Genetic variation articles within Nature Communications

Featured

  • Article
    | Open Access

    Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

    • John T. Lovell
    • , Nolan B. Bentley
    •  & Jennifer J. Randall

  • Article
    | Open Access

    The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

    • Alexis Groppi
    • , Shuo Liu
    •  & Véronique Decroocq

  • Article
    | Open Access

    Ethiopia is one of the most ethnically and culturally diverse countries. Here, the authors look at genetic and cultural variation in 1,214 Ethiopians to unravel the relationship between genetic admixture and cultural factors.

    • Saioa López
    • , Ayele Tarekegn
    •  & Garrett Hellenthal

  • Article
    | Open Access

    Karyotyping of cancer genomes at the base-level is technically challenging. Here, the authors introduce InfoGenomeR, an algorithm that can infer cancer genome karyotypes from whole-genome sequencing data, and test their model on breast, ovarian and brain cancer samples; and identify private and shared mutations between primary and metastatic cancer samples.

    • Yeonghun Lee
    •  & Hyunju Lee

  • Article
    | Open Access

    Prioritising genes as potential drug targets is challenging and often unsuccessful once testing efficacy in humans. Here, the authors propose an approach to identifying drug targets that uses evidence from gain- or loss-of-function mutations associated with bidirectional effects on phenotypes.

    • Karol Estrada
    • , Steven Froelich
    •  & Lon R. Cardon

  • Article
    | Open Access

    Identifying structural variants (SVs) from whole genome sequence data has been a significant bioinformatic challenge. Here, the authors describe PopDel, which uses a joint SV detection approach to reliably and efficiently identify 500-10,000 bp deletions across large population cohorts.

    • Sebastian Niehus
    • , Hákon Jónsson
    •  & Birte Kehr

  • Article
    | Open Access

    Sequencing and mapping of long repetitive regions can be challenging due to technical difficulties in sequencing and assembly of the sequence data. Here authors report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe to reveal highly polymorphic and hot spots for genome variation features.

    • Yusuke Oizumi
    • , Takuto Kaji
    •  & Junko Kanoh

  • Article
    | Open Access

    The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits.

    • Myung-Shin Kim
    • , Roberto Lozano
    •  & Soon-Chun Jeong

  • Article
    | Open Access

    Gene flow is classically thought to impede local adaptation via parallel evolution. However, a genomic study on Hawaiian crickets from different island populations finds evidence of parallel adaptation to the same lethal parasitoid in spite of strong ongoing gene flow.

    • Xiao Zhang
    • , Jack G. Rayner
    •  & Nathan W. Bailey

  • Article
    | Open Access

    Ancient, asexual lineages are rare as a lack of recombination is usually an evolutionary dead end. Here, authors compare complete genomes of 11 individual bdelloid rotifers that suggest evidence of regular genetic exchange between individuals in a species that was previously thought to be asexual.

    • Olga A. Vakhrusheva
    • , Elena A. Mnatsakanova
    •  & Alexey S. Kondrashov

  • Article
    | Open Access

    Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.

    • Xin Wang
    • , Lei Gao
    •  & Zhangjun Fei

  • Article
    | Open Access

    The human reference genome does not fully reflect human genetic diversity. Here, the authors analyse 338 human genome assemblies from diverse populations to identify missing sequences, define non-reference unique insertions and construct a Human Diversity Reference.

    • Karen H. Y. Wong
    • , Walfred Ma
    •  & Pui-Yan Kwok

  • Article
    | Open Access

    The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.

    • Therese Mitros
    • , Adam M. Session
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    This study presents and validates a novel approach to reliably identify structural variations (SVs) in non-model genomes using whole genome sequencing, which was used to detect 15,483 SVs in 492 Atlantic salmon, shedding light on their roles in genome evolution and the genetic architecture of domestication.

    • Alicia C. Bertolotti
    • , Ryan M. Layer
    •  & Daniel J. Macqueen

  • Article
    | Open Access

    Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

    • Michael Abrouk
    • , Hanin Ibrahim Ahmed
    •  & Simon G. Krattinger

  • Article
    | Open Access

    Pleistocene population dynamics can inform the consequences of current climate change. This phylogeography of 35 complete American mastodon mitochondrial genomes suggests distinct lineages in this species repeatedly expanded northwards and then went locally extinct in response to glacial cycles.

    • Emil Karpinski
    • , Dirk Hackenberger
    •  & Hendrik N. Poinar

  • Article
    | Open Access

    Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.

    • Weiyi Zhang
    • , Youjun Zhang
    •  & Weiwei Wen

  • Article
    | Open Access

    Structural genomic variation can fuel evolution. Here, authors present genome data from seven Corvus species and unearth structural variants that vary between incipient crow species in Europe, with implications for premating isolation involving plumage patterning.

    • Matthias H. Weissensteiner
    • , Ignas Bunikis
    •  & Jochen B. W. Wolf

  • Article
    | Open Access

    Evidence that somatic mutation rates in introns exceed those in exons challenges the molecular evolution tenet that mutation rate and sequence function are independent. Here, authors analyze germline de novo mutations and reveal no evidence for mutation rate differences between exons and introns.

    • Miguel Rodriguez-Galindo
    • , Sònia Casillas
    •  & Antonio Barbadilla

  • Article
    | Open Access

    Structural variants (SVs) contribute to the genetic architecture of many brain-related disorders. Here, the authors integrate SV calls from genome sequencing (n = 755) with RNA-seq data (n = 629) from post-mortem dorsal lateral prefrontal cortex to annotate the gene regulatory effects of SVs in the human brain and their potential to contribute to disease.

    • Lide Han
    • , Xuefang Zhao
    •  & Douglas M. Ruderfer

  • Article
    | Open Access

    Reduction of pollen grain number is widespread in selfing plants, but the determining gene is unknown. Here, the authors show that a ribosome-biogenesis factor encoding gene RDP1 is responsible for adaptive reduction of male gamete number in Arabidopsis thaliana.

    • Takashi Tsuchimatsu
    • , Hiroyuki Kakui
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    Multi-nucleotide variants (MNV) are genetic variants in close proximity of each other on the same haplotype whose functional impact is difficult to predict if they reside in the same codon. Here, Wang et al. use the gnomAD dataset to assemble a catalogue of MNVs and estimate their global mutation rate.

    • Qingbo Wang
    • , Emma Pierce-Hoffman
    •  & Daniel G. MacArthur

  • Article
    | Open Access

    Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.

    • Wai Yee Low
    • , Rick Tearle
    •  & John L. Williams

  • Article
    | Open Access

    Mutations in PTEN have been associated with various human disease, including autism spectrum disorder (ASD) and cancer. Here, the authors assess the function of 106 PTEN variants in yeast, invertebrate models and cell culture and report that PTEN variants generally decrease protein stability.

    • Kathryn L. Post
    • , Manuel Belmadani
    •  & Kurt Haas

  • Article
    | Open Access

    Recent evidence has questioned the dogma of strict maternal transmission of mitochondrial DNA (mtDNA) in humans. Wei et al. saw no evidence of paternal transmission of mtDNA in 11,035 human trios, and show that nuclear-mitochondrial segments (NUMTs) can give the impression of paternal mtDNA transmission, but are actually inherited through the nuclear genome.

    • Wei Wei
    • , Alistair T. Pagnamenta
    •  & Patrick F. Chinnery

  • Article
    | Open Access

    Polygenic scores are believed to hold future promise for trait prediction and personalized medicine, but are sensitive to demographic history. Here, Marnetto et al. develop partial polygenic scores supplemented with local ancestry deconvolution which improves prediction accuracy into recently admixed European populations.

    • Davide Marnetto
    • , Katri Pärna
    •  & Luca Pagani

  • Article
    | Open Access

    Population structure, even subtle differences within seemingly homogenous populations, can have an impact on the accuracy of polygenic prediction. Here, Sakaue et al. use dimensionality reduction methods to reveal fine-scale structure in the Biobank Japan cohort and explore the performance of polygenic risk scores.

    • Saori Sakaue
    • , Jun Hirata
    •  & Yukinori Okada

  • Article
    | Open Access

    Mutations in human pluripotent stem cells (PSC) and whether any form during culture prior to use in a human clinical context are a concern. Here, the authors use hPSCs derived to cGMP standards and show they have low mutation rates after culture, noting this decreases on culturing in low (5%) oxygen conditions.

    • Oliver Thompson
    • , Ferdinand von Meyenn
    •  & Peter W. Andrews

  • Article
    | Open Access

    GWAS analysis currently relies mostly on linear mixed models, which do not account for linkage disequilibrium (LD) between tested variants. Here, Sesia et al. propose KnockoffZoom, a non-parametric statistical method for the simultaneous discovery and fine-mapping of causal variants, assuming only that LD is described by hidden Markov models (HMMs).

    • Matteo Sesia
    • , Eugene Katsevich
    •  & Chiara Sabatti

  • Article
    | Open Access

    Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.

    • Wen-Biao Jiao
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Few studies empirically pinpoint how balanced polymorphisms are maintained. “Mérot et al”. identify an inversion polymorphism that is maintained in seaweed fly populations because of antagonistic pleiotropy that mediates a classic life history tradeoff between larval survival and adult reproduction.

    • Claire Mérot
    • , Violaine Llaurens
    •  & Maren Wellenreuther

  • Article
    | Open Access

    Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery.

    • Pilar Cacheiro
    • , Violeta Muñoz-Fuentes
    •  & Coleen Kane

  • Article
    | Open Access

    Population-based association analyses of rare genetic variants with complex traits are limited by the availability of data from sufficiently large cohorts. Here, Cirulli et al. report gene-based collapsing analysis of exomes from 49,960 participants of the UK Biobank and 21,866 participants of the Healthy Nevada Project over a total of 4377 traits.

    • Elizabeth T. Cirulli
    • , Simon White
    •  & Nicole L. Washington

  • Article
    | Open Access

    G-quadruplexes (G4s) are secondary structures that can form in both DNA and RNA from guanine-rich sequences which are enriched in untranslated regions (UTRs). Here, Lee et al. find that putative G4-forming sequences are evolutionarily constrained, enriched for RNA-binding protein interactions and enriched for disease genetic associations.

    • David S. M. Lee
    • , Louis R. Ghanem
    •  & Yoseph Barash

  • Article
    | Open Access

    Healthspan and healthy aging are areas of research with potential socioeconomic impact. Here, the authors present the Medical Genome Reference Bank (MGRB) which consist of over 4,000 individuals aged 70 years and older without a history of the major age-related diseases and report on results from whole-genome sequencing and association analyses.

    • Mark Pinese
    • , Paul Lacaze
    •  & David M. Thomas

  • Article
    | Open Access

    Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.

    • Yun Rose Li
    • , Joseph T. Glessner
    •  & Hakon Hakonarson

  • Article
    | Open Access

    RNA-sequencing is mostly used to assess gene expression; however, it can also give information about genetic variants. Here, the authors present CaSpER, a statistical framework that utilises RNA-sequencing reads to identify and visualise CNV events by integrating transcriptome-wide expression and allelic shift profiles.

    • Akdes Serin Harmanci
    • , Arif O. Harmanci
    •  & Xiaobo Zhou

  • Article
    | Open Access

    Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.

    • Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    •  & Pall Melsted

Browse broader subjects

Browse narrower subjects

Browse Genetic variation across other nature.com journals