Genome articles within Nature Communications

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  • 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

    The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.

    • Lulu Xu
    • , Yandong Ren
    •  & Gang Li

  • 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

    It has been suggested that transposable elements (TE) play a role in tumourigenesis, but the associated mechanisms remain unclear. Here, the authors show, using colorectal cancer data and Bayesian Networks, that TEs can mediate the effect of expression quantitative trait loci and contribute to the regulation of cancer-related genes.

    • Nikolaos M. R. Lykoskoufis
    • , Evarist Planet
    •  & Emmanouil T. Dermitzakis

  • Article
    | Open Access

    Frogs are an ancient and ecologically diverse group of amphibians that include important model systems. This paper reports genome sequences of multiple frog species, revealing remarkable stability of frog chromosomes and centromeres, along with highly recombinogenic extended subtelomeres.

    • Jessen V. Bredeson
    • , Austin B. Mudd
    •  & Daniel S. Rokhsar

  • 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

    Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.

    • Bob Zimmermann
    • , Juan D. Montenegro
    •  & Ulrich Technau

  • Article
    | Open Access

    In Saccharomyces cerevisiae, the left arm of chromosome XII only requires 12 genes to maintain cell viability, whereas 25 genes are needed for robust fitness. Here the authors demonstrate that the entire arm can be replaced by a neochromosome with completely artificial sequences.

    • Shuangying Jiang
    • , Zhouqing Luo
    •  & Junbiao Dai

  • 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

    In Drosophila, insulators may be involved in the organization of Topological Associated Domains, but the mechanism of action is a still a matter of investigation. Here the authors investigate the role of insulators in the 3D organization of the Drosophila genome by combining bioinformatics analysis and Hi-M, an imaging-based methods developed to detect the 3D positions of multiple genomic loci in single cells.

    • Olivier Messina
    • , Flavien Raynal
    •  & Marcelo Nollmann

  • Article
    | Open Access

    Ddd-Aderived cytosine base editors (DdCBEs) are important for research of mitochondrial DNA mutation diseases. Here the authors report a strategy for screening and characterising dsDNA cytidine deaminases, and identify 7 DddA homologs which they optimise to minimise nuclear and mitochondrial off-target editing.

    • Haifeng Sun
    • , Zhaojun Wang
    •  & Bin Shen

  • 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

    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

    Horseradish is a spicy root vegetable and it also produces horseradish peroxidase, an enzyme widely used in biochemistry applications. Here, the authors report its telomere-to-telomere reference genome, reveal subgenome diversification and the effect on the biosynthesis of glucosinolates and horseradish peroxidases.

    • Fei Shen
    • , Shixiao Xu
    •  & Martin A. Lysak

  • 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

  • Article
    | Open Access

    Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.

    • Liang Ma
    • , Ke-Wei Liu
    •  & Zhong-Jian Liu

  • Article
    | Open Access

    Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.

    • Xing Guo
    • , Fang Wang
    •  & Huan Liu

  • Article
    | Open Access

    While the organelle genome is commonly considered to be a single circular DNA molecule, extensive variation exists. Here, the authors report multipartite minicircular genomes in red algae and indicate an origin driven by recombination due to loss of DNA replication, recombination, and repair genes.

    • Yongsung Lee
    • , Chung Hyun Cho
    •  & Hwan Su Yoon

  • 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

    The precise inference of structural variants (SVs) requires suitable sequencing technologies and computational tools. Here, in order to analyse SVs with haplotype resolution, the author applies high-resolution long-read sequencing and long-range Hi-C to a melanoma cell line and develops an efficient graph-based computational framework, pstools.

    • Shilpa Garg

  • Article
    | Open Access

    Pachytene Piwi-interacting RNAs (piRNAs) expressed in mammalian germ lines are abundant, but their evolution and function are not fully understood. Here, the authors find that pachytene piRNA loci are hotspots of structural variation, which underlies rapid piRNA birth, divergence, and loss.

    • Yu H. Sun
    • , Hongxiao Cui
    •  & Xin Zhiguo Li

  • Article
    | Open Access

    Few genetic loci have been associated with tuberculosis infection, possibly because of the influence of genetic variation in the pathogen. Here, the authors integrate human and Mycobacterium tuberculosis genetics to find genome-genome interactions associated with infection.

    • Jody Phelan
    • , Paula Josefina Gomez-Gonzalez
    •  & Taane G. Clark

  • Article
    | Open Access

    Understanding origin and adaptation of weeds is important for their management. Here, via genome assembly, population genomics, and QTL mapping, the authors establish Cardamine occulta as a model to study weed ruderality and show FLC and CRY2 as genetic drivers for the establishment of short life cycle.

    • Ling-Zi Li
    • , Zhou-Geng Xu
    •  & Jia-Wei Wang

  • Article
    | Open Access

    The human genome harbors more than 4.5 million transposable element (TE)-derived insertions, the result of recurrent waves of invasion and internal propagation. Here they show that TEs belonging to evolutionarily recent subfamilies go on to regulate later stages of human embryonic development, notably conditioning the expression of genes involved in gastrulation and early organogenesis.

    • Julien Pontis
    • , Cyril Pulver
    •  & Didier Trono

  • Article
    | Open Access

    Here the authors characterize structural variations (SVs) in a cohort of individuals with complex genomic rearrangements, identifying breakpoints by employing short- and long-read genome sequencing and investigate their impact on gene expression and the three-dimensional chromatin architecture. They find breakpoints are enriched in inactive regions and can result in chromatin domain fusions.

    • Robert Schöpflin
    • , Uirá Souto Melo
    •  & Stefan Mundlos

  • Article
    | Open Access

    Identifying structural variants (SVs) under positive selection in cancer is challenging. Here, the authors develop CSVDriver, a method that computes SV breakpoint proximity and the contribution of elements such as topologically associating domains, and identifies loci that show signs of positive selection and contain known and putative drivers.

    • Alexander Martinez-Fundichely
    • , Austin Dixon
    •  & Ekta Khurana

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