Genomics articles within Nature Communications

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  • Article
    | Open Access

    Topologically associating domains (TADs) are critical structural units in 3D genome organization, and their reorganization between health and disease states is associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the early stages of development. Here, the authors present an algorithm leveraging random matrix theory to identify reorganized TADs.

    • Dunming Hua
    • , Ming Gu
    •  & Dechao Tian

  • Article
    | Open Access

    Copy number variants (CNV) are shown to contribute to the etiology of various genetic disorders. Here, authors present ECOLE, a deep learning-based somatic and germline CNV caller for WES data. Utilising a variant of the transformer architecture, the model is trained to call CNVs per exon.

    • Berk Mandiracioglu
    • , Furkan Ozden
    •  & A. Ercument Cicek

  • Article
    | Open Access

    Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.

    • Jiao Yang
    • , Ying Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    The integration of single-cell and spatial data can provide a more comprehensive picture of the network of cells within the tumour microenvironment. Here the authors use a combination of single-cell and spatial technologies including 10x Xenium to characterise serial formalin-fixed, paraffin-embedded human breast cancer sections.

    • Amanda Janesick
    • , Robert Shelansky
    •  & Sarah E. B. Taylor

  • Article
    | Open Access

    Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

    • Senne Heeren
    • , Ilse Maes
    •  & Frederik Van den Broeck

  • Article
    | Open Access

    Cyprinids fish species contain multiple subgenomes as a result of past duplications. Here, Xu et al. report new genomes of 21 cyprinid fish and conclude that observed subgenome dominance patterns are likely due to both maternal dominance and transposable element densities in each polyploid.

    • Min-Rui-Xuan Xu
    • , Zhen-Yang Liao
    •  & Hua-Hao Zhang

  • 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

    Human ADAR1 and ADAR2 edit millions of adenosines transcriptome-wide, altering RNA structure. Here the authors show that variations in RNA binding domains influence site-specific editing, enhancing ADAR2-targeted therapeutics.

    • Marlon S. Zambrano-Mila
    • , Monika Witzenberger
    •  & Schraga Schwartz

  • Article
    | Open Access

    The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.

    • Youjie Zhao
    • , Chengyong Su
    •  & Jiasheng Hao

  • Article
    | Open Access

    Here the authors show that in activated B cells, RIF1 primarily binds early-replicating active chromatin and promotes early replication. RIF1 and MCM proteins establish early replication timing signatures genome-wide and ensure early replication of highly transcribed genes.

    • Daniel Malzl
    • , Mihaela Peycheva
    •  & Rushad Pavri

  • Article
    | Open Access

    It has recently been reported a link between Alzheimer’s disease and mobilization of transposable elements (TEs) in heterochromatic regions. Here the authors demonstrate that dysregulation of the pioneer transcription factor c-JUN (AP-1) underlies aberrant transposable element mobilization, associated innate immune 2 response, and impaired neurogenesis in Alzheimer’s disease.

    • Chiara Scopa
    • , Samantha M. Barnada
    •  & Marco Trizzino

  • Article
    | Open Access

    Long-read single-cell RNA sequencing is capable of detecting isoform-level gene expression and genomic alterations such as mutations and gene fusions, thereby providing cell-specific genotype-phenotype information. Here, the authors use long-read scRNA-seq on metastatic ovarian cancer samples and detect cell-type specific isoforms and gene fusions that may otherwise be misclassified in short-read data.

    • Arthur Dondi
    • , Ulrike Lischetti
    •  & Niko Beerenwinkel

  • Article
    | Open Access

    Epigenetic drift has been hypothesized to contribute to epigenetic clock signals and variation in lifespan across species. Here, the authors show that an empirical measure of epigenetic drift scales with maximum lifespan across four mammal species and accumulates in non-random genomic locations.

    • Emily M. Bertucci-Richter
    •  & Benjamin B. Parrott

  • Perspective
    | Open Access

    Endangered polar ecosystems play critical roles in the Earth’s climate system and comprise many different habitats with unique organisms. Here, the authors propose a community road map to use multi-omics data from polar organisms for conservation, ecosystem services and societal gain.

    • M. S. Clark
    • , J. I. Hoffman
    •  & T. Mock

  • Article
    | Open Access

    Pneumococcal vaccination has been shown to promote emergence of non-vaccine S. pneumoniae serotypes. Here, the authors use data from Malawi to investigate whether vaccine introduction also results in changes in metabolic, virulence, and antimicrobial resistance profiles of circulating strains.

    • Uri Obolski
    • , Todd D. Swarthout
    •  & Robert S. Heyderman

  • Article
    | Open Access

    The direct impacts of transposable element dynamics on polyploid regulation and developmental specificity remain unclear. Here, the authors show that a large proportion of enhancer-like elements (ELEs) are mainly originated from RLG_famc7.3 specifically expanded in subgenome A, producing active nascent transcripts and influencing wheat spike development.

    • Yilin Xie
    • , Songbei Ying
    •  & Yijing Zhang

  • Article
    | Open Access

    Understanding T cell behaviour in cancers is vital for improving immunotherapies. Here, the authors present spatially resolved T cell receptor sequencing (SPTCR-seq), a technology that annotates T cell receptors within the tumour ecosystem.

    • Jasim Kada Benotmane
    • , Jan Kueckelhaus
    •  & Dieter Henrik Heiland

  • Article
    | Open Access

    Verticillum wilt is an important cotton disease caused by fungal pathogen Verticillium dahiae. Here, the authors assemble the genomes of defoliating and non-defoliating isolates of the pathogen, identify virulence gene SP3, and develop a disease control strategy using polyethyleneimine-coated MXene quantum dots.

    • Ping Qiu
    • , Jiayue Li
    •  & Longfu Zhu

  • Article
    | Open Access

    Bacteria usually have at least one rRNA operon on the chromosome, suggesting that the exclusive presence of rRNA operons on a plasmid is rare and unlikely to be stably maintained. Here, Anda et al. find that at least four bacterial clades in different phyla lost their chromosomal rRNA operons independently, and one of the clades has maintained this peculiar genome organization for hundreds of millions of years.

    • Mizue Anda
    • , Shun Yamanouchi
    •  & Wataru Iwasaki

  • Article
    | Open Access

    Pseudotime analysis is prevalent in single-cell RNA-seq, but it remains challenging to perform it across multiple samples and experimental conditions. Here, the authors develop Lamian, a computational framework for multi-sample pseudotime analysis that adjusts for biological and technical variation to detect gene program changes along cell trajectories and across conditions.

    • Wenpin Hou
    • , Zhicheng Ji
    •  & Hongkai Ji

  • Article
    | Open Access

    The study reveals limitations in widely used RNA-seq aligners, which create 'phantom' introns in reference databases. The authors introduce EASTR, a computational tool that not only enhances alignment accuracy but also uncovers existing annotation errors. This improvement bolsters the dependability of subsequent RNA-seq analyses.

    • Ida Shinder
    • , Richard Hu
    •  & Mihaela Pertea

  • Article
    | Open Access

    Paediatric liver cancer is rare, and often associated with a predisposition syndrome. Here, the authors show that 11p15.5 mosaic alteration in the liver is a pre-neoplastic lesion associated with hepatoblastoma, and spatial transcriptomics together with single-nucleus RNAseq identify a an altered zonation in the liver of these patients.

    • Jill Pilet
    • , Theo Z. Hirsch
    •  & Jessica Zucman-Rossi

  • Article
    | Open Access

    Staphylococcus pseudintermedius has a wide host-range in domesticated and wild animals, yet it has also been isolated as an opportunistic pathogen in human wounds. In this work, the authors genotypically analyse S. pseudintermedius isolates from veterinary diagnostic laboratories and medical care centres, alongside household surfaces and inhabitants.

    • Sanjam S. Sawhney
    • , Rhiannon C. Vargas
    •  & Gautam Dantas

  • Article
    | Open Access

    The meninges protect the central nervous system at the brain border, and its dysfunction can lead to neural inflammation and cell damage. Here, the authors uncover the gene signatures of diverse cell types in the aged human leptomeninges and highlight their changes in Alzheimer’s Disease.

    • Nicola A. Kearns
    • , Artemis Iatrou
    •  & Yanling Wang

  • Article
    | Open Access

    Human embryo development involves extensive transcriptional remodeling. In this study, the authors apply long- and short-read RNA-Seq to profile the transcriptomes of 73 human preimplantation embryos spanning zygotic to blastocyst stages, identifying tens of thousands of additional isoforms transcribed from both known and unannotated gene loci.

    • Denis Torre
    • , Nancy J. Francoeur
    •  & Robert Sebra

  • Article
    | Open Access

    The death cap mushroom Amanita phalloides is invading California but little is known about how it spreads through forests. Wang et al. discover that this fungus can develop mushrooms and sporulate without mating; the nuclei involved in unisexuality appear to have persisted in invaded habitats for decades.

    • Yen-Wen Wang
    • , Megan C. McKeon
    •  & Anne Pringle

  • Article
    | Open Access

    Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.

    • Ashley T. Sendell-Price
    • , Frank J. Tulenko
    •  & Manfred Schartl

  • 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

    A wide variety of tissues exhibit nested hierarchical organisation of cells in gene expression and activities. Here, authors present NeST, a method for spatial transcriptomics to identify such structures and uncover their functions via ligand-receptor communication, in both two and three dimensions.

    • Benjamin L. Walker
    •  & Qing Nie

  • Article
    | Open Access

    The brushtail possum is a treasured Australian marsupial, but also a harmful pest introduced into New Zealand. Here, using functional genomics and a new chromosome-level genome assembly of New Zealand possums, Bond et al. quantify their genome admixture and identify unique parent-specific and weaning associated gene expression.

    • Donna M. Bond
    • , Oscar Ortega-Recalde
    •  & Timothy A. Hore

  • Article
    | Open Access

    Despite the significance of mosquitos for human health, little research has focused on their phylogeny. Here, the authors present a resolved phylogenetic history of mosquitoes based on phylogenomics showing that these major disease vectors radiated coincidentally with geologic events and the diversification of their hosts.

    • John Soghigian
    • , Charles Sither
    •  & Brian M. Wiegmann

  • 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

    In the absence of recombination, the number of transposable elements (TEs) increases, but their accumulation dynamics are not well characterized. This study shows that TEs rapidly accumulated in non-recombining fungal mating-type chromosomes before reaching a plateau, possibly forming a TE reservoir.

    • Marine Duhamel
    • , Michael E. Hood
    •  & Tatiana Giraud

  • Article
    | Open Access

    Haplotype-resolved long, complex tandem repeats remain largely hidden despite their potential relevance to disease. Here, the authors reveal and analyze the genome-wide landscape of these repeats using a high-precision algorithm.

    • Kazuki Ichikawa
    • , Riki Kawahara
    •  & Shinichi Morishita

  • 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

    Evolutionary relationships among green plants are unresolved and, in particular, the phylogenetic position of Prasinodermophyta remains controversial. Here, the authors conduct phylogenomic analyses to resolve relationships within Viridiplantae, suggesting that this group diverged between the Great Oxidation Event and the Neoproterozoic Oxygenation Event.

    • Zhiping Yang
    • , Xiaoya Ma
    •  & Bojian Zhong

  • Article
    | Open Access

    Lotto et al. delineate cell diversity and mechanisms during heart valve development using scRNA-seq. They identify distinct cell types and states, the emergence of epithelial-mesenchymal plasticity, and cell interactions that may govern this process.

    • Jeremy Lotto
    • , Rebecca Cullum
    •  & Pamela A. Hoodless

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