Genomics articles within Nature Communications

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  • Article
    | Open Access

    Differential impact of genetic and environmental influences on DNA methylation may result in sex- and age-related physiological variation and disease susceptibility. By analysing DNA methylome of 2,603 individuals from twin families, here, the authors establish a catalogue of between-individual variation in DNA methylation.

    • Jenny van Dongen
    • , Michel G. Nivard
    •  & Dorret I. Boomsma

  • Article
    | Open Access

    Nitrogen fixation in oceans is facilitated by associations between marine phytoplankton and cyanobacteria such as UCYN-A. Here, Cornejo-Castillo et al. show that UCYN-A diversified in the late Cretaceous under strong purifying selection to become lineage-specific symbiont partners with different prymnesiophytes.

    • Francisco M. Cornejo-Castillo
    • , Ana M. Cabello
    •  & Silvia G. Acinas

  • Article
    | Open Access

    Nuclear bodies can nucleate at sites of active transcription and are beneficial for efficient gene expression. Here, the authors show that Cajal bodies, a prominent type of nuclear body, contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

    • Qiuyan Wang
    • , Iain A. Sawyer
    •  & Miroslav Dundr

  • Article
    | Open Access

    Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.

    • Felix M. Key
    • , Qiaomei Fu
    •  & Aida M. Andrés

  • Article
    | Open Access

    The human genome is highly organized, with one-dimensional chromatin states packaged into higher level three-dimensional architecture. Here, the authors present EpiTensor that can identify 3D spatial associations from 1D epigenetic information.

    • Yun Zhu
    • , Zhao Chen
    •  & Wei Wang

  • Article
    | Open Access

    Helitron elements are proposed rolling-circle transposons in eukaryotic genomes, but experimental evidence for their transposition has been lacking. Here, Grabundzija et al. reconstruct an active Helitron from bats which they name Helraiser, and characterize its mechanism of transposition in cell-free reactions and in human cell cultures in vitro.

    • Ivana Grabundzija
    • , Simon A. Messing
    •  & Zoltán Ivics

  • Article
    | Open Access

    It is feared that reprogramming may introduce DNA mutations. Here Bhutani et al. take three different reprogramming methods and using comparative whole genome analyses do identify nucleotide variations that are different in reprogrammed cells from the original fibroblasts, but none convey oncogenic potential.

    • Kunal Bhutani
    • , Kristopher L. Nazor
    •  & Jeanne F. Loring

  • Article
    | Open Access

    Ticks transmit a large number of pathogens that cause human diseases. Here, the authors sequence the genome of the tick Ixodes scapularisand uncover expansion of genes associated with parasitic processes unique to ticks and tick-host interactions.

    • Monika Gulia-Nuss
    • , Andrew B. Nuss
    •  & Catherine A. Hill

  • Article
    | Open Access

    The common bedbug is a pest for humans, yet its molecular biology is poorly understood. Here, the authors sequence the common bedbug genome and profile gene expression across all life stages to show major changes in gene expression after feeding on human blood.

    • Jeffrey A. Rosenfeld
    • , Darryl Reeves
    •  & Christopher E. Mason

  • Article
    | Open Access

    Trichinellosis is a globally important food-borne disease caused by roundworms of the Trichinella complex. Here the authors present genomic sequences representing all 12 recognized Trichinellaspecies and genotypes, and reconstruct their phylogeny and biogeography.

    • Pasi K. Korhonen
    • , Edoardo Pozio
    •  & Robin B. Gasser

  • Article
    | Open Access

    The great tit (Parus major) is known for its complex social-cognitive behaviour. Here, the authors sequence genomes of the great tit and show genes related to learning and cognition in regions under positive selection, as well as neuronal non-CpG methylation patterns similar to those observed in mammals.

    • Veronika N. Laine
    • , Toni I. Gossmann
    •  & Martien A. M. Groenen

  • Article
    | Open Access

    Toxoplasma gondii is a parasite that causes zoonotic infections in humans. Here, the authors identify tandem amplification and diversification of secretory pathogenesis determinants in the T. gondiigenome and show that clade-specific inheritance of conserved haploblocks enriched for these determinants shapes population structure.

    • Hernan Lorenzi
    • , Asis Khan
    •  & L. David Sibley

  • Article
    | Open Access

    RNA interference inadvertently represses off-target transcripts. Here, Lee et al.report that substituting nucleotide in position 6 of the seed region of the small interfering RNAs with abasic spacers can significantly decrease miRNA-like off-target repression while preserving on-target activity.

    • Hye-Sook Lee
    • , Heeyoung Seok
    •  & Sung Wook Chi

  • Article
    | Open Access

    Environmental DNA from unculturable microorganisms contains genes with useful functions that remain difficult to identify and isolate. Here Colin, Kintses et al.demonstrate the screening of millions of samples in pL volumes to directly identify new enzymatic activities and complements sequence-based approaches.

    • Pierre-Yves Colin
    • , Balint Kintses
    •  & Florian Hollfelder

  • Article
    | Open Access

    Unravelling the molecular basis of hypertension remains a major challenge. Here, the authors identify the transcription factor GATA5 as a novel regulator of blood pressure and potential genetic determinant of human hypertension and describe a unique mouse model for research of salt-sensitive hypertension.

    • Smail Messaoudi
    • , Ying He
    •  & Mona Nemer

  • Article
    | Open Access

    Genetic and environmental factors affect genome-wide patterns of epigenetic variation. Here, the authors show that while current habitat and historical lifestyle impact the methylome of rainforest hunter-gatherers and sedentary farmers, the biological functions affected and the degree of genetic control differ.

    • Maud Fagny
    • , Etienne Patin
    •  & Lluis Quintana-Murci

  • Article
    | Open Access

    Geckos are small, agile reptiles with nocturnal habits. Here, the authors sequence the genome of the Schlegel’s Japanese Gecko and reveal gene family expansions and reductions associated with formation of adhesive setae, nocturnal vision, tail regeneration, and diversification of olfactory sensation.

    • Yan Liu
    • , Qian Zhou
    •  & Xiaosong Gu

  • Article
    | Open Access

    Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.

    • Marius Roesti
    • , Benjamin Kueng
    •  & Daniel Berner

  • Article
    | Open Access

    In intergenic trans-splicing, exons from two independent primary transcripts are joined. Here, the authors show that evolutionarily trans-splicing activity in insects is tightly controlled, with mod(mdg4)being a unique case of functional diversification involving trans-splicing.

    • Yimeng Kong
    • , Hongxia Zhou
    •  & Xuan Li

  • Article
    | Open Access

    Sesame is a valuable oilseed crop with a small diploid genome and high seed-oil content making it an attractive model for genetic studies. Here, Wei et al.sequence more than 705 sesame varieties and perform a genome-wide association study to identify genes associated with important agronomic traits.

    • Xin Wei
    • , Kunyan Liu
    •  & Xiurong Zhang

  • Article
    | Open Access

    The burying beetle shows flexible parenting behaviour. Here, the authors show that offspring fare equally well regardless of the sex or number of parents present and find similar gene expression profiles in uniparental and biparental females and in uniparental males, which suggests no specialization in parenting.

    • Darren J. Parker
    • , Christopher B. Cunningham
    •  & Allen J. Moore

  • Article
    | Open Access

    How genetic variation contributes to brain morphology is still poorly understood. Here Chenet al. combine brain imaging with single-nucleotide polymorphism data to discover that a substantial degree of cortical variation is derived from underlying genetic differences.

    • Chi-Hua Chen
    • , Qian Peng
    •  & Anders M. Dale

  • Article
    | Open Access

    Anaplastic oligodendrogliomas are rare and incurable primary brain tumours with few treatment options. Here Labrecheet al. perform whole-exome sequencing and identify recurring mutations in transcription factor TCF12, which are associated with aggressive tumours.

    • Karim Labreche
    • , Iva Simeonova
    •  & Michel Wager

  • Article
    | Open Access

    Adverse drug reactions are an important clinical problem. Here the authors combine information about drug-induced gene expression changes and genetic variability of patients with a genome-scale metabolic model to identify drug-induced changes in cellular metabolism that may be linked to drug side effects.

    • Daniel C. Zielinski
    • , Fabian V. Filipp
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.

    • Linnéa Smeds
    • , Vera Warmuth
    •  & Hans Ellegren

  • Article
    | Open Access

    Kelps are ecologically and economically important seaweeds. Here the authors sequence the genome of Saccharina japonicato gain insights into the evolutionary adaptation of polysaccharide biosynthesis, iodine concentration and antioxidation mechanisms and the population genetics of kelp domestication.

    • Naihao Ye
    • , Xiaowen Zhang
    •  & Fangqing Zhao

  • Article
    | Open Access

    Horizontal gene transfer is important for bacterial evolution but the molecular basis of its fitness costs remain unclear. Here the authors show that fitness costs produced by a plasmid in P. aeruginosaare alleviated by mutations in recently acquired genes encoded in mobile genetic elements.

    • Alvaro San Millan
    • , Macarena Toll-Riera
    •  & R. Craig MacLean

  • Article |

    Characterizing mammalian gene expression regulation by enhancer elements is complicated by the size and complexity of the genome. Here Vanhille et al.demonstrate CapStarr-Seq, a novel high-throughput method for assessing potential enhancers and deciphering the mechanisms regulating transcription

    • Laurent Vanhille
    • , Aurélien Griffon
    •  & Salvatore Spicuglia

  • Article |

    Basal-like breast cancer is a heterogeneous disease with poor prognosis; however, its cellular origins and aetiology are poorly understood. Here the authors provide evidence that ID4 is a key controller of mammary stem/progenitor cell self-renewal, acting upstream of Notch signalling to repress luminal fate commitment.

    • Simon Junankar
    • , Laura A. Baker
    •  & Alexander Swarbrick

  • Article
    | Open Access

    Efficacy of anticancer treatments vary across patients, imposing a need for personalized approaches. Here the authors show that responsiveness to chemotherapy can be predicted using tumour explant cultures in a patient-matched microenvironment, coupled with a machine-learning algorithm.

    • Biswanath Majumder
    • , Ulaganathan Baraneedharan
    •  & Pradip K. Majumder

  • Article
    | Open Access

    Suppression of MutS HOMOLOGUE 1 (MSH1), a plant protein targeted to mitochondria and plastids, causes a variety of phenotypes. Here Virdi et al. show that MSH1 depletion in Arabidopsisresults in heritable changes in nuclear DNA methylation, which can lead to enhanced growth vigour.

    • Kamaldeep S. Virdi
    • , John D. Laurie
    •  & Sally A. Mackenzie

  • Article
    | Open Access

    Epigenetic changes associated with post-natal differentiation have been characterized. Here the authors generate epigenomic and transcriptional profiles from primary human breast cells, providing insights into the transcriptional and epigenetic events that define post-natal cell differentiation in vivo.

    • Philippe Gascard
    • , Misha Bilenky
    •  & Martin Hirst

  • Article
    | Open Access

    Many loci in the mammalian genome are intermediately methylated. Here, by comprehensively identifying these loci and quantifying their relationship with gene activity, the authors show that intermediate methylation is an evolutionarily conserved epigenomic signature of gene regulation.

    • GiNell Elliott
    • , Chibo Hong
    •  & Joseph F. Costello

  • Article
    | Open Access

    Pheochromocytomas and paragangliomas (PCCs/PGLs) are rare neuroendocrine tumours with a significant genetic component. Here, the authors carry out a multi-omic integrative characterization of PCC/PGL and reveal potential genomic alterations and regulatory mechanisms involved in the disease.

    • Luis Jaime Castro-Vega
    • , Eric Letouzé
    •  & Anne-Paule Gimenez-Roqueplo

  • Article |

    Body plan complexity is associated with the number of different cell types, yet the processes that create this diversity are unclear. Here the authors use transcriptomics to test the hypothesis that unlike cancer cells, novel normal cell types arise through sub-specialization of an ancestral cell type.

    • Cong Liang
    • , Alistair R.R. Forrest
    •  & Günter P. Wagner

  • 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

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