Genome evolution articles within Nature Communications

Featured

  • Article
    | Open Access

    Head-on replication-transcription collisions occur within genes encoded on the lagging DNA strand. Here, the authors show that a large number of originally co-oriented (leading strand) genes have inverted to the head-on orientation, increasing both gene-specific mutation rates, and the overall evolvability of several bacterial pathogens.

    • Christopher N. Merrikh
    •  & Houra Merrikh

  • Article
    | Open Access

    Ducks, one of the most common domestic fowls, originated from mallards. Here, the authors perform whole-genome sequencing of mallards, indigenous-breed ducks, and Pekin ducks, as well as 1026 ducks from a population generated by wild × domestic crosses to identify selection signals and map variants associated with body size and plumage color.

    • Zhengkui Zhou
    • , Ming Li
    •  & Yu Jiang

  • Article
    | Open Access

    Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.

    • Giulia I. M. Pasquesi
    • , Richard H. Adams
    •  & Todd A. Castoe

  • Article
    | Open Access

    Parasitic lifestyles leave unique genomic footprints. Here, the authors describe the genome sequence of a parasitic plant, Cuscuta campestris, and find that gene losses and host gene acquisitions reflect the independence from photosynthesis and the ability to retain and express chunks of foreign genomic DNA.

    • Alexander Vogel
    • , Rainer Schwacke
    •  & Kirsten Krause

  • Article
    | Open Access

    It is unclear if experimental evolution is a good model for natural processes. Here, Clerissi et al. find parallels between the evolution of symbiosis in rhizobia after horizontal transfer of a plasmid over 10 million years ago and experimentally evolved symbionts.

    • Camille Clerissi
    • , Marie Touchon
    •  & Eduardo P. C. Rocha

  • Article
    | Open Access

    Giant viruses are visible by light microscopy and have unusually long genomes. Here, the authors report three new members of the Pandoraviridae family and investigate their evolution and diversity.

    • Matthieu Legendre
    • , Elisabeth Fabre
    •  & Jean-Michel Claverie

  • Article
    | Open Access

    The use of synthetic chromosomes and the recombinase-based SCRaMbLE system could enable rapid strain evolution through massive chromosome rearrangements. Here the authors present ReSCuES, which uses auxotrophic markers to rapidly identify yeast with rearrangements for strain engineering.

    • Zhouqing Luo
    • , Lihui Wang
    •  & Junbiao Dai

  • Article
    | Open Access

    SCRaMbLE has been used to rearrange synthetic chromosomes that have been introduced into host yeast. Here the authors produce semi-synthetic heterozygous diploid strains for rapid selection of phenotypes and map the rearrangements underlying selected phenotypes such as thermoresistance and caffeine resistance.

    • Michael J. Shen
    • , Yi Wu
    •  & Jef D. Boeke

  • Article
    | Open Access

    The SCRaMbLE system integrated into Sc2.0’s synthetic yeast chromosome project allows rapid strain evolution. Here the authors use a genetic logic gate to control induction of recombination in a haploid and diploid yeast carrying synthetic chromosomes.

    • Bin Jia
    • , Yi Wu
    •  & Ying-Jin Yuan

  • Article
    | Open Access

    Animals, the Metazoa, co-opted numerous unicellular genes in their transition to multicellularity. Here, the authors use phylogenomic analyses to infer the genome composition of the ancestor of extant animals and show there was also a burst of novel gene groups associated with this transition.

    • Jordi Paps
    •  & Peter W. H. Holland

  • Article
    | Open Access

    The American cockroach (Periplaneta americana) is an hemimetabolous insect with rapid growth, high fecundity, and remarkable tissue-regeneration capability. Here Li et al sequence its 3.38-Gb genome and perform the functional studies, yielding insights into its environmental adaptation and developmental plasticity.

    • Sheng Li
    • , Shiming Zhu
    •  & Shuai Zhan

  • Article
    | Open Access

    The population of Madagascar arose from admixture of Austronesian and Bantu genetic backgrounds. Analyzing local ancestry in genomes of 700 Malagasy, Pierron et al. identify signals of recent positive selection for African ancestry in a region on chromosome 1 with implications for physiology and disease risk.

    • Denis Pierron
    • , Margit Heiske
    •  & Thierry Letellier

  • Article
    | Open Access

    The canonical scenario of sex chromosome evolution is through the differentiation of ancestral pairs of autosomes. Here, Fraïsse and colleagues use a comparative genomic analysis that shows the deep conservation of the Z chromosome in Lepidoptera and supports a non-canonical origin of the W chromosome.

    • Christelle Fraïsse
    • , Marion A. L. Picard
    •  & Beatriz Vicoso

  • Article
    | Open Access

    Several models have been proposed to explain the emergence of sex chromosomes. Here, through comparative genomics and mutant analysis, Harkess et al. show that linked but separate genes on the Y chromosome are responsible for sex determination in Asparagus, supporting a two-gene model for sex chromosome evolution.

    • Alex Harkess
    • , Jinsong Zhou
    •  & Guangyu Chen

  • Article
    | Open Access

    The European continent is thought to have played a major role in the origins of modern dogs. Here, analysing two ancient dog genomes from Germany, the authors find significant genetic continuity throughout the Neolithic period and time dog domestication to ∼20,000–40,000 years ago.

    • Laura R. Botigué
    • , Shiya Song
    •  & Krishna R. Veeramah

  • Article
    | Open Access

    In the absence of complete genomes, the metabolic capabilities of uncultured ARMAN-like archaea have been uncertain. Here, Golyshina et al. apply an enrichment culture technique and find that the ungapped genome of the ARMAN-like archaeon Mia14 has lost key metabolic pathways, suggesting dependence on the host archaeon Cuniculiplasma divulgatum.

    • Olga V. Golyshina
    • , Stepan V. Toshchakov
    •  & Peter N. Golyshin

  • Article
    | Open Access

    Hosts vary in how dependent they are on their beneficial symbionts. Here, Fisher and colleagues analyse the results of symbiont-removal experiments from 106 symbioses in a phylogenetic context and show that host dependence is associated with symbiont transmission mode, function, and genome size.

    • Roberta M. Fisher
    • , Lee M. Henry
    •  & Stuart A. West

  • Article
    | Open Access

    Sexual dimorphism is likely the result of differential gene expression. Here, the authors examine the role of thedsxgene in beetles and find that this gene acts in a sex- and tissue-specific manner, either by regulating sex-specific targets or by acting in opposite directions in males and females.

    • C. C. Ledón-Rettig
    • , E. E. Zattara
    •  & A. P. Moczek

  • Article
    | Open Access

    Tarsiers occupy a key node between strepsirrhines and anthropoids in the primate phylogeny. Here, Warren and colleagues present the genome of Tarsius syrichta, including a survey of transposable elements, an unusual mitochondrial insertion, and evidence for positive gene selection.

    • Jürgen Schmitz
    • , Angela Noll
    •  & Wesley C. Warren

  • Article
    | Open Access

    Attine ants, including the leaf-cutting ants, cultivate fungi as their sole source of food. Here, Nygaard et al. use whole genome and transcriptome sequences from seven ant species and their fungal cultivars to reconstruct the reciprocal genetic changes underlying the evolution of the ant-fungus mutualism.

    • Sanne Nygaard
    • , Haofu Hu
    •  & Jacobus J. Boomsma

  • Article
    | Open Access

    Transcription factors Distal-less(Dll) and spalt were co-opted during the evolution of butterfly eyespots. Here, Zhang and Reed use CRISPR/Cas9 genome editing to show that while spalt is a positive regulator of eyespots as predicted, Dll knockouts have positive effects on both eyespot size and number, thus suggesting that Dllis an eyespot repressor, not an activator as previously thought.

    • Linlin Zhang
    •  & Robert D. Reed

  • Article
    | Open Access

    Helitron elements are proposed rolling-circle transposons in eukaryotic genomes, but experimental evidence for their transposition has been lacking. Here, Grabundzija et al. reconstruct an active Helitron from bats which they name Helraiser, and characterize its mechanism of transposition in cell-free reactions and in human cell cultures in vitro.

    • Ivana Grabundzija
    • , Simon A. Messing
    •  & Zoltán Ivics

  • Article |

    The structure of insect odorant receptors (ORs) has remained elusive due to their lack of homology to other proteins and the inability to obtain OR crystals. Here, the authors use amino acid evolutionary covariation patterns to fold these proteins de novoand generate the first three-dimensional models of insect ORs.

    • Thomas A. Hopf
    • , Satoshi Morinaga
    •  & Richard Benton

  • Article
    | Open Access

    The lancelet, or amphioxus, is an extant basal chordate that diverged from other chordate lineages about 550 million years ago. Here the authors sequence and assemble the diploid genome of a male adult of the Chinese lancelet, B. belcheri, and highlight genomic features that may have played an important role in the origin and evolution of vertebrates.

    • Shengfeng Huang
    • , Zelin Chen
    •  & Anlong Xu

  • Article |

    Helicobacter pylori chronically infects humans, and this is associated with high mutation and recombination rates in the bacterium. Here the authors provide evidence that genome evolution in H. pyloriduring acute infection of the host is orders of magnitude faster than any previously determined mutation rates in bacteria.

    • Bodo Linz
    • , Helen M. Windsor
    •  & Barry J. Marshall

  • Article
    | Open Access

    Brassica oleracea is plant species comprising economically important vegetable crops. Here, the authors report the draft genome sequence of B. oleracea and, through a comparative analysis with the closely related B. rapa, reveal insights into Brassicaevolution and divergence of interspecific genomes and intraspecific subgenomes.

    • Shengyi Liu
    • , Yumei Liu
    •  & Andrew H Paterson

  • Article
    | Open Access

    Horizontal transfer of DNA is common among eukaryotes but the vectors involved remain elusive. Here, Gilbert et al. show high frequency of in vivotransposition from the cabbage looper moth into genomes of a baculovirus, suggesting that viruses can act as vectors of horizontal transfer between animals.

    • Clément Gilbert
    • , Aurélien Chateigner
    •  & Richard Cordaux

  • Article |

    Little is known about the genes that confer salt tolerance in trees. Here, Ma et al. report the genome sequence of the desert poplar, Populus euphratica, and provide insight into the genetic architecture and adaptation of this salt tolerant desert poplar.

    • Tao Ma
    • , Junyi Wang
    •  & Jianquan Liu

  • Article
    | Open Access

    Phytophthora infestanscaused the potato famine in the nineteenth century. Martinet al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans.

    • Michael D. Martin
    • , Enrico Cappellini
    •  & M. Thomas P. Gilbert

  • Article
    | Open Access

    Cyanobacterial symbionts of marine diatoms can localize intracellularly or externally to their host partners. Here Hilton et al. describe the genomes of two diazotroph cyanobacterial symbionts of diatoms and show that the location of the symbiont affects expression of nitrogen assimilation genes.

    • Jason A. Hilton
    • , Rachel A. Foster
    •  & Tracy A. Villareal

  • Article
    | Open Access

    The wild rice species can be used as germplasm resources for this crop’s genetic improvement. Here Chen and colleagues report the de novo sequencing of the O. brachyanthagenome, and identify the origin of genome size variation, the role of gene movement and its implications on heterochromatin evolution in the rice genome.

    • Jinfeng Chen
    • , Quanfei Huang
    •  & Mingsheng Chen

  • Article |

    APOBEC3 is a DNA editing enzyme that is important for antiviral responses. In this study, Carmi and colleagues show that APOBEC3 editing of retrotransposon sequences in mammalian genomes is widespread, with implications for the evolution of retrotransposons.

    • Shai Carmi
    • , George M. Church
    •  & Erez Y. Levanon

  • Article
    | Open Access

    A comparison of related genomes provides valuable information about how they evolve. Here, the complete sequence of the smallest known nuclear genome from the microsporidiaE. intestinalis is described and compared with its larger sister E. cuniculi, revealing what parts are indispensable in even the most reduced genomes.

    • Nicolas Corradi
    • , Jean-François Pombert
    •  & Patrick J. Keeling

Browse broader subjects

Browse Genome evolution across other nature.com journals