Genome informatics articles within Nature

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  • Article
    | Open Access

    We build a polyploid reference genome for hybrid sugarcane cultivar R570, improving on its current ‘mosaic monoploid’ representation, enabling fine-grain description of genome architecture and the exploration of candidate genes underlying the Bru1 brown rust resistance locus.

    • A. L. Healey
    • , O. Garsmeur
    •  & A. D’Hont

  • Article
    | Open Access

    We analysed 149,842 environmental genomes from multiple habitats and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel gene families exclusive to uncultivated prokaryotic taxa spanning multiple species.

    • Álvaro Rodríguez del Río
    • , Joaquín Giner-Lamia
    •  & Jaime Huerta-Cepas

  • Article |

    We present the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference.

    • Arang Rhie
    • , Sergey Nurk
    •  & Adam M. Phillippy

  • Article |

    A study reports the development of an algorithm, BISCUT, that detects genomic loci under selective pressure by relying on the distribution of breakpoints across chromosome arms, and uses it to explore how aneuploidies affect tumorigenesis.

    • Juliann Shih
    • , Shahab Sarmashghi
    •  & Rameen Beroukhim

  • Article
    | Open Access

    A study reports data from the first phase of the Chinese Pangenome Consortium including 116 de novo assemblies from 58 core samples representing 36 minority Chinese ethnic groups.

    • Yang Gao
    • , Xiaofei Yang
    •  & Shuhua Xu

  • Article
    | Open Access

    An initial draft of the human pangenome is presented and made publicly available by the Human Pangenome Reference Consortium; the draft contains 94 de novo haplotype assemblies from 47 ancestrally diverse individuals.

    • Wen-Wei Liao
    • , Mobin Asri
    •  & Benedict Paten

  • Article
    | Open Access

    Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.

    • Mireia Valles-Colomer
    • , Aitor Blanco-Míguez
    •  & Nicola Segata

  • Article
    | Open Access

    A new framework enables a pan-cancer reference set of copy number signatures derived from allele-specific profiles from different experimental assays.

    • Christopher D. Steele
    • , Ammal Abbasi
    •  & Nischalan Pillay

  • Analysis
    | Open Access

    A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.

    • Diane P. Genereux
    • , Aitor Serres
    •  & Elinor K. Karlsson

  • Article
    | Open Access

    High-coverage, ultra-long-read nanopore sequencing is used to create a new human genome assembly that improves on the coverage and accuracy of the current reference (GRCh38) and includes the gap-free, telomere-to-telomere sequence of the X chromosome.

    • Karen H. Miga
    • , Sergey Koren
    •  & Adam M. Phillippy

  • Article
    | Open Access

    A large empirical assessment of sequence-resolved structural variants from 14,891 genomes across diverse global populations in the Genome Aggregation Database (gnomAD) provides a reference map for disease-association studies, population genetics, and diagnostic screening.

    • Ryan L. Collins
    • , Harrison Brand
    •  & Michael E. Talkowski

  • Article |

    The GLASS Consortium studies the evolutionary trajectories of 222 patients with a diffuse glioma to aid in our understanding of tumour progression and treatment failure

    • Floris P. Barthel
    • , Kevin C. Johnson
    •  & Roel G. W. Verhaak

  • Article |

    The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.

    • David Zeevi
    • , Tal Korem
    •  & Eran Segal

  • Article
    | Open Access

    Draft prokaryotic genomes from faecal metagenomes of diverse human populations enrich our understanding of the human gut microbiome by identifying over two thousand new species-level taxa that have numerous disease associations.

    • Stephen Nayfach
    • , Zhou Jason Shi
    •  & Nikos C. Kyrpides

  • Letter |

    RNA velocity, estimated in single cells by comparison of spliced and unspliced mRNA, is a good indicator of transcriptome dynamics and will provide a useful tool for analysis of developmental lineage.

    • Gioele La Manno
    • , Ruslan Soldatov
    •  & Peter V. Kharchenko

  • Letter
    | Open Access

    An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize.

    • Yinping Jiao
    • , Paul Peluso
    •  & Doreen Ware

  • Letter |

    A conformation capture sequencing method is developed to link multiple genomic loci into three-dimensional proximity chains called chromosomal walks (C-walks), adding to our understanding of how higher-order chromosomal structures participate in genome regulation.

    • Pedro Olivares-Chauvet
    • , Zohar Mukamel
    •  & Amos Tanay

  • Article |

    Insights into the genomic architecture of heterosis for grain yield in rice are presented, and further mapping of grain yield loci resolves candidate genes that could be useful for breeding.

    • Xuehui Huang
    • , Shihua Yang
    •  & Bin Han

  • Article |

    Eukaryotes acquired their prokaryotic genes in two episodes of evolutionary influx corresponding to the origin of mitochondria and plastids, respectively, followed by extensive differential gene loss, uncovering a massive imprint of endosymbiosis in the nuclear genomes of complex cells.

    • Chuan Ku
    • , Shijulal Nelson-Sathi
    •  & William F. Martin

  • Article |

    The emRiboSeq sequencing method is used to track polymerase activity genome-wide in vivo; despite Okazaki fragment processing, DNA synthesized by error-prone polymerase-α (Pol-α) is retained in vivo and comprises ∼1.5% of the genome, establishing Pol-α as an important source of genomic variability and providing a mechanism for site-specific variation in nucleotide substitution rates.

    • Martin A. M. Reijns
    • , Harriet Kemp
    •  & Martin S. Taylor

  • Article |

    Family-based exome sequencing in a large autism study has identified 27 high-confidence gene targets and accurately estimates the contribution of both de novo gene-disrupting and missense mutations to the incidence of simplex autism, with target genes in affected females overlapping those in males of lower but not higher IQ; targets also overlap known targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes.

    • Ivan Iossifov
    • , Brian J. O’Roak
    •  & Michael Wigler

  • Article |

    DNA double-stranded breaks (DSBs) are shown to form in greater numbers in yeast cells lacking ZMM proteins, which are traditionally regarded as acting strictly downstream of DSB formation; these findings shed light on how cells balance the beneficial and deleterious outcomes of DSB formation.

    • Drew Thacker
    • , Neeman Mohibullah
    •  & Scott Keeney

  • Letter
    | Open Access

    A full genome sequence is presented of sugar beet Beta vulgaris, the first plant belonging to Caryophyllales to have its genome sequenced; spinach was sequenced to enable inter-clade comparisons, and intraspecific variation was analysed by comparative genomics of a progenitor of all beet crops and additional sugar beet accessions.

    • Juliane C. Dohm
    • , André E. Minoche
    •  & Heinz Himmelbauer

  • Letter |

    In synthetic biology, the use of regulatory proteins that bind either DNA or RNA to reprogram mammalian cellular functions allows a variety of computational ‘logic circuits’ to be built in a plug-and-play manner, which may pave the way for precise and robust control of future gene-based and cell-based therapies.

    • Simon Ausländer
    • , David Ausländer
    •  & Martin Fussenegger

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