Genomics articles within Nature Communications

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  • Article
    | Open Access

    The analysis of mammalian transcriptomes could provide new insights into human biology. Here the authors carry out RNA sequencing in a large collection of mouse tissues and compare these data to human transcriptome profiles, identifying a set of constrained genes that carry out basic cellular functions with remarkably constant expression levels across tissues and species.

    • Dmitri D. Pervouchine
    • , Sarah Djebali
    •  & Thomas R. Gingeras

  • Article |

    The structure of insect odorant receptors (ORs) has remained elusive due to their lack of homology to other proteins and the inability to obtain OR crystals. Here, the authors use amino acid evolutionary covariation patterns to fold these proteins de novoand generate the first three-dimensional models of insect ORs.

    • Thomas A. Hopf
    • , Satoshi Morinaga
    •  & Richard Benton

  • Article
    | Open Access

    The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.

    • Shengfeng Huang
    • , Zelin Chen
    •  & Anlong Xu

  • Article
    | Open Access

    The correct assembly of genomes from sequencing data remains a challenge due to difficulties in correctly assigning the location of repeated DNA elements. Here the authors describe GRAAL, an algorithm that utilizes genome-wide chromosome contact data within a probabilistic framework to produce accurate genome assemblies.

    • Hervé Marie-Nelly
    • , Martial Marbouty
    •  & Romain Koszul

  • Article
    | Open Access

    Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. In this study, the authors use RNA sequencing analyses to characterize differences in the transcriptome between autistic and typically developing brains.

    • Simone Gupta
    • , Shannon E. Ellis
    •  & Dan E. Arking

  • Article
    | Open Access

    The expansion of Bantu agriculturalists 3,800 years ago in sub-Saharan Africa established first contact with Khoisan hunter-gatherers living in parts of Southern Africa. Sequencing the genomes of five Namibian-Khoisan hunter-gatherers and one Bantu individual tells a tale of admixture and isolation in the early history of modern human populations.

    • Hie Lim Kim
    • , Aakrosh Ratan
    •  & Stephan C. Schuster

  • Article |

    Molecular and functional differences between induced pluripotent stem cells (iPSCs) derived from distinct cell types have been described. Here the authors show, by comparing human iPSCs derived from fibroblasts or cord blood, that the competence in activating developmental genes upon differentiation is influenced by the donor cell of origin.

    • Jong-Hee Lee
    • , Jung Bok Lee
    •  & Mickie Bhatia

  • Article
    | Open Access

    Knowing which genetic variants exist on either parental chromosome requires diploid human genomes to be phased. Here the authors generate haplotype-resolved genomes and identify a large diversity of haploid and diploid gene forms, a common diplotypic proteome, and an abundance of cisconfigurations of mutations, highlighting the functional importance of diploidy.

    • Margret R. Hoehe
    • , George M. Church
    •  & Thomas Huebsch

  • Article |

    Epigenomes are thought to retain molecular memories of their developmental history. Here, by comparing differentially methylated regions of genomes from different cells, the authors reveal an epigenetic signature that underlies a shared gene regulatory network with a common developmental origin.

    • Rebecca F. Lowdon
    • , Bo Zhang
    •  & Jeffrey B. Cheng

  • Article |

    Genome editing has yet to be performed in non-bilaterian phyla. Here, Ikmi et al. develop techniques to use both TALEN and CRISPR/Cas9 in the sea anemone, Nematostella vectensis, and further leverage a locus expressing an endogenous fluorescent protein as a landing site for homologous recombination-mediated transgenesis.

    • Aissam Ikmi
    • , Sean A. McKinney
    •  & Matthew C. Gibson

  • Article
    | Open Access

    The large yellow croaker, Larimichthys crocea, is an economically important marine fish in China. Here, the authors sequence the draft genome of a wild large yellow croaker and highlight genes that may have played a role in the development of innate immunity in this species.

    • Changwen Wu
    • , Di Zhang
    •  & Yun Liu

  • Article
    | Open Access

    Mungbean is a fast-growing and warm-season legume crop, cultivated mainly in Asia. Here, the authors sequence the genomes of both wild and domesticated mungbean varieties and, together with detailed transcriptome data, provide insight into mungbean domestication, polyploidization and speciation.

    • Yang Jae Kang
    • , Sue K. Kim
    •  & Suk-Ha Lee

  • Article
    | Open Access

    Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.

    • Andrew D. W. Geering
    • , Florian Maumus
    •  & Pierre-Yves Teycheney

  • Article
    | Open Access

    The jujube is a major dry fruit crop in China and is commonly used for medicinal purposes. Here the authors sequence the genome and transcriptome of the most widely cultivated jujube cultivar, Dongzao, and highlight the genetic and molecular basis of agronomically important jujube traits, such as vitamin C content.

    • Meng-Jun Liu
    • , Jin Zhao
    •  & Long-Hai Luo

  • Article
    | Open Access

    Recent advances in high-throughput sequencing techniques have enabled the analysis of ancient human genomes. Here the authors sequence ancient human genomes that span a period of 5,000 years, to understand the ancestral influence on Europe's genetic landscape.

    • Cristina Gamba
    • , Eppie R. Jones
    •  & Ron Pinhasi

  • Article |

    Comparative genomics can provide valuable insights on adaptations to hostile environments. Here, the authors sequence the genomes and transcriptomes of the Bactrian camel, dromedary and alpaca, to reveal the demographic history of the group as well as metabolic adaptations to the desert environment.

    • Huiguang Wu
    • , Xuanmin Guang
    •  & Jun Wang

  • Article
    | Open Access

    Populations of the cave fish Astyanax mexicanus exhibit a variety of traits that evolved repeatedly and independently from its surface counterparts. Here the authors present a de novo genome assembly for A. mexicanusand identify candidate genes for eye loss and reduced pigmentation.

    • Suzanne E. McGaugh
    • , Joshua B. Gross
    •  & Wesley C. Warren

  • Article |

    Chloroplasts originate from endosymbiosis between a cyanobacterium and a eukaryotic mitochondriate ancestor. Here, the authors show that the plastid ancestor is related to a cyanobacterial lineage that include N2-fixing filamentous cyanobacteria and species with specialized nitrogen-fixing cells.

    • Jesús A. G. Ochoa de Alda
    • , Rocío Esteban
    •  & Jean Houmard

  • Article
    | Open Access

    The African chironomid midge, Polypedilum vanderplanki, is able to withstand extreme desiccation. Here the authors sequence the genomes of a desiccation-tolerant and desiccation-sensitive species of chironomid midge and pinpoint genes that may have a role in conferring resistance to desiccation.

    • Oleg Gusev
    • , Yoshitaka Suetsugu
    •  & Takahiro Kikawada

  • Article
    | Open Access

    Kinases activated by gene fusions represent potentially important targets for the development of cancer drugs. Here, the authors develop a method for detecting gene fusion events in RNA sequencing data from The Cancer Genome Atlas and identify several novel recurrent fusions involving kinases.

    • Nicolas Stransky
    • , Ethan Cerami
    •  & Christoph Lengauer

  • Article
    | Open Access

    Butterflies and moths (Lepidoptera) vary in chromosome number. Here, the authors sequence the genome of the Glanville fritillary butterfly, Melitaea cinxia, show it has the ancestral lepidopteran karyotype and provide insight into how chromosomal fusions have shaped karyotype evolution in butterflies and moths.

    • Virpi Ahola
    • , Rainer Lehtonen
    •  & Ilkka Hanski

  • Article
    | Open Access

    Genetic variation in Mycobacterium tuberculosiscomplex (MTBC) bacteria is responsible for differences in factors such as virulence and transmissibility. Here, the authors analyse the genomes of 1,601 MTBC isolates from diverse geographic locations and identify 62 SNPs that may be used to resolve lineages and sublineages of these strains.

    • Francesc Coll
    • , Ruth McNerney
    •  & Taane G. Clark

  • Article |

    Nanoparticles can be used for therapeutic and diagnostic purposes. Here, the authors report that nanoparticles made of a single chemical building block, called nanoporphyrins, incorporate eight different functionalities, including various types of imaging, drug delivery and cancer therapy.

    • Yuanpei Li
    • , Tzu-yin Lin
    •  & Kit S. Lam

  • Article
    | Open Access

    Protein biomarkers could play an important role in the diagnosis and management of diseases. Here the authors investigate the impact of genetic, clinical and lifestyle factors on 92 protein biomarkers for cancer and inflammation and suggest that personalized biomarker thresholds should be used in cancer management.

    • Stefan Enroth
    • , Åsa Johansson
    •  & Ulf Gyllensten

  • Article
    | Open Access

    The advancement of sensitive, accurate and non-invasive methods to identify the allergen that drives allergic disease in an individual remains a challenge. Here, the authors develop a synthetic biology approach using human designer cells to profile allergic reactions against an array of allergens measuring histamine release from whole blood.

    • David Ausländer
    • , Benjamin Eggerschwiler
    •  & Martin Fussenegger

  • Article
    | Open Access

    The identification of genes that control economically important traits is an essential step towards crop improvement. Here the authors sequence the genome of the wild soybean and, through a combined genetic and functional approach, identify a new gene affecting salt tolerance in soybean.

    • Xinpeng Qi
    • , Man-Wah Li
    •  & Hon-Ming Lam

  • Article |

    Helicobacter pylori chronically infects humans, and this is associated with high mutation and recombination rates in the bacterium. Here the authors provide evidence that genome evolution in H. pyloriduring acute infection of the host is orders of magnitude faster than any previously determined mutation rates in bacteria.

    • Bodo Linz
    • , Helen M. Windsor
    •  & Barry J. Marshall

  • Article |

    The blind mole rat (BMR), Spalax galili, is perfectly adapted to life underground. Here, the authors sequence the BMR genome and transcriptome and highlight genomic features that may have played a role in adaptation to extreme underground stressors, such as darkness hypercapnia and hypoxia.

    • Xiaodong Fang
    • , Eviatar Nevo
    •  & Jun Wang

  • Article
    | Open Access

    Plant colonization of land is an important evolutionary event. Here, the authors sequence the genome of a filamentous terrestrial alga and, through a comparative analysis with related algae and land plant species, provide insight into how aquatic algae adapted to terrestrial environments.

    • Koichi Hori
    • , Fumito Maruyama
    •  & Hiroyuki Ohta

  • Article
    | Open Access

    Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

    • Shengyi Liu
    • , Yumei Liu
    •  & Andrew H Paterson

  • Article
    | Open Access

    Horizontal gene transfer occurs in most bacteria, yet it is unclear whether it happens in clonal species. Here, Everitt et al. show widespread within-species recombination, driven by mobile elements, in the genome of the pathogen Staphylococcus aureus, but no recombination between closely related strains.

    • Richard G. Everitt
    • , Xavier Didelot
    •  & Daniel J. Wilson

  • Article
    | Open Access

    Rice false smut, caused by the pathogenic ascomycete fungus Ustilaginoidea virens (Cooke) Takah, has a significant economic impact on crop production. Here, Zhang et al. report the draft genome sequence of U. virensand provide insight into the evolution of genes involved in pathogenicity and adaptation to a biotrophic and floret-infecting lifestyle.

    • Yong Zhang
    • , Kang Zhang
    •  & Wenxian Sun

  • Article
    | Open Access

    Common tobacco (Nicotiana tabacum) is a widely cultivated and economically important non-food crop. Here, the authors report the draft genome sequences for three of the most common tobacco varieties and provide insights into the evolution of tobacco through a comparative analysis with closely related species.

    • Nicolas Sierro
    • , James N.D. Battey
    •  & Nikolai V. Ivanov

  • Article
    | Open Access

    Spiders use self-produced venom and silk for their daily survival. Here, the authors report the assembled genome of the social velvet spider and a draft assembly of the tarantula genome and, together with proteomic data, provide insights into the evolution of genes that affect venom and silk production.

    • Kristian W. Sanggaard
    • , Jesper S. Bechsgaard
    •  & Jun Wang

  • Article |

    Mass mortality events of fish and invertebrates are increasingly frequent in coastal zones, yet it is often difficult to identify their causes. Here, the authors provide evidence that a combined field and genomics approach could help identifying the specific cause of mass mortality events.

    • Pierre De Wit
    • , Laura Rogers-Bennett
    •  & Stephen R. Palumbi

  • Article
    | Open Access

    Horizontal transfer of DNA is common among eukaryotes but the vectors involved remain elusive. Here, Gilbert et al. show high frequency of in vivotransposition from the cabbage looper moth into genomes of a baculovirus, suggesting that viruses can act as vectors of horizontal transfer between animals.

    • Clément Gilbert
    • , Aurélien Chateigner
    •  & Richard Cordaux

  • Article
    | Open Access

    Locusts are destructive agricultural pests and serve as a model organism for studies of insects. Here, the authors report a draft genome sequence of the migratory locust, Locusta migratoria, and provide insight into genes associated with key survival traits such as phase-change, long-distance migration and feeding.

    • Xianhui Wang
    • , Xiaodong Fang
    •  & Le Kang

  • Article |

    Little is known about the genes that confer salt tolerance in trees. Here, Ma et al. report the genome sequence of the desert poplar, Populus euphratica, and provide insight into the genetic architecture and adaptation of this salt tolerant desert poplar.

    • Tao Ma
    • , Junyi Wang
    •  & Jianquan Liu

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