Genome evolution articles within Nature Communications

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  • Article
    | Open Access

    Through regeneration, the endometrium accumulates somatic mutations that can lead to diseases like endometriosis and cancer. Here, the authors use genomics to analyse normal endometrial glands from different patient cohorts, detect rhizome structures with common clonal ancestors and infer clonal expansion dynamics.

    • Manako Yamaguchi
    • , Hirofumi Nakaoka
    •  & Takayuki Enomoto

  • Article
    | Open Access

    Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.

    • Dongya Wu
    • , Enhui Shen
    •  & Chu-Yu Ye

  • Article
    | Open Access

    Gamma triplication arises via two whole-genome duplications early in eudicot history, but the relative timing of these is unclear. Here, the authors report the genomes of Buxales and Trochodendrales and reject the hypothesis of gamma arising via inter-lineage hybridization between ancestral eudicot lineages.

    • Andre S. Chanderbali
    • , Lingling Jin
    •  & Pamela S. Soltis

  • Article
    | Open Access

    Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus sesilifolius and show that both hybridization and incomplete lineage sorting may have contributed to the phylogenetic incongruities in the literature.

    • Jianxiang Ma
    • , Pengchuan Sun
    •  & Yongzhi Yang

  • Article
    | Open Access

    Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus spicatus and show its contribution to deepen our understanding on diversification, phylogeny, and genome evolution in angiosperms.

    • Xing Guo
    • , Dongming Fang
    •  & Huan Liu

  • Article
    | Open Access

    Trait genetic architecture influences how populations evolve and adapt. Genomic analysis finds that an inversion links genetic variation controlling redpoll finch color and bill shape, allowing the maintenance of latitudinal ecotypes despite a genome largely homogenized by gene flow.

    • Erik R. Funk
    • , Nicholas A. Mason
    •  & Scott A. Taylor

  • Article
    | Open Access

    Muntjac deer underwent rapid species radiation and dramatic chromosome fusions within a short period of time. Here the authors reveal that repeat sequences likely mediated illegitimate recombination to result in chromosome fusions and that 3D chromatin architecture around fusion sites have no significant change, while significant interactions across fusion sites were gradually established after speciation.

    • Yuan Yin
    • , Huizhong Fan
    •  & Fuwen Wei

  • Article
    | Open Access

    Hybrids are often considered evolutionary dead ends because they do not generate viable offspring. Here, the authors show that sterile yeast hybrids generate genetic diversity through meiotic-like recombination by aborting meiosis and return to asexual growth.

    • Simone Mozzachiodi
    • , Lorenzo Tattini
    •  & Gianni Liti

  • Article
    | Open Access

    It is commonly thought that horizontal transfer of most bacterial chromosomal genes is limited, in comparison with the frequent transfer of mobile genetic elements. Humphrey et al. show that, actually, phage-mediated lateral transduction of core chromosomal genes can be more efficient than the transfer of mobile genetic elements via conjugation or generalized transduction.

    • Suzanne Humphrey
    • , Alfred Fillol-Salom
    •  & José R. Penadés

  • Article
    | Open Access

    Despite extensive characterization of crassulacean acid metabolism (CAM) in terrestrial angiosperms, little attention has been given to aquatics and early diverging land plants. Here, the authors assemble the genome of Isoetes taiwanensis and investigate the genetic factors driving CAM in this aquatic lycophyte.

    • David Wickell
    • , Li-Yaung Kuo
    •  & Fay-Wei Li

  • Article
    | Open Access

    Existing methods to identify the presence of DNA from other hominin species can be limited in the ability to accurately estimate introgression waves, or can only be applied to specific populations. Here, the authors have developed a generalizable method to identify introgression in multi-wave situations.

    • Kai Yuan
    • , Xumin Ni
    •  & Shuhua Xu

  • Article
    | Open Access

    Papaver species P. setigerum, P. rhoeas, and P. somniferum accumulates different levels of morphine and noscapine. Here, the authors report the improved genome assembly of P. somniferum and de novo assembly of the other two species, and reveal the evolution of the benzylisoquinoline alkaloids biosynthetic pathway.

    • Xiaofei Yang
    • , Shenghan Gao
    •  & Kai Ye

  • Article
    | Open Access

    Early vertebrate genomes were shaped by multiple whole-genome duplication (WGD) events of debated timings. Here the authors’ reconstruction of ancestral genomes using the probabilistic macrosynteny model supports a WGD shared by all vertebrates and a gnathostome-specific WGD, and reveals evidence of a cyclostome-specific genome triplication.

    • Yoichiro Nakatani
    • , Prashant Shingate
    •  & Byrappa Venkatesh

  • Article
    | Open Access

    Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.

    • Tao Zhao
    • , Arthur Zwaenepoel
    •  & Yves Van de Peer

  • Article
    | Open Access

    Many obligate symbionts, including parasites, have reduced genomes. A comparison of leaf-cutter ant genomes reveals parallel gene losses, particularly in olfactory receptors, in socially parasitic species compared to their closely-related hosts, consistent with relaxed selection for cooperative colony life in the parasites.

    • Lukas Schrader
    • , Hailin Pan
    •  & Christian Rabeling

  • Article
    | Open Access

    Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle. Using 12 new genomes, this study finds evidence that Nitrososphaerales evolution was marked by lateral gene transfer followed by gene duplication.

    • Paul O. Sheridan
    • , Sebastien Raguideau
    •  & Cécile Gubry-Rangin

  • Article
    | Open Access

    Pseudogenes are key markers of genome remodelling processes. Here the authors present genome-wide annotation of the pseudogenes in the mouse reference genome and 18 inbred mouse strains, update human pseudogene annotations, and characterise the transcription and evolution of mouse pseudogenes.

    • Cristina Sisu
    • , Paul Muir
    •  & Mark Gerstein

  • Article
    | Open Access

    Reconstructing the early molecular evolution of animals requires genomic resources for non-bilaterian animals. Here, the authors present the chromosome-level genome of a freshwater sponge together with analyses of its genome architecture, methylation, developmental gene expression, and microbiome.

    • Nathan J. Kenny
    • , Warren R. Francis
    •  & Sally P. Leys

  • Article
    | Open Access

    Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.

    • Weiyi Zhang
    • , Youjun Zhang
    •  & Weiwei Wen

  • Article
    | Open Access

    Streptococcus pneumoniae is an opportunistic pathogen and asymptomatic colonization is a precursor for invasive disease. Here the authors show rapid within-host evolution of naturally acquired pneumococci in ninety-eight infants driven by high nucleotide substitution rates and intra-host homologous recombination.

    • Chrispin Chaguza
    • , Madikay Senghore
    •  & Brenda A. Kwambana-Adams

  • Article
    | Open Access

    Many nematode worms, including Caenorhabditis elegans have XX/XO sex determination, while other species have XY. The authors use a new genome assembly of the filarial parasite Brugia malayi and published data to show that nematode sex chromosome evolution is highly plastic.

    • Jeremy M. Foster
    • , Alexandra Grote
    •  & Elodie Ghedin

  • Article
    | Open Access

    Litsea cubeba belongs to the Lauraceae family within the Magnoliids clade. Here, the authors assemble its genome and reveal divergence of inflorescence and sexual differentiation, the phylogenetic relationships across the Lauraceae and related species, and biosynthetic genes related to essential oil synthesis.

    • Yi-Cun Chen
    • , Zhen Li
    •  & Yang-Dong Wang

  • Article
    | Open Access

    White lupin is a legume crop that develops cluster roots for efficient phosphate acquisition. Here, the authors assemble its triplicated genome, reveal gene expression difference among sub-genomes, and characterize possible pathways related to high phosphorus-use efficiency.

    • Weifeng Xu
    • , Qian Zhang
    •  & Feng Cheng

  • Article
    | Open Access

    Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.

    • Wen-Biao Jiao
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

    • Cormac M. Kinsella
    • , Francisco J. Ruiz-Ruano
    •  & Alexander Suh

  • Article
    | Open Access

    A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.

    • Jaime Iranzo
    • , Yuri I. Wolf
    •  & Itamar Sela

  • Article
    | Open Access

    The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.

    • Deborah J. Weinstein
    • , Sarah E. Allen
    •  & John R. Bracht

  • Article
    | Open Access

    The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.

    • Thomas W. Scott
    •  & Stuart A. West

  • Article
    | Open Access

    Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

    • JunMo Lee
    • , Dongseok Kim
    •  & Hwan Su Yoon

  • Article
    | Open Access

    Hybridization across species can lead to offspring with reduced fertility. Here, the authors experimentally evolve yeast and show that whole-genome duplication during asexual reproduction can restore fertility in hybrids over a relatively short evolutionary timespan.

    • Guillaume Charron
    • , Souhir Marsit
    •  & Christian R. Landry

  • Article
    | Open Access

    The Chloropicophyceae represent an important group of green algae in tropical oceans, but there is only limited genomic resource available. Here, the authors present the genome sequence of Chloropicon primus, revealing a diploid structure and the presence of a propionate detoxification pathway.

    • Claude Lemieux
    • , Monique Turmel
    •  & Jean-François Pombert

  • Article
    | Open Access

    Wild relatives of crop plants are invaluable germplasm for genetic improvement. Here, Xie et al. report a reference-grade wild soybean genome and show that it can be used to identify structural variation and refine quantitative trait loci.

    • Min Xie
    • , Claire Yik-Lok Chung
    •  & Hon-Ming Lam

  • Article
    | Open Access

    The Pacific white shrimp Litopenaeus vannamei is an important aquaculture species and a promising model for crustacean biology. Here, the authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.

    • Xiaojun Zhang
    • , Jianbo Yuan
    •  & Jianhai Xiang

  • Article
    | Open Access

    Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.

    • Marie-Christine Carpentier
    • , Ernandes Manfroi
    •  & Olivier Panaud

  • Article
    | Open Access

    Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

    • John T. Lovell
    • , Jerry Jenkins
    •  & Thomas E. Juenger

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