Fernandes
    • , Kendra A. Sirak
    •  & David Reich
  • Article |

    A high-throughput, chromosome-wide analysis of DNA looping reveals its contribution to the organization of chromatin, and provides insight into how nucleosomes are deposited and organised de novo.

    • Aakash Basu
    • , Dmitriy G. Bobrovnikov
    •  & Taekjip Ha
  • Article
    | Open Access

    Chromosome-scale sequence assemblies of 20 diverse varieties of barley are used to construct a first-generation pan-genome, revealing previously hidden genetic variation that can be used by studies aimed at crop improvement

    • Murukarthick Jayakodi
    • , Sudharsan Padmarasu
    •  & Nils Stein