Genome articles within Nature Communications

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  • Article
    | Open Access

    Maize was domesticated from wild lowland progenitors that co-existed with upland subspecies in Southwestern Mexico. Here Yang et al. use a meta-assembly approach to assemble an upland mexicana genome and find evidence of introgression suggesting it contributed to modern maize adaptation

    • Ning Yang
    • , Xi-Wen Xu
    •  & Jianbing Yan

  • Article
    | Open Access

    Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here Ichikawa et al perform de novo long-read genome assembly of three inbred medaka strains, and report long-range structure of centromeres and their methylation as well as correlation of structural variants with differential gene expression.

    • Kazuki Ichikawa
    • , Shingo Tomioka
    •  & Shinich Morishita

  • Article
    | Open Access

    Bivalve molluscs have evolved various characteristics to adapt to benthic filter-feeding. Here, Li et al investigate the genome, transcriptomes and proteomes of scallop Chlamys farreri, revealing evidences of molecular adaptations to semi-sessile life and neurotoxins.

    • Yuli Li
    • , Xiaoqing Sun
    •  & Zhenmin Bao

  • Article
    | Open Access

    The repertoire of tissue-specific distal regulators of gene transcription enhancers defines homeostasis or disease. Here, the authors reveal the enhancer and super-enhancer signature of vascular smooth muscle cells under normal and angiotensin II stimuli, providing new insight into the transcriptional regulation of vascular pathologies.

    • Sadhan Das
    • , Parijat Senapati
    •  & Rama Natarajan

  • Article
    | Open Access

    The detection of structural variants can be difficult with short-read sequencing technology, especially when variants are highly complex. Here, the authors use a MinION nanopore sequencer to analyse two patient genomes and develop NanoSV to map known and novel structural variants in long read data.

    • Mircea Cretu Stancu
    • , Markus J. van Roosmalen
    •  & Wigard P. Kloosterman

  • Article
    | Open Access

    Cancer driver mutations can occur within noncoding genomic sequences. Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.

    • Matteo D′Antonio
    • , Donate Weghorn
    •  & Kelly A Frazer

  • Article
    | Open Access

    Spinach is an economically important vegetable crop but previous genomic resources were of limited use for comparative and functional analyses. Here, Xuet al. present a high quality draft spinach genome and transcriptome data for multiple Spinaciaaccessions providing insight into Caryophyllales genome evolution.

    • Chenxi Xu
    • , Chen Jiao
    •  & Quanhua Wang

  • Article
    | Open Access

    Biomphalaria glabrata is a fresh water snail that acts as a host for trematode Schistosoma mansoni that causes intestinal infection in human. This work describes the genome and transcriptome analyses from 12 different tissues of B glabrata, and identify genes for snail behavior and evolution.

    • Coen M. Adema
    • , LaDeana W. Hillier
    •  & Richard K. Wilson

  • Article
    | Open Access

    In ancient cultures without a writing system, it is difficult to infer the basis of status and rank. Here the authors analyse ancient DNA from nine presumed elite individuals buried successively over a 300-year period at Chaco Canyon, and show evidence of matrilineal relationships.

    • Douglas J. Kennett
    • , Stephen Plog
    •  & George H. Perry

  • Article
    | Open Access

    Fission yeastSchizosaccharomyces pombe has diverse traits. Jeffares et al. characterize large copy number variations (CNVs) and rearrangements in S. pombe, and show that CNVs are transient with effects on quantitative traits and gene expression, whereas rearrangements influence intrinsic reproductive isolation.

    • Daniel C. Jeffares
    • , Clemency Jolly
    •  & Fritz J. Sedlazeck

  • Article
    | Open Access

    Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleraceareference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits

    • Agnieszka A. Golicz
    • , Philipp E. Bayer
    •  & David Edwards

  • Article
    | Open Access

    Japanese morning glory (Ipomoea nil) has diverse flowering traits. Here, the authors describe the reference genome sequence of I. nil, annotations of genes and transposons, and compare evolution of the I. nilgenome to other Convolvulaceae and Solanales genomes.

    • Atsushi Hoshino
    • , Vasanthan Jayakumar
    •  & Yasubumi Sakakibara

  • Article
    | Open Access

    Tarsiers occupy a key node between strepsirrhines and anthropoids in the primate phylogeny. Here, Warren and colleagues present the genome of Tarsius syrichta, including a survey of transposable elements, an unusual mitochondrial insertion, and evidence for positive gene selection.

    • Jürgen Schmitz
    • , Angela Noll
    •  & Wesley C. Warren

  • Article
    | Open Access

    Analysis of cancer genome sequencing data has been used to predict genes associated with the pathogenesis of cancer. Here, the authors propose a new algorithm entitled RUBIC that predicts breaks in DNA as opposed to previously published methods that predict amplifications and deletions of DNA.

    • Ewald van Dyk
    • , Marlous Hoogstraat
    •  & Lodewyk F. A. Wessels

  • Article
    | Open Access

    Copper (Cu) is an essential mineral nutrient but high concentrations in rice grain can cause toxicity. Here the authors provide evidence that natural variation in rice grain Cu concentration is caused by altered sequestration of Cu into root vacuoles due to a single amino acid substitution in the OsHMA4 transporter.

    • Xin-Yuan Huang
    • , Fenglin Deng
    •  & Jian Feng Ma

  • Article
    | Open Access

    Short-read sequencing has inherent limitations in the characterisation of long repeat elements. Shi and Guo et al.combine single-molecule real-time sequencing and IrysChip to construct a Chinese reference genome that fills many gaps in the reference genome, and identify novel spliced genes.

    • Lingling Shi
    • , Yunfei Guo
    •  & Kai Wang

  • Article
    | Open Access

    It has been increasingly recognised that tumours are not made up of a homogeneous population of cells. Here, the authors show heterogeneous expression of five protein markers in renal cell cancer and demonstrate that the progression of the tumour does not influence the degree of heterogeneity in the tumour.

    • Rouven Hoefflin
    • , Bernd Lahrmann
    •  & Stefan Duensing

  • Article
    | Open Access

    Clinical RNA-seq datasets can predict clinical outcomes. Here, Shen et al. report a statistical method for survival analysis of mRNA isoform variation using clinical RNA-seq datasets, and the identified isoform based survival predictors outperform gene expression based survival predictors using TCGA data on six cancer types.

    • Shihao Shen
    • , Yuanyuan Wang
    •  & Yi Xing

  • Article
    | Open Access

    The T300A substitution in ATG16L is associated with Crohn’s disease risk and disrupts clearance of intracellular pathogens by autophagy. Here the authors show that the mutation impairs interaction of ATG16L with TMEM59 and disrupts unconventional TMEM-induced autophagy, an aspect of innate immunity.

    • Emilio Boada-Romero
    • , Inmaculada Serramito-Gómez
    •  & Felipe X. Pimentel-Muiños

  • Article
    | Open Access

    3D genome structures are plastic and vary from cell to cell even in an isogenic sample. Here, the authors present an approach to identify frequent 3D chromatin clusters across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data.

    • Chao Dai
    • , Wenyuan Li
    •  & Xianghong Jasmine Zhou

  • Article
    | Open Access

    The variability in patient response to radiation treatment is difficult to predict. Here, using more than 500 cell lines the authors measure response to radiation exposure and a large panel of compounds, and show that response can be predicted by genetic alterations of the cells.

    • Brian D. Yard
    • , Drew J. Adams
    •  & Mohamed E. Abazeed

  • Article
    | Open Access

    Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.

    • Jonathan D. Mosley
    • , John S. Witte
    •  & Joshua C. Denny

  • Article
    | Open Access

    Understanding the genetic influences on human aging requires a large number of subjects for a study of sufficient power. Here, Jim Wilson and colleagues use information on parental ages at death to show that common variants near the genes for apolipoprotein E and nicotinic acetylcholine receptor subunit alpha 5 are associated with longer lifespan.

    • Peter K. Joshi
    • , Krista Fischer
    •  & James F. Wilson

  • Article
    | Open Access

    COBRA1 is a BRCA1-binding protein and, as part of the negative elongation factor, regulates RNA polymerase II pausing and transcription elongation. Here, the authors show that tissue-specific deletion of mouse Cobra1 inhibits postnatal mammary gland development and that the mammary defects can be rescued by additional deletion of Brca1in a DNA repair-independent manner.

    • Sreejith J. Nair
    • , Xiaowen Zhang
    •  & Rong Li

  • Article
    | Open Access

    Phenome-wide association is a novel method that links sequence variants to a spectrum of phenotypes and diseases. Here the authors generate detailed mouse genetic and phenome data which links their phenome-wide association study (PheWAS) of mouse to corresponding PheWAS in human.

    • Xusheng Wang
    • , Ashutosh K. Pandey
    •  & Robert W. Williams

  • Article
    | Open Access

    Tsai et al. here utilize a multi-stage genome-wide association study in Taiwanese population to show a copy number variation in the intron of potassium interacting channel 1 gene (KCNIP1) to be strongly associated with atrial fibrillation. The study also examines the functionality of KCNIP1 in heart electrophysiological function using cultured myocytes and zebrafish.

    • Chia-Ti Tsai
    • , Chia-Shan Hsieh
    •  & Jiunn-Lee Lin

  • Article
    | Open Access

    Reduced glomerular filtration rate (eGFR) is a hallmark of chronic kidney disease. Here, Pattaro et al. conduct a meta-analysis to discover several new loci associated with variation in eGFR and find that genes associated with eGFR loci often encode proteins potentially related to kidney development.

    • Cristian Pattaro
    • , Alexander Teumer
    •  & Caroline S. Fox

  • Article
    | Open Access

    Here, Martiniano et al. examine the genetic structure of northern Britain in the late BC/early AD using ancient genome sequencing of 9 individuals. They uncover evidence of far-reaching Roman and later Anglo-Saxon migrations within a background of Britons similar to the earlier Iron Age.

    • Rui Martiniano
    • , Anwen Caffell
    •  & Daniel G. Bradley

  • Article
    | Open Access

    Published sequencing data sets of cancer samples could be used to identify genetic variants associated with the risk of developing cancer. Here, Luet al. analyse over 4,000 tumour-normal pairs to reveal variable frequencies of inherited susceptibilities across 12 cancer types and find enrichment of functionally validated missense variants of unknown significance.

    • Charles Lu
    • , Mingchao Xie
    •  & Li Ding

  • Article
    | Open Access

    The mushroom bodies (MBs) in an insect brain integrate and process sensory information. Using fully sequenced/inbred lines of the Drosophila Genetic Reference Panel, this study performs genome wide association analyses and identifies candidate genes affecting MB size, and uses RNAi to functionally validate the identified loci.

    • Liesbeth Zwarts
    • , Lies Vanden Broeck
    •  & Patrick Callaerts

  • Article
    | Open Access

    DICER1 is required for the maturation of miRNAs which regulate expression of thousands of genes. Here the authors show significantly reduced levels of DICER1in individuals having post-traumatic stress disorder and comorbid depression suggestive of a role in the molecular mechanism of the condition.

    • Aliza P. Wingo
    • , Lynn M. Almli
    •  & Kerry J. Ressler

  • Article
    | Open Access

    One of the key aspects for controlling infectious diseases is understanding how pathogens cross host species. Here the authors conduct a genome-wide analysis of Salmonella and show a high degree of variation, enabling host-adapted colonization among Salmonellaintestinal and systemic serovars.

    • Min Yue
    • , Xiangan Han
    •  & Dieter M. Schifferli

  • Article
    | Open Access

    Previous studies have linked over 100 genomic loci to age-at-menarche but that work was restricted to common autosomal variation. Here, Lunetta et al. identify associations with rare protein-coding and X-linked variants, implicating new mechanisms that regulate puberty timing.

    • Kathryn L. Lunetta
    • , Felix R. Day
    •  & John R. B. Perry

  • Article
    | Open Access

    In order to effectively design interventions, it is useful to understand the complex interplay between multiple syndromes. Here, Ahmad et al. use genome-wide association study data and Mendelian randomisation to examine the influence of Type 2 diabetes and fasting glucose levels on coronary heart disease.

    • Omar S. Ahmad
    • , John A. Morris
    •  & J. Brent Richards

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