Genetic variation articles within Nature Communications

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  • Article
    | Open Access

    Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage

    • Crystal M. Tomlin
    • , Sitaram Rajaraman
    •  & Charlotte Lindqvist

  • Article
    | Open Access

    Left-handedness is a common and partly heritable trait. Here, the authors perform a genome-wide screen for rare, protein-altering genetic variants associated with handedness in over 350,000 people, and implicate the tubulin gene TUBB4B.

    • Dick Schijven
    • , Sourena Soheili-Nezhad
    •  & Clyde Francks

  • Article
    | Open Access

    Comparing to other biological systems, our understanding of plant extrachromosomal circular DNA (eccDNA) is limited. Here, the authors profile eccDNA from six rice tissues and investigate eccDNA characteristics, formation mechanisms, distribution, and functional implications.

    • Jundong Zhuang
    • , Yaoxin Zhang
    •  & Tingting Lu

  • Article
    | Open Access

    Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.

    • Wai Kuan Ho
    • , Alberto Stefano Tanzi
    •  & Sean Mayes

  • Article
    | Open Access

    Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.

    • Rong Wang
    • , Chao-Nan Liu
    •  & Xiao-Yong Chen

  • Article
    | Open Access

    Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.

    • Lin-Feng Li
    • , Tonapha Pusadee
    •  & Kenneth M. Olsen

  • Article
    | Open Access

    The contribution of rare variants to complex traits has not been well studied. Here, the authors present RARity, a method to assess rare variant heritability without assuming a particular genetic architecture and enabling both gene-level and exome-wide heritability estimation of continuous traits.

    • Nazia Pathan
    • , Wei Q. Deng
    •  & Guillaume Paré

  • Article
    | Open Access

    Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. Here the authors present an engineered yeast strain with 83 sparsely distributed loxPsym sites across the genome can genrerate large-scale genomic rearrangements, which benefits cell fitness under stress and boosts the SCRaMbLE system when combined with synthetic chromosomes.

    • Li Cheng
    • , Shijun Zhao
    •  & Junbiao Dai

  • Article
    | Open Access

    Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.

    • Simone Scalabrin
    • , Gabriele Magris
    •  & Michele Morgante

  • Editorial
    | Open Access

    Orphan crops hold the potential to diversify our food systems. Considering their unique characteristics, our deep understanding of major crops, and the availability of modern genomic tools, taking a different research path from what major crops have gone through could accelerate the genetic improvement of orphan crops.

  • Comment
    | Open Access

    Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.

    • Oluwaseyi Shorinola
    • , Rose Marks
    •  & Mark A. Chapman

  • Article
    | Open Access

    Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.

    • Lewis Stevens
    • , Isaac Martínez-Ugalde
    •  & Mark Blaxter

  • Article
    | Open Access

    A pan-genome can reduce bias in genetic diversity analysis inherent in using a single reference genome. Here, the authors assemble genomes of 10 diverse apple accessions, conduct pan-genome analysis together with three existing genomes, and reveal the role of mitogen-activated protein kinase homolog MMK2 in fruit coloration.

    • Ting Wang
    • , Shiyao Duan
    •  & Ting Wu

  • Article
    | Open Access

    Ecogeographic rules link spatial patterns in phenotype and environment, potentially reflecting adaptation. This study identifies nine genes associated with body mass variation in song sparrow populations, supporting Bergmann’s Rule and highlighting the role of natural selection in local adaptation.

    • Katherine Carbeck
    • , Peter Arcese
    •  & Jennifer Walsh

  • Article
    | Open Access

    Arabs account for 5% of the world population and have a high burden of cardiometabolic disease. Here, the authors optimize polygenic scores for 10 cardiometabolic traits in 5399 Arabs, achieving a performance on par with that among European-ancestry individuals.

    • Injeong Shim
    • , Hiroyuki Kuwahara
    •  & Akl C. Fahed

  • Article
    | Open Access

    Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.

    • Minghui Kang
    • , Haolin Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    Reninomas are very rare kidney tumours of juxtaglomerular cells. Here, the authors analyse reninomas using whole-genome and transcriptome sequencing, and reveal the presence and functional effects of NOTCH1 rearrangements.

    • Taryn D. Treger
    • , John E. G. Lawrence
    •  & Tanzina Chowdhury

  • Article
    | Open Access

    Yaks have been subject to natural selection, human domestication and interspecific introgression during their evolution. Here, the authors have identified genomic structural variations and the linked genes involved in these processes in domestic yaks, to reveal new insight into genetic basis of phenotypic diversity.

    • Xinfeng Liu
    • , Wenyu Liu
    •  & Jianquan Liu

  • Article
    | Open Access

    Industrial whaling drove several species to near extinction. From an analysis of 50 whole-genomes from fin whale populations, this study shows that the fin whale population in the Eastern North Pacific was reduced 99% during whaling but has maintained genomic diversity, whereas the Gulf of California population remained small and isolated, resulting in increased genetic load.

    • Sergio F. Nigenda-Morales
    • , Meixi Lin
    •  & Robert K. Wayne

  • Article
    | Open Access

    Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.

    • Feng Liu
    • , Jiantao Zhao
    •  & Xuexiao Zou

  • Article
    | Open Access

    This study presents a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences. From over 2 million mtDNA sequences, they find a negative quadratic latitudinal gradient in genetic diversity evenness, peaking in the subtropics and correlating with hot, stable environments.

    • Connor M. French
    • , Laura D. Bertola
    •  & Michael J. Hickerson

  • Article
    | Open Access

    Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene EPSPS in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of EPSPS could lead to glyphosate resistance.

    • Chun Zhang
    • , Nicholas A. Johnson
    •  & Eric L. Patterson

  • Article
    | Open Access

    Understanding the genetic basis of rubber tree domestication is critical for improving natural rubber production. Here, the authors assemble the genome of the rubber tree clone CATAS8-79 and conduct population and genetic association analyses to reveal the function of phytosulfokine in regulating number of laticifer rings.

    • Jinquan Chao
    • , Shaohua Wu
    •  & Wei-Min Tian

  • Article
    | Open Access

    Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function.

    • Stephen A. Schlebusch
    • , Jakub Rídl
    •  & Radka Reifová

  • Article
    | Open Access

    Detection of resistance to the antibiotic metronidazole in C. difficile often requires the presence of heme in the media, for unclear reasons. Here, the authors show that most metronidazole-resistant strains carry a mutation that promotes expression of a heme-dependent enzyme that degrades nitroimidazoles, and the mutation often co-occurs with an amino-acid substitution in DNA gyrase that confers resistance to another class of antibiotics, fluoroquinolones.

    • Abiola O. Olaitan
    • , Chetna Dureja
    •  & Julian G. Hurdle

  • Article
    | Open Access

    There are challenges with transferring genetic risk scores from ancestry in which they were generated to another. Here, the authors investigate the use of multi-ancestry versus single-ancestry training sets to construct polygenic scores and find that the optimal strategy varies across traits.

    • Brieuc Lehmann
    • , Maxine Mackintosh
    •  & Chris Holmes

  • Article
    | Open Access

    A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis. Here, the authors investigate copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men.

    • Elise A. Lucotte
    • , Valdís Björt Guðmundsdóttir
    •  & Kari Stefansson

  • Article
    | Open Access

    Gastric cancers (GC) are driven by genomic alterations, but the underlying molecular mechanisms remain unclear. Here, the authors analyse the structural rearrangement landscape of 170 GCs using whole-genome sequencing, identify recurrent structural variant hotspots and find oncogene amplicons driven by extrachromosomal DNA.

    • Mihoko Saito-Adachi
    • , Natsuko Hama
    •  & Tatsuhiro Shibata

  • Comment
    | Open Access

    Whole genome sequencing has enabled new insights into the genetic architecture of complex traits, especially through access to low-frequency and rare variation. This Comment highlights the key contributions from this technology and discusses considerations for its use and future perspectives.

    • Ozvan Bocher
    • , Cristen J. Willer
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    Current methods for detecting insertions from short read sequencing data generally have low sensitivity. Here, the authors develop a new tool that runs quickly and detects significantly more true positive insertions compared to any combination of existing methods.

    • Ramesh Rajaby
    • , Dong-Xu Liu
    •  & Wing-Kin Sung

  • Article
    | Open Access

    Epidemiological models are commonly fit to case and pathogen sequence data to estimate parameters and to reconstruct disease dynamics. Here, the authors present an inference approach based on sequence data that is well suited for model fitting early on during the expansion of a viral lineage.

    • Yeongseon Park
    • , Michael A. Martin
    •  & Katia Koelle

  • Article
    | Open Access

    Repeated evolution provides valuable insight into adaptation. In this study, the authors found that repeated evolution of cave-adapted phenotypes of a fish (Astyanax mexicanus) was driven by selection on standing genetic variation and novel mutations and genes repeatedly under selection are longer compared to the rest of the genome.

    • Rachel L. Moran
    • , Emilie J. Richards
    •  & Suzanne E. McGaugh

  • Article
    | Open Access

    Lablab is a legume native to Africa and cultivated throughout the tropics for food and forage; however, as an orphan crop, limited genomic resources hampers its genetic improvement. Here, an African-led South-North plant genome collaboration produces an improved genome assembly and population genomic resource to accelerate its breeding.

    • Isaac Njaci
    • , Bernice Waweru
    •  & Chris S. Jones

  • Article
    | Open Access

    Short tandem repeat studies in humans have often focused on European populations. Here, the authors report a comprehensive map of 366,013 polymorphic short tandem repeats in Chinese individuals and their mutational patterns, functional properties, gene regulatory effects and population characteristics.

    • Yirong Shi
    • , Yiwei Niu
    •  & Shunmin He

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