Genomics articles within Nature Communications

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  • Article
    | Open Access

    The contribution of transposable elements (TEs) to the creation of heritable mutations is unknown. Here the authors show in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner.

    • Leandro Quadrana
    • , Mathilde Etcheverry
    •  & Vincent Colot

  • Article
    | Open Access

    Genetic adaptation and physiological acclimation can potentially buffer species against climate change. Here, the authors perform a long-term warming experiment of Antarctic encrusting communities and show that focal animal species failed to acclimate and lacked genetic variation in tolerance to warming.

    • Melody S. Clark
    • , Leyre Villota Nieva
    •  & Lloyd S. Peck

  • Article
    | Open Access

    A number of computational methods have been developed for calling structural variants (SVs) using short read sequencing data. Here, the authors perform a comprehensive benchmarking analysis comparing 10 general-purpose callers and provide recommendations for both users and methods developers.

    • Daniel L. Cameron
    • , Leon Di Stefano
    •  & Anthony T. Papenfuss

  • Article
    | Open Access

    The transcription factor p63 is a master regulator of ectoderm development. Here the authors show that zebrafish p63 binds enhancers associated with neural genes to limit Sox3 binding and gene expression while also acting as a pioneer factor by promoting chromatin opening at epidermal gene enhancers.

    • José M. Santos-Pereira
    • , Lourdes Gallardo-Fuentes
    •  & Juan J. Tena

  • Article
    | Open Access

    Dosage compensation (DC) on the X chromosome has predictable effects on genetic and phenotypic trait variance. Here, the authors use information for 20 quantitative traits in the UK Biobank and across-tissue gene expression to compare X-linked heritability and the effects of trait-associated SNPs between the sexes.

    • Julia Sidorenko
    • , Irfahan Kassam
    •  & Peter M. Visscher

  • Article
    | Open Access

    Systematic analysis of postzygotic mosaicism (PZM) is difficult due to challenges in detecting such events. Here, Wright et al. analyse trio exome sequencing data from blood and saliva of 4,293 probands with developmental disorders from the DDD Study and estimate that >3% of causative de novo mutations result from PZM.

    • C. F. Wright
    • , E. Prigmore
    •  & M. E. Hurles

  • Article
    | Open Access

    Bulk RNA-seq data harbors valuable information about gene expression levels from different cell types in tissue samples. Here, the authors develop DWLS, a computational method for estimating cell-type composition of bulk data by leveraging single-cell RNA-seq-derived cell-type signatures.

    • Daphne Tsoucas
    • , Rui Dong
    •  & Guo-Cheng Yuan

  • Article
    | Open Access

    The Atlantic salmon has suffered widespread population declines over the last century. Here, Lehnert et al. reconstruct changes in effective population size of 172 populations based on genomic linkage information revealing mostly temperature-associated population declines with over 60% of populations in decline since 1975.

    • S. J. Lehnert
    • , T. Kess
    •  & I. R. Bradbury

  • Article
    | Open Access

    Mutational signature analysis provides important information about the mutational processes underpinning different stages of tumorigenesis. Here, the authors compare publicly available signature extraction tools and suggest a framework for the generation of accurate and reproducible signature data.

    • Francesco Maura
    • , Andrea Degasperi
    •  & Niccolò Bolli

  • Article
    | Open Access

    Genetic variants in RP1 can cause hereditary retinal degeneration (HRD). Here, in a genomic screen of 331 Japanese HRD patients, the authors identify a near-polymorphic RP1 variant that causes Mendelian HRD in trans with an Alu insertion and otherwise is associated with HRD according to a complex model of inheritance.

    • Konstantinos Nikopoulos
    • , Katarina Cisarova
    •  & Carlo Rivolta

  • Article
    | Open Access

    The oomycete Bremia lactucae is a highly variable pathogen that causes lettuce downy mildew. Here, the authors generate a high-quality genome assembly for B. lactucae, detect a high prevalence of heterokaryosis, and investigate its pathogenic consequences.

    • Kyle Fletcher
    • , Juliana Gil
    •  & Richard Michelmore

  • Article
    | Open Access

    Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.

    • Yong Peng
    • , Dan Xiong
    •  & Xingwang Li

  • Article
    | Open Access

    Chromatin is folded into Topologically Associating domains (TADs), with the organization and folding hierarchy of the TADs being highly dynamic. Here the authors develop a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency encounters present in Hi-C data within and between TADs and reconstruct TADs across cell differentiation, revealing local chromatin re-organization.

    • O. Shukron
    • , V. Piras
    •  & D. Holcman

  • Article
    | Open Access

    Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.

    • En Li
    • , Han Liu
    •  & Jinsheng Lai

  • Article
    | Open Access

    Our understanding of the functional link between differential DNA methylation and type 2 diabetes and obesity remains limited. Here the authors present a blood-based EWAS of fasting glucose and insulin among 4808 non-diabetic Europeans and identify nine CpGs not previously implicated in glucose, insulin homeostasis and diabetes.

    • Jun Liu
    • , Elena Carnero-Montoro
    •  & Cornelia M. van Duijn

  • Article
    | Open Access

    Risk loci for type 2 diabetes (T2D) reside in pancreatic islet enhancers. Here, the authors generate high-resolution maps of islet chromatin conformation using Hi-C which they combine with ATAC-seq and ChIP-seq data to annotate candidate target genes of enhancers and validate IGF2BP2 activity in mouse islets.

    • William W. Greenwald
    • , Joshua Chiou
    •  & Kyle J. Gaulton

  • Article
    | Open Access

    The pygmy hog (Porcula salvania), now highly endangered and restricted in a small region at the southern foothills of the Himalaya, is the only suid species in mainland Eurasia that outlived the expansion of wild boar (Sus scrofa). Here, the authors analyze genomes of pygmy hog and related suid species, and identify signals of introgression among these species.

    • Langqing Liu
    • , Mirte Bosse
    •  & Ole Madsen

  • Article
    | Open Access

    Understanding gene regulation will require mapping specific chromain features in a small number of cells at high resolution. Here the authors describe CUT&Tag, which uses antibody-mediated tethering of Tn5 transposase to a chromatin protein to generate high resolution libraries.

    • Hatice S. Kaya-Okur
    • , Steven J. Wu
    •  & Steven Henikoff

  • Article
    | Open Access

    Alignment is an important stage in the analysis of sequencing data. Here, the authors present a fast and accurate alignment approach suitable for long and short reads, and introduce two line sweep-based techniques which can replace the often-used chaining approach.

    • Markus Schmidt
    • , Klaus Heese
    •  & Arne Kutzner

  • Article
    | Open Access

    Analysis of Hi-C datasets is limited by the current existing methods for data normalization, with detection of features such as TADs and chromatin loops being inconsistent amongst different approaches. Here the authors develop Binless, a method that allows for reproducible normalization of Hi-C data independent of its resolution and compare how Binless performs in comparison with other methods.

    • Yannick G. Spill
    • , David Castillo
    •  & Marc A. Marti-Renom

  • Article
    | Open Access

    Nanopore sequencing technology generates longer reads than current technologies, but with more errors. Here, the authors develop new analytical tools to improve accuracy and evaluate the potential of nanopore sequencing for clinical human genomics.

    • Rory Bowden
    • , Robert W. Davies
    •  & Peter Donnelly

  • Article
    | Open Access

    The increasing accessibility of single cell omics technologies beyond transcriptomics demands parallel advances in analysis. Here, the authors introduce STREAM, a pipeline for reconstruction and visualization of differentiation trajectories from both single-cell RNA-seq and ATAC-seq data.

    • Huidong Chen
    • , Luca Albergante
    •  & Luca Pinello

  • Article
    | Open Access

    Personalized approaches to diagnosis and treatment monitoring could improve the management of cystic fibrosis patients. Here the authors show that multiscale differential dynamic microscopy can assess changes in cilia beating dynamics and coordination in patient-derived airway epithelial cells, in response to different CFTR-modulating drugs, in a patient-specific manner.

    • M. Chioccioli
    • , L. Feriani
    •  & P. Cicuta

  • Article
    | Open Access

    Any DNA sequence can be represented by a chiral partner sequence – an exact copy arranged in reverse nucleotide order. Here, the authors show that chiral DNA sequence pairs share important properties and show the utility of synthetic chiral sequences (sequins) as controls for clinical genomics.

    • Ira W. Deveson
    • , Bindu Swapna Madala
    •  & Tim R. Mercer

  • Article
    | Open Access

    While the role of effective population size (Ne) in explaining variation in genetic diversity has received much attention, the role of spontaneous mutation rate is largely ignored. Here, Xu et al. show that giant duckweed has a high Ne yet low genetic diversity, likely due to its low mutation rate.

    • Shuqing Xu
    • , Jessica Stapley
    •  & Meret Huber

  • Article
    | Open Access

    Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.

    • Min Xie
    • , Claire Yik-Lok Chung
    •  & Hon-Ming Lam

  • Article
    | Open Access

    Wolbachia bacteria live within the cells of many insects, including the mosquito Culex pipiens. Here, the authors analyse new and existing Wolbachia metagenomes from C. pipiens mosquitoes and find evidence of a plasmid, which may facilitate genetic manipulation of these bacteria for vector control applications.

    • Julie Reveillaud
    • , Sarah R. Bordenstein
    •  & A. Murat Eren

  • Article
    | Open Access

    It is currently unclear how quantitative changes in chromatin loop propensity contribute to differential gene regulation. Here, the authors use phased Hi-C, RNA-seq, and ChIP-seq to show that subtle changes in loop propensity associate with differential gene regulation across cell types and haplotypes.

    • William W. Greenwald
    • , He Li
    •  & Kelly A. Frazer

  • Article
    | Open Access

    Somatic mutations are crucial to the understanding of cancer genesis, progression, and treatment, but are still challenging to detect. Here the authors present NeuSomatic, a convolutional neural network approach for accurate somatic mutation detection across various sequencing scenarios.

    • Sayed Mohammad Ebrahim Sahraeian
    • , Ruolin Liu
    •  & Hugo Y. K. Lam

  • Article
    | Open Access

    N6-methyladenine is involved in many biological pathways for microbial survival and host interaction. Here the authors train a neural network for improved m6A detection in nanopore sequencing data and validate methylomes for a microbial reference community.

    • Alexa B. R. McIntyre
    • , Noah Alexander
    •  & Christopher E. Mason

  • Article
    | Open Access

    The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

    • Chuan-Chao Wang
    • , Sabine Reinhold
    •  & Wolfgang Haak

  • Article
    | Open Access

    Broomcorn millet is one of the earliest domesticated plants and has the highest water use efficiency among cereals. Here, the authors report its genome assembly and annotation, which provides a valuable resource for breeders and paves the way for studying plant drought tolerance and C4 photosynthesis.

    • Changsong Zou
    • , Leiting Li
    •  & Heng Zhang

  • Article
    | Open Access

    Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet.

    • Junpeng Shi
    • , Xuxu Ma
    •  & Jinsheng Lai

  • Article
    | Open Access

    Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.

    • Xia Jiang
    • , Hilary K. Finucane
    •  & Sara Lindström

  • Article
    | Open Access

    The Pacific white shrimp Litopenaeus vannamei is an important aquaculture species and a promising model for crustacean biology. Here, the authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.

    • Xiaojun Zhang
    • , Jianbo Yuan
    •  & Jianhai Xiang

  • Article
    | Open Access

    DNA methylation is an epigenetic mark involved in gene regulation. Here the authors investigate the extent to which genetics, sex and pregnancy influence genomic DNA methylation in mice, providing evidence of the stability of CpG methylation across generation and suggest that CpG methylation may serve as an epigenetic record of life events in somatic tissues at loci whose expression is linked to the relevant biology.

    • Sara A. Grimm
    • , Takashi Shimbo
    •  & Paul A. Wade

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