Comparative genomics articles within Nature

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  • 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

    An insertion of an Alu element into an intron of the TBXT gene is identified as a genetic mechanism of tail-loss evolution in humans and apes, with implications for human health today.

    • Bo Xia
    • , Weimin Zhang
    •  & Itai Yanai

  • 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

    Whole-genome sequencing is used to analyse the landscape of somatic mutation in intestinal crypts from 16 mammalian species, revealing that rates of somatic mutation inversely scale with the lifespan of the animal across species.

    • Alex Cagan
    • , Adrian Baez-Ortega
    •  & Iñigo Martincorena

  • Article
    | Open Access

    A revised, universal nomenclature for the vertebrate genes that encode the oxytocin and vasopressin–vasotocin ligands and receptors will improve our understanding of gene evolution and facilitate the translation of findings across species.

    • Constantina Theofanopoulou
    • , Gregory Gedman
    •  & Erich D. Jarvis

  • Article
    | Open Access

    New reference genomes of the two extant monotreme lineages (platypus and echidna) reveal the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution.

    • Yang Zhou
    • , Linda Shearwin-Whyatt
    •  & Guojie Zhang

  • Article
    | Open Access

    Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

    • Sean Walkowiak
    • , Liangliang Gao
    •  & Curtis J. Pozniak

  • Article |

    A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

    • Shaohong Feng
    • , Josefin Stiller
    •  & Guojie Zhang

  • 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

    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 |

    A transcriptome dataset from seven organs and seven mammalian species throughout development is used to analyse the expression of long noncoding RNAs in tissues within and between species, and at different stages of organ development.

    • Ioannis Sarropoulos
    • , Ray Marin
    •  & Henrik Kaessmann

  • Article
    | Open Access

    Sequencing and assembly of the 32-Gb genome of the Mexican axolotl reveals that it lacks the developmental gene Pax3, which is essential in other vertebrates; the genome sequence could improve our understanding of the evolution of the axolotl’s remarkable regenerative capabilities.

    • Sergej Nowoshilow
    • , Siegfried Schloissnig
    •  & Eugene W. Myers

  • Letter |

    The class 2 type VI RNA-guided RNA-targeting CRISPR–Cas effector Cas13 can be engineered for RNA knockdown and binding, expanding the CRISPR toolset with a flexible platform for studying RNA in mammalian cells and therapeutic development.

    • Omar O. Abudayyeh
    • , Jonathan S. Gootenberg
    •  & Feng Zhang

  • Article
    | Open Access

    Sequencing the genomes of two enteropneusts reveals complex genomic organization and developmental innovation in the ancestor of deuterostomes, a group of animals including echinoderms (starfish and their relatives) and chordates (which includes humans).

    • Oleg Simakov
    • , Takeshi Kawashima
    •  & John Gerhart

  • 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 |

    Single-molecule, real-time DNA sequencing is used to analyse a haploid human genome (CHM1), thus closing or extending more than half of the remaining 164 euchromatic gaps in the human genome; the complete sequences of euchromatic structural variants (including inversions, complex insertions and tandem repeats) are resolved at the base-pair level, suggesting that a greater complexity of the human genome can now be accessed.

    • Mark J. P. Chaisson
    • , John Huddleston
    •  & Evan E. Eichler

  • 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

  • Letter
    | Open Access

    Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

    • Mark B. Gerstein
    • , Joel Rozowsky
    •  & Robert Waterston

  • Letter
    | Open Access

    A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

    • Alan P. Boyle
    • , Carlos L. Araya
    •  & Michael Snyder

  • Outlook |

    A subterranean species that seems to be cancer-proof is providing promising clues on how we might prevent the disease in humans.

    • Sarah Deweerdt

  • Article
    | Open Access

    The draft genome of the ctenophore Pleurobrachia bachei (Pacific sea gooseberry) is presented, together with ten other ctenophore transcriptomes — these genomes have a very different neurogenic, immune and developmental gene content when compared with other animal genomes, and it is proposed that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.

    • Leonid L. Moroz
    • , Kevin M. Kocot
    •  & Andrea B. Kohn

  • 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

  • Letter |

    The phenomenon of sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio — now, a single gene, doublesex, is shown to control supergene mimicry, a finding that is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci.

    • K. Kunte
    • , W. Zhang
    •  & M. R. Kronforst

  • Article
    | Open Access

    Whole-genome analysis of the elephant shark, a cartilaginous fish, shows that it is the slowest evolving of all known vertebrates, lacks critical bone formation genes and has an unusual adaptive immune system.

    • Byrappa Venkatesh
    • , Alison P. Lee
    •  & Wesley C. Warren

  • 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

  • Letter
    | Open Access

    A high-quality sequence assembly of the zebrafish genome reveals the largest gene set of any vertebrate and provides information on key genomic features, and comparison to the human reference genome shows that approximately 70% of human protein-coding genes have at least one clear zebrafish orthologue.

    • Kerstin Howe
    • , Matthew D. Clark
    •  & Derek L. Stemple

  • Letter |

    To identify comprehensively factors involved in RNAi and microRNA-mediated gene expression regulation, this study performed a phylogenetic analysis of 86 eukaryotic species; the candidates this approach highlighted were subjected to Bayesian analysis with transcriptional and proteomic interaction data, identifying protein orthologues of already known RNAi silencing factors, as well as other hits involved in splicing, suggesting a connection between the two processes.

    • Yuval Tabach
    • , Allison C. Billi
    •  & Gary Ruvkun

  • Article
    | Open Access

    Sequencing the nuclear genomes of Guillardia theta and Bigelowiella natans, transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of certain eukaryotic algae, reveals unprecedented alternative splicing for a single-celled organism (B. natans) and extensive genetic and biochemical mosaicism, shedding light on why nucleomorphs persist in these species but not other algae.

    • Bruce A. Curtis
    • , Goro Tanifuji
    •  & John M. Archibald

  • Letter
    | Open Access

    Sequencing of the bonobo genome shows that more than three per cent of the human genome is more closely related to either the bonobo genome or the chimpanzee genome than those genomes are to each other.

    • Kay Prüfer
    • , Kasper Munch
    •  & Svante Pääbo

  • News & Views |

    The genetic basis of traits can be understood by comparing the DNA of varieties of the same species. The genomes of many varieties of a model plant organism have now been sequenced, and the results are revelatory. See Article p.419

    • Michael Bevan

  • Letter
    | Open Access

    The genome of the southeast Asian orang-utan has been sequenced. The draft assembly of a Sumatran individual alongside sequence data from five Sumatran and five Bornean orang-utan genomes is presented. The resources and analyses described offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.

    • Devin P. Locke
    • , LaDeana W. Hillier
    •  & Richard K. Wilson

  • News & Views |

    Analysis of ancient nuclear DNA, recovered from 40,000-year-old remains in the Denisova Cave, Siberia, hints at the multifaceted interaction of human populations following their migration out of Africa. See Article p.1053

    • Carlos D. Bustamante
    •  & Brenna M. Henn

  • Article
    | Open Access

    Using DNA from a finger bone, the genome of an archaic hominin from southern Siberia has been sequenced to about 1.9-fold coverage. The group to which this individual belonged shares a common origin with Neanderthals, and although it was not involved in the putative gene flow from Neanderthals into Eurasians, it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. A tooth whose mitochondrial genome is very similar to that of the finger bone further suggests that these hominins are evolutionarily distinct from Neanderthals and modern humans.

    • David Reich
    • , Richard E. Green
    •  & Svante Pääbo

  • News & Views |

    Comparative genomics studies reveal molecular signatures of the controversial 'phylotypic' stage — a time when embryos of members of an animal phylum all look more alike than at other embryonic stages. See Letters p.811 & p.815

    • Benjamin Prud'homme
    •  & Nicolas Gompel

  • Article
    | Open Access

    Fungi from the genus Fusarium are important pathogens of animals and crop plants. Some have a wide host range, whereas others are more specific in the organisms they infect. Here, clues are provided as to how differences in specificity come about. The genomes of two Fusarium fungi with differing host ranges have been sequenced, and compared with the genome of a third species. Experiments show that transferring two whole chromosomes turns a non-pathogenic Fusarium strain into a pathogenic one.

    • Li-Jun Ma
    • , H. Charlotte van der Does
    •  & Martijn Rep

  • Article |

    The genome of the wild grass Brachypodium distachyon (Brachypodium), a member of the Pooideae subfamily, is sequenced. The Pooideae are one of three subfamilies of grasses that provide the bulk of human nutrition and may become major sources of renewable energy. Availability of the genome sequence should help establish Brachypodium as a model for developing new energy and food crops.

    • John P. Vogel
    • , David F. Garvin
    •  & Ivan Baxter

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