Genetics articles within Nature Communications

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  • 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

  • Article |

    Palindromic DNA sequences in the genome can cause gross chromosomal rearrangements. Inagaki et al.demonstrate how the pathways of Holliday-junction resolution and antigen-receptor gene rearrangement interact to process cruciform conformation of palindrome DNA into chromosomal translocations in human embryonic kidney cells.

    • Hidehito Inagaki
    • , Tamae Ohye
    •  & Hiroki Kurahashi

  • Article
    | Open Access

    Tillering is a multigenic complex trait that influences grain yield in cereal; however, the molecular network for its regulation remains unclear. Guo et al.show that OsMADS57, a transcription factor controlled by miR444a, interacts with OsTEOSINTE BRANCHED1 and targets DWARF14 to control tillering in rice.

    • Siyi Guo
    • , Yunyuan Xu
    •  & Kang Chong

  • Article
    | Open Access

    The factors that modulate growth rate of the human malaria parasite Plasmodium falciparum remain poorly understood. Here Scherf and collaborators demonstrate that the Plasmodiumsirtuin PfSir2a regulates the transcription of ribosomal DNA, thereby modulating parasite proliferation rate and virulence.

    • Liliana Mancio-Silva
    • , Jose Juan Lopez-Rubio
    •  & Artur Scherf

  • Article
    | Open Access

    Sorghum is a drought-adapted cereal, but the grains have lower digestibility than other cereal crops. This work shows that a low-frequency allele type in the starch metabolic gene pullulanase is associated with increased digestibility, which may help improve sorghum yield and therefore food security.

    • Edward K. Gilding
    • , Celine H. Frère
    •  & Ian D. Godwin

  • Article
    | Open Access

    The Chinese tree shrew, Tupaia belangeri chinensis, has been proposed as a potential animal model in biomedical research and drug safety testing. This study presents the full genome of the Chinese tree shrew, identifying common features between the tree shrew and primates.

    • Yu Fan
    • , Zhi-Yong Huang
    •  & Yong-Gang Yao

  • Article
    | Open Access

    A variant in the IFITM3gene increases the risk of severe influenza, but homozygosity is rare in Caucasians. The authors show that the variant gene is homozygous in 25% of healthy Chinese people, and 69% of those with severe pandemic influenza, suggesting that this gene influences the epidemiology of influenza in South-East Asia.

    • Yong-Hong Zhang
    • , Yan Zhao
    •  & Tao Dong

  • Article
    | Open Access

    The mitochondrial protease CLPP is found in most eukaryotic organisms but its biological role has been unclear. Here Osiewacz and colleagues show that deletion of CLPP extends lifespan of the filamentous fungus Podospora anserina, and that human and fungal CLPP are functionally conserved.

    • Fabian Fischer
    • , Andrea Weil
    •  & Heinz D. Osiewacz

  • Article
    | Open Access

    Plant pathogens encode effector proteins that trigger immunity in plants carrying appropriate resistance genes. Here Qutob et al. show non-Mendelian interactions between naturally occurring Phytophthora sojaealleles that result in transgenerational gene silencing and gain of virulence in soybean plants.

    • Dinah Qutob
    • , B. Patrick Chapman
    •  & Mark Gijzen

  • Article
    | Open Access

    The Prunus mume was domesticated in China over 3,000 years ago and is an important ornamental plant and fruit. Here Qixiang Zhang et al.obtain the first assembly of its genome with a combination of next-generation sequencing, whole-genome mapping and restriction-site-associated DNA.

    • Qixiang Zhang
    • , Wenbin Chen
    •  & Jun Wang

  • Article |

    During embryonic development, midline fluid flow results in asymmetric nodal gene expression. Using genetic manipulations and mathematical modelling, Nakamura et al. find that expression of the nodal antagonist Cerl2 is regulated post-transcriptionally, and that asymmetry is maintained by Wnt-Cerl2 feedback loops.

    • Tetsuya Nakamura
    • , Daisuke Saito
    •  & Hiroshi Hamada

  • Article
    | Open Access

    Genetic modification in insects mostly involves the use of fluorescent markers to identify successful transformation. Here Osanai-Futahashi et al.report a marker system based on changes in melanin pigmentation that allows the identification of genetically modified insects with the naked eye.

    • Mizuko Osanai-Futahashi
    • , Takahiro Ohde
    •  & Hideki Sezutsu

  • Article |

    RNA viruses are known to rapidly evolve new features through errors in replication and reshuffling of genomic segments. These authors report another strategy used by the measles virus to improve infectivity; the cooperation between wild-type and mutant fusion proteins in the same viral particle.

    • Yuta Shirogane
    • , Shumpei Watanabe
    •  & Yusuke Yanagi

  • Article |

    The amount of data supplied by next-generation sequencing technologies presents a challenge for traditional algorithms to detect single-nucleotide polymorphisms. Xu et al.develop an efficient detection program and demonstrate its utility by identifying polymorphisms in cancer genomes and human populations.

    • Feng Xu
    • , Weixin Wang
    •  & Junwen Wang

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