Genomics articles within Nature

Featured

  • Letter
    | Open Access

    The genome of Ectocarpus siliculosis, a model for the study of brown algae, has been sequenced. These seaweeds are complex photosynthetic organisms that have adapted to rocky coastal environments. Genome analysis sheds light on this adaptation, revealing an extended set of light-harvesting and pigment biosynthesis genes, and new metabolic processes such as halide metabolism. Comparative analyses are also significant with respect to the evolution of multicellularity in plants, animals and brown algae.

    • J. Mark Cock
    • , Lieven Sterck
    •  & Patrick Wincker

  • Letter |

    Transcriptional enhancers are segments of regulatory DNA located some distance from the coding region of a gene, and several of them may sometimes serve apparently redundant functions. These authors demonstrate in Drosophila that such 'redundant' enhancers, by contributing higher overall levels of transcription, ensure robustness of phenotypes against both genetic and environmental perturbations, for example mutations in other genes or temperature changes that would otherwise lead to aberrant development.

    • Nicolás Frankel
    • , Gregory K. Davis
    •  & David L. Stern

  • News |

    A technology that simultaneously reads a DNA sequence and its crucial modifications makes its debut.

    • Alla Katsnelson

  • Letter |

    The topologies of, and spatial relationships between, chromosomes are important but poorly understood. Here, a high-throughput method is used to study intra- and inter-chromosomal interactions in Saccharomyces cerevisiae. A map of the haploid genome is generated at kilobase resolution, and is used to construct a three-dimensional model of the yeast genome. The findings provide a glimpse of the interface between the form and function of a eukaryotic genome.

    • Zhijun Duan
    • , Mirela Andronescu
    •  & William S. Noble

  • News & Views |

    A challenge in biology is to understand complex traits, which are influenced by many genetic variants. Studies in yeast provide the prospect of analysing such genetic variation in detail in other organisms, including humans.

    • David B. Goldstein
    •  & Mohamed A. F. Noor

  • Letter |

    Mutations in mitochondrial DNA (mtDNA) are a common cause of human genetic disease. It has been shown in non-human primates that nuclear transfer techniques might be an approach to prevent the transmission of mtDNA mutations. The proof of principle has now been extended to human embryos. Pronuclei were transferred between human zygotes, which developed onwards to the blastocyst stage in vitro. Carry-over of mtDNA from the donor zygotes to the recipients was minimal.

    • Lyndsey Craven
    • , Helen A. Tuppen
    •  & Douglass M. Turnbull

  • Letter
    | Open Access

    Studies of identical twins are widely used to dissect the contributions of genes and the environment to human diseases. In multiple sclerosis, an autoimmune demyelinating disease, identical twins often show differences. This might suggest that environmental effects are most significant in this case, but genetic and epigenetic differences between identical twins have been described. Here, however, studies of identical twins show no evidence for genetic, epigenetic or transcriptome differences that could explain disease discordance.

    • Sergio E. Baranzini
    • , Joann Mudge
    •  & Stephen F. Kingsmore

  • Letter |

    'Horizontal gene transfer' refers to the passage of genetic material between non-mating species. Transposable elements (transposons) may be especially prone to horizontal gene transfer, but the mechanisms by which they can spread across diverged species have been elusive. Here it is shown that transposons can spread by hitchhiking in the genomes of parasites. The amount of DNA that can be transferred in this way underscores the impact of horizontal gene transfer on genome evolution.

    • Clément Gilbert
    • , Sarah Schaack
    •  & Cédric Feschotte

  • Opinion |

    Looking back over the past decade of human genomics, Francis Collins finds five key lessons for the future of personalized medicine — for technology, policy, partnerships and pharmacogenomics.

    • Francis Collins

  • Editorial |

    Nearly a decade on from the completion of the draft sequence of the human genome, researchers should work with the same intensity and focus to apply the results to health.

  • Opinion |

    Genomic data will soon become a commodity; the next challenge — linking human genetic variation with physiology and disease — will be as great as the one genomicists faced a decade ago, says J. Craig Venter.

    • J. Craig Venter

  • Opinion |

    There is little to show for all the time and money invested in genomic studies of cancer, says Robert Weinberg — and the approach is undermining tried-and-tested ways of doing, and of building, science. This Opinion piece is part of a linked pair; see also Counterpoint: Data First by Todd Golub.

    • Robert Weinberg

  • Books & Arts |

    Bringing genetic information into health care is welcome but its utility in the clinic needs to be rigorously reviewed, caution Muin J. Khoury, James Evans and Wylie Burke.

    • Muin J. Khoury
    • , James Evans
    •  & Wylie Burke

  • News Feature |

    What was it like to participate in the fastest, fiercest research race in biology? Alison Abbott talks to some of the genome competitors about the rivalries and obstacles they faced then — and now.

    • Alison Abbott

  • Column |

    The Human Genome Project attracted investment beyond what a rational analysis would have predicted. There are pros and cons to that, says Philip Ball.

    • Philip Ball

  • Letter
    | Open Access

    The genome of the black truffle - one of the most popular truffles on the market - has been sequenced. This is the first genome of a symbiotic ascomycete to be analysed. Comparison with the genome of another ectomycorrhizal symbiotic fungus indicates that a genetic predisposition to symbiosis evolved differently in ascomycetes and basidiomycetes. The study also offers insight into fungal sex and fruiting.

    • Francis Martin
    • , Annegret Kohler
    •  & Patrick Wincker

  • Letter
    | Open Access

    Ancient mitochondrial DNA from a hominin individual who lived in the mountains of Central Asia between 48,000–30,000 years ago has been sequenced. Comparative genomics suggest that this mitochondrial DNA derives from an out-of-Africa migration distinct from the ones that gave rise to Neanderthals and modern humans. It also seems that this hominin lived in close spatio-temporal proximity to Neanderthals and modern humans.

    • Johannes Krause
    • , Qiaomei Fu
    •  & Svante Pääbo

  • Article
    | Open Access

    Fungi from the genus Fusarium are important pathogens of animals and crop plants. Some have a wide host range, whereas others are more specific in the organisms they infect. Here, clues are provided as to how differences in specificity come about. The genomes of two Fusarium fungi with differing host ranges have been sequenced, and compared with the genome of a third species. Experiments show that transferring two whole chromosomes turns a non-pathogenic Fusarium strain into a pathogenic one.

    • Li-Jun Ma
    • , H. Charlotte van der Does
    •  & Martijn Rep

  • Letter |

    Here, sequencing has been used to characterize the mRNA fraction of the transcriptome in Caucasian individuals, to provide a fine-scale view of transcriptomes and to identify genetic variants that affect alternative splicing. Measuring allele-specific expression identified rare expression quantitative trait loci (eQTLs) and allelic differences in transcript structure, revealing new properties of genetic effects on the transcriptome.

    • Stephen B. Montgomery
    • , Micha Sammeth
    •  & Emmanouil T. Dermitzakis

  • Article
    | Open Access

    Deep metagenomic sequencing and characterization of the human gut microbiome from healthy and obese individuals, as well as those suffering from inflammatory bowel disease, provide the first insights into this gene set and how much of it is shared among individuals. The minimal gut metagenome as well as the minimal gut bacterial genome is also described.

    • Junjie Qin
    • , Ruiqiang Li
    •  & Jun Wang

  • News Feature |

    The bold ambitions of one institute could make China the world leader in genome sequencing. David Cyranoski asks if its science will survive the industrial ramp-up.

    • David Cyranoski

  • Article |

    The transcriptome of Helicobacter pylori, an important human pathogen involved in gastric ulcers and cancer, is presented. The approach establishes a model for mapping and annotating the primary transcriptomes of many living species.

    • Cynthia M. Sharma
    • , Steve Hoffmann
    •  & Jörg Vogel

  • Article |

    The genome of the wild grass Brachypodium distachyon (Brachypodium), a member of the Pooideae subfamily, is sequenced. The Pooideae are one of three subfamilies of grasses that provide the bulk of human nutrition and may become major sources of renewable energy. Availability of the genome sequence should help establish Brachypodium as a model for developing new energy and food crops.

    • John P. Vogel
    • , David F. Garvin
    •  & Ivan Baxter

  • Books & Arts |

    The director of the US National Institutes of Health, Francis Collins, calls for a revolution in personalized medicine. Such advances should be shared beyond the developed world, says Abdallah S. Daar.

    • Abdallah S. Daar

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