Genome evolution articles within Nature

Featured

  • Article
    | Open Access

    Patagia—the mammalian gliding membrane—repeatedly originated through a process of convergent genomic evolution, whereby the regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species.

    • Jorge A. Moreno
    • , Olga Dudchenko
    •  & Ricardo Mallarino

  • Article
    | Open Access

    A comparison of two complete sets of human centromeres reveals that the centromeres show at least a 4.1-fold increase in single-nucleotide variation compared with their unique flanks, and up to 3-fold variation in size, resulting from an accelerated mutation rate.

    • Glennis A. Logsdon
    • , Allison N. Rozanski
    •  & Evan E. Eichler

  • 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

    Introduction of a long synthetic DNA into yeast genomic loci results in high default transcriptional activity in yeast but low activity in mouse, suggesting distinct default levels of genomic activity in these organisms.

    • Brendan R. Camellato
    • , Ran Brosh
    •  & Jef D. Boeke

  • Article
    | Open Access

    A chromosome-scale genome assembly for the hagfish Eptatretus atami, combined with a series of phylogenetic analyses, sheds light on ancient polyploidization events that had a key role in the early evolution of vertebrates.

    • Ferdinand Marlétaz
    • , Nataliya Timoshevskaya
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    Whole-genome alignment of 239 primate species reveals noncoding regulatory elements that are under selective constraint in primates but not in other placental mammals, that are enriched for variants that affect human gene expression and complex traits in diseases.

    • Lukas F. K. Kuderna
    • , Jacob C. Ulirsch
    •  & Kyle Kai-How Farh

  • Article
    | Open Access

    An engineered minimal cell evolves to escape the negative consequences of genome streamlining.

    • R. Z. Moger-Reischer
    • , J. I. Glass
    •  & J. T. Lennon

  • Article
    | Open Access

    Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as the sister group to all other animals.

    • Darrin T. Schultz
    • , Steven H. D. Haddock
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    A study comparing the pattern of single-nucleotide variation between unique and duplicated regions of the human genome shows that mutation rate and interlocus gene conversion are elevated in duplicated regions.

    • Mitchell R. Vollger
    • , Philip C. Dishuck
    •  & Evan E. Eichler

  • Article
    | Open Access

    Comparisons within the human pangenome establish that homologous regions on short arms of heterologous human acrocentric chromosomes actively recombine, leading to the high rate of Robertsonian translocation breakpoints in these regions.

    • Andrea Guarracino
    • , Silvia Buonaiuto
    •  & Erik Garrison

  • Article
    | Open Access

    Sequencing of individual human lymphocyte clones shows that they are highly prone to mutations, with higher burdens in memory cells than in naive cells arising from mutational processes associated with differentiation and tissue residency.

    • Heather E. Machado
    • , Emily Mitchell
    •  & Peter J. Campbell

  • Article
    | Open Access

    The complete assembly of human chromosome 8 resolves previous gaps and reveals hidden complex forms of genetic variation, enabling functional and evolutionary characterization of primate centromeres.

    • Glennis A. Logsdon
    • , Mitchell R. Vollger
    •  & Evan E. Eichler

  • Article |

    Single-cell analysis of genomes from primary human breast tumours and cell lines shows that chromosomal aberrations continue to evolve during primary tumour expansion, resulting in a milieu of subclones within the tumour.

    • Darlan C. Minussi
    • , Michael D. Nicholson
    •  & Nicholas E. Navin

  • Article
    | Open Access

    The genome of the biofuel crop switchgrass (Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

    • John T. Lovell
    • , Alice H. MacQueen
    •  & Jeremy Schmutz

  • Article
    | Open Access

    A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.

    • Axel Meyer
    • , Siegfried Schloissnig
    •  & Manfred Schartl

  • Article
    | Open Access

    The approximately 5-Gb tuatara (Sphenodon punctatus) genome assembly provides a resource for analysing amniote evolution, and highlights the imperative for meaningful cultural engagement with Indigenous communities in genome-sequencing endeavours.

    • Neil J. Gemmell
    • , Kim Rutherford
    •  & Haydn Edmonds

  • Article
    | Open Access

    The genome of the tropical blue-petal water lily Nymphaea colorata and the transcriptomes from 19 other Nymphaeales species provide insights into the early evolution of angiosperms.

    • Liangsheng Zhang
    • , Fei Chen
    •  & Haibao Tang

  • Article
    | Open Access

    Whole-genome sequencing of 1,011 natural isolates of the yeast Saccharomyces cerevisiae reveals its evolutionary history, including a single out-of-China origin and multiple domestication events, and provides a framework for genotype–phenotype studies in this model organism.

    • Jackson Peter
    • , Matteo De Chiara
    •  & Joseph Schacherer

  • Letter
    | Open Access

    A combination of advanced sequencing and mapping techniques is used to produce a reference genome of Aegilops tauschii, progenitor of the wheat D genome, providing a valuable resource for comparative genetic studies.

    • Ming-Cheng Luo
    • , Yong Q. Gu
    •  & Jan Dvořák

  • Letter
    | Open Access

    The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from the genomes of its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness.

    • Thomas Mock
    • , Robert P. Otillar
    •  & Igor V. Grigoriev

  • Article
    | Open Access

    The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

    • Adam M. Session
    • , Yoshinobu Uno
    •  & Daniel S. Rokhsar

  • Letter |

    The observations that introns are acquired in bursts and that exons are often nucleosome-sized can be explained by the generation of introns from DNA transposons, which insert between nucleosomes.

    • Jason T. Huff
    • , Daniel Zilberman
    •  & Scott W. Roy

  • Letter |

    Whole-genome sequencing of individuals from 125 populations provides insight into patterns of genetic diversity, natural selection and human demographic history during the peopling of Eurasia and finds evidence for genetic vestiges of an early expansion of modern humans out of Africa in Papuans.

    • Luca Pagani
    • , Daniel John Lawson
    •  & Mait Metspalu

  • Article
    | Open Access

    The genome sequence is presented for the Atlantic salmon (Salmo salar), providing information about a rediploidization following a salmonid-specific whole-genome duplication event that resulted in an autotetraploidization.

    • Sigbjørn Lien
    • , Ben F. Koop
    •  & William S. Davidson

  • Letter
    | Open Access

    Oropetium thomaeum is a resurrection plant that can survive extreme water stress through desiccation to complete dryness, providing a model for drought tolerance; here, whole-genome sequencing and assembly of the Oropetium genome using single-molecule real-time sequencing is reported.

    • Robert VanBuren
    • , Doug Bryant
    •  & Todd C. Mockler

  • Letter |

    Enamel is a tissue unique to vertebrates, and nowadays associated with teeth; here, histological material from a fossil bony fish and genomic data from an extant, armour-plated fish are analysed to show that enamel originated on the body surface and only later colonized the teeth.

    • Qingming Qu
    • , Tatjana Haitina
    •  & Per Erik Ahlberg

  • 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
    | Open Access

    Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification.

    • David Brawand
    • , Catherine E. Wagner
    •  & Federica Di Palma

  • Article
    | Open Access

    The Eucalyptus grandis genome has been sequenced, revealing the greatest number of tandem duplications of any plant genome sequenced so far, and the highest diversity of genes for specialized metabolites that act as chemical defence and provide unique pharmaceutical oils; genome sequencing of the sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression.

    • Alexander A. Myburg
    • , Dario Grattapaglia
    •  & Jeremy Schmutz

  • Article |

    A study comparing the Y chromosome across mammalian species reveals that selection to maintain the ancestral dosage of homologous X–Y gene pairs preserved a handful of genes on the Y chromosome while the rest were lost; the survival of broadly expressed dosage-sensitive regulators of gene expression suggest that the human Y chromosome is essential for male viability.

    • Daniel W. Bellott
    • , Jennifer F. Hughes
    •  & David C. Page

  • Article |

    A computational approach for predicting the future evolution of the human influenza virus, based on population-genetic data of previous strains, is presented; this model holds promise for improving vaccine strain selection for seasonal influenza.

    • Marta Łuksza
    •  & Michael Lässig

  • Letter
    | Open Access

    The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells.

    • Jean-François Flot
    • , Boris Hespeels
    •  & Karine Van Doninck

  • Article
    | Open Access

    Genome sequencing and phylogenomic analysis show that the lungfish, not the coelacanth, is the closest living relative of tetrapods, that coelacanth protein-coding genes are more slowly evolving than those of tetrapods and lungfish, and that the genes and regulatory elements that underwent changes during the vertebrate transition to land reflect adaptation to a new environment.

    • Chris T. Amemiya
    • , Jessica Alföldi
    •  & Kerstin Lindblad-Toh

Browse broader subjects

Browse Genome evolution across other nature.com journals