Genetics articles within Nature Communications

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  • Article
    | Open Access

    Tigers are an endangered species and therefore understanding their genetic architecture could aid conservation efforts. Here, the authors report the first genome sequence of the Amur tiger and, through close species comparative genomic analysis, provide insight into the genome organization, evolutionary divergence and diversity of big cats.

    • Yun Sung Cho
    • , Li Hu
    •  & Jong Bhak

  • Article
    | Open Access

    FGFR2 gene variation is associated with breast cancer risk but the molecular mechanism is unknown. Fletcher et al. provide a link between FGFR2 signalling and breast cancer susceptibility by demonstrating that FGFR2 signalling activates the ERa transcriptional network, which drives transcription of risk genes.

    • Michael N. C. Fletcher
    • , Mauro A. A. Castro
    •  & Kerstin B. Meyer

  • Article |

    Mutually exclusive splicing of genes is a mechanism for generating proteome diversity. Here Kollmar et al. determine the mutually exclusive spliced exome of Drosophila melanogaster and reveal insights into its evolutionary history within the Drosophilagroup.

    • Klas Hatje
    •  & Martin Kollmar

  • Article |

    The metabolic reaction catalysed by the isocitrate dehydrogenase 1 (IDH1) enzyme is commonly perturbed in some glioma subtypes due to gain-of-function mutations in the IDH1 gene. Here, Chaumeil et al.present a method that detects mutant IDH1 activity by measuring the levels of different hyperpolarized metabolites produced by wild-type and mutant IDH1.

    • Myriam M. Chaumeil
    • , Peder E. Z. Larson
    •  & Sabrina M. Ronen

  • Article
    | Open Access

    It is still not clear when the introduction of animal domestication in northwestern Europe occurred. Here the authors provide evidence that Mesolithic hunter-gatherers in Northern Germany already possessed domestic pigs, and pigs were present in the region ~500 years earlier than previously thought.

    • Ben Krause-Kyora
    • , Cheryl Makarewicz
    •  & Almut Nebel

  • Article
    | Open Access

    Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).

    • Cindy J. Castelle
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Article |

    The distance that individuals disperse to between birth and first breeding determines the dynamics and genetic composition of natural populations. Here the authors show that in great tits (Parus major), the distance of local dispersal is genetically coupled with exploratory behaviour measured in the lab.

    • Peter Korsten
    • , Thijs van Overveld
    •  & Erik Matthysen

  • Article
    | Open Access

    Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.

    • Volker Winstel
    • , Chunguang Liang
    •  & Guoqing Xia

  • Article |

    MADS-box genes regulate flowering plant development, but their evolutionary origins are unclear. Here, Ruelens et al.show that three major, apparently flowering plant-specific, MADS-box gene clades are derived from a single ancestral tandem duplication, and identify FLOWERING LOCUS C-like genes in cereals.

    • Philip Ruelens
    • , Ruud A. de Maagd
    •  & Kerstin Kaufmann

  • Article
    | Open Access

    The date palm is one of the most economically important plants of the palm family. Here, the authors present a high-quality genome assembly of the date palm Phoenix dactylifera, and reveal insights into the unique sugar metabolism underlying fruit ripening.

    • Ibrahim S. Al-Mssallem
    • , Songnian Hu
    •  & Jun Yu

  • Article |

    Uncovering the factors that influence the generation of copy number variation (CNV) across the genome may increase our understanding of the role of CNVs in disease. Here, Makino et al.provide insights into the mechanisms underlying CNV formation and suggest a method for identifying disease-associated CNVs.

    • Takashi Makino
    • , Aoife McLysaght
    •  & Masakado Kawata

  • Article |

    Clinical trials of γ-secretase inhibitors to treat Alzheimer’s disease show that side effects occur from their non-selective action. Dimitrov et al.show that improved second generation γ-secretase modulators spare cleavage sites of substrate proteins that are implicated in the side effects.

    • Mitko Dimitrov
    • , Jean-René Alattia
    •  & Patrick C. Fraering

  • Article |

    Genetic effects on gene expression by variants at expression quantitative trait loci (eQTLs), can contribute to human genetic diseases. Here, Liet al. present a method to study eQTLs with effects on protein translation on a transcriptome-wide scale.

    • Quan Li
    • , Angeliki Makri
    •  & Hui-Qi Qu

  • Article
    | Open Access

    Telomerase reverse-trancriptase promoter mutations have been recently found in human melanomas. Here, Nault et al.identify telomerase reverse-trancriptase promoter mutations as the most frequent somatic genetic alterations in hepatocellular carcinomas and as the first mutation identified in cirrhotic preneoplastic lesions.

    • Jean Charles Nault
    • , Maxime Mallet
    •  & Jessica Zucman-Rossi

  • Article
    | Open Access

    Transition from a spread panicle typical of ancestral wild rice to the compact panicle of present cultivars was a crucial event in rice domestication. Here the authors show that this panicle architecture is controlled by the transcription factor OsLG1 and that a mutation in its regulatory region led to the compact panicle phenotype.

    • Zuofeng Zhu
    • , Lubin Tan
    •  & Chuanqing Sun

  • Article |

    Chemical modifications of CpG dinucleotides form part of the epigenetic code and various methods for the detection of modified CpG sites exist. Here Kriukiene and colleagues report a complementary method that allows the profiling of unmodified CpG sites within the genome, which they call the 'unmethylome'.

    • Edita Kriukienė
    • , Viviane Labrie
    •  & Saulius Klimašauskas

  • Article
    | Open Access

    Phytophthora infestanscaused the potato famine in the nineteenth century. Martinet al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans.

    • Michael D. Martin
    • , Enrico Cappellini
    •  & M. Thomas P. Gilbert

  • Article
    | Open Access

    Cell lines are widely used in cancer research to study tumour biology. Here Domcke et al.compare genomic data from ovarian cancer cell lines with those from clinical ovarian tumour samples and identify cell lines that most closely resemble the genomic features of high-grade serous ovarian cancer.

    • Silvia Domcke
    • , Rileen Sinha
    •  & Nikolaus Schultz

  • Article
    | Open Access

    DNA double-strand breaks commonly occur in all replicating cells. Wimberly and colleagues show that in non-replicating cells, aborted transcription/translation forms RNA/DNA hybrid R-loops that prime origin-independent replication, leading to DNA breakage, point mutations and chromosomal rearrangements.

    • Hallie Wimberly
    • , Chandan Shee
    •  & P. J. Hastings

  • Article
    | Open Access

    Quantitative trait loci mapping has traditionally been used to discover desirable alleles in plants. In this study, Lyu et al. use a comparative genome approach to identify an allele that is prevalent in upland rice varieties and alters the function of a protein involved in abscisic acid biosynthesis.

    • Jun Lyu
    • , Shilai Zhang
    •  & Wen Wang

  • Article
    | Open Access

    Mutations in the E3 ubiquitin ligase parkin are associated with juvenile Parkinson’s disease. Here the authors report the solution structure of the Parkin RING2 domain, revealing how disease-associated mutations affect its function and providing a molecular explanation for the recessive nature of the disease.

    • Donald E. Spratt
    • , R Julio Martinez-Torres
    •  & Gary S. Shaw

  • Article |

    Red algae form one of the most ancient eukaryotic lineages, and have undergone multiple symbioses. Here, Price et al. report the first genome sequence for a mesophilic red alga, and reveal significant differences between these organisms and hyperthermopilic algae.

    • Debashish Bhattacharya
    • , Dana C. Price
    •  & Hwan Su Yoon

  • Article |

    Dehydrated hereditary stomatocytosis is a genetic condition in which the permeability of red blood cells to cations in increased. Albuisson and colleagues find that mutations in the mechanically-activated PIEZO1 ion channel are the major cause of the disease and result in more slowly inactivating currents.

    • Juliette Albuisson
    • , Swetha E Murthy
    •  & Ardem Patapoutian

  • Article
    | Open Access

    5,000 years ago, the Minoans established the first advanced civilization of Europe, but their origin remains unclear. Here the authors show that the Minoans were a European population, genetically similar to other ancient European populations and to the present inhabitants of the island of Crete.

    • Jeffery R. Hughey
    • , Peristera Paschou
    •  & George Stamatoyannopoulos

  • Article
    | Open Access

    The endemic Tibetan antelope is adapted to high-altitude environments with low partial pressure of oxygen and high level of ultraviolet radiation. Here Ge et al. report a draft genome of this species and by comparison with other mammals, present possible genetic bases of highland adaptation.

    • Ri-Li Ge
    • , Qingle Cai
    •  & Jian Wang

  • Article |

    Differentiated genomic regions among conserved loci, known as speciation islands, are believed to form because of reduced inter-population gene flow near loci under divergent selection. Renault et al.show that reduced recombination, rather than slower gene flow, accounts for the formation of these regions in sunflowers.

    • S. Renaut
    • , C. J. Grassa
    •  & L. H. Rieseberg

  • Article |

    With paleovirology it is possible to identify ancient endogenous viral elements within eukaryotic genomes. Here Suh and colleagues report a genomic record of hepatitis endogenizations through bird’s evolution; they find a complete hepatitis genome sequence, the first discovery of a Mesozoic paleovirus genome.

    • Alexander Suh
    • , Jürgen Brosius
    •  & Jan Ole Kriegs

  • Article |

    Here, Brotherton and colleagues sequence 39 mitochondrial genomes from ancient human remains. They track population changes across Central Europe and find that the foundations of the European mitochondrial DNA pool were formed during the Neolithic rather than the post-glacial period.

    • Paul Brotherton
    • , Wolfgang Haak
    •  & Janet S. Ziegle

  • Article |

    Even though both embryonic stem cells and primordial germ cells express pluripotency markers, they differ in their developmental potential. Maeda et al. show that, in embryonic stem cells, the Myc family member Max mediates epigenetic repression of genes involved in germ cell development.

    • Ikuma Maeda
    • , Daiji Okamura
    •  & Yasuhisa Matsui

  • Article
    | Open Access

    Cyanobacterial symbionts of marine diatoms can localize intracellularly or externally to their host partners. Here Hilton et al. describe the genomes of two diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont affects expression of nitrogen assimilation genes.

    • Jason A. Hilton
    • , Rachel A. Foster
    •  & Tracy A. Villareal

  • Article
    | Open Access

    HNF1B is overexpressed in the clear cell subtype and epigenetically silenced in the serous subtype of ovarian cancer. Pearce and colleagues now show that genetic variants in HNF1B are differentially associated with risks of developing these two cancer subtypes, possibly through an epigenetic mechanism.

    • Hui Shen
    • , Brooke L. Fridley
    •  & Celeste Leigh Pearce

  • Article
    | Open Access

    The wild rice species can be used as germplasm resources for this crop’s genetic improvement. Here Chen and colleagues report the de novo sequencing of the O. brachyanthagenome, and identify the origin of genome size variation, the role of gene movement and its implications on heterochromatin evolution in the rice genome.

    • Jinfeng Chen
    • , Quanfei Huang
    •  & Mingsheng Chen

  • Article
    | Open Access

    Expansion of polyglutamines correlates with neuronal death in Huntington’s disease. Here the authors show that, in haploid yeast cells, the toxic effect of polyglutamine expression is associated with the disruption of the septin ring and cells may escape from toxicity by hyperploidization.

    • Christoph J.O. Kaiser
    • , Stefan W. Grötzinger
    •  & Klaus Richter

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