Article
|
Open Access
Featured
-
-
Article
| Open AccessEvolution of giant pandoravirus revealed by CRISPR/Cas9
Until today, genetic tools have been lacking to enable manipulation of amoebal giant viruses (GVs) by CRISPR/Cas9 technology. Here, Bisio et al. apply S. pyogenes Cas9 together with pU6- driven guide RNAs to investigate the replication of pandoravirus, a GV replication in the nucleus. Using this tool, they provide evidence for stepwise evolution and genetic expansion of viral gigantism.
- Hugo Bisio
- , Matthieu Legendre
- & Chantal Abergel
-
Article
| Open AccessUncovering a miltiradiene biosynthetic gene cluster in the Lamiaceae reveals a dynamic evolutionary trajectory
A diterpenoid biosynthetic gene cluster (BGC) has been identified in a few species in the Lamiaceae (mint) family, but its origin and evolution remain unclear. Here, the authors report assembly of genomes of three species within the family and reveal the dynamic evolutionary trajectory of the BGC.
- Abigail E. Bryson
- , Emily R. Lanier
- & Björn Hamberger
-
Article
| Open AccessCommon evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds
Understanding origin and adaptation of weeds is important for their management. Here, via genome assembly, population genomics, and QTL mapping, the authors establish Cardamine occulta as a model to study weed ruderality and show FLC and CRY2 as genetic drivers for the establishment of short life cycle.
- Ling-Zi Li
- , Zhou-Geng Xu
- & Jia-Wei Wang
-
Article
| Open AccessMigration direction in a songbird explained by two loci
The genetic determinants of long-distance migration in birds are largely unknown. Sokolovskis et al. tracked genotyped hybrid willow warblers from a migratory divide in Sweden and find that autumn migration direction is consistent with a dominant inheritance pattern of two large effect loci that interact through epistasis.
- Kristaps Sokolovskis
- , Max Lundberg
- & Staffan Bensch
-
Article
| Open AccessThe HAPSTR2 retrogene buffers stress signaling and resilience in mammals
The recently described protein HAPSTR1 governs cellular stress resilience. Here, the authors discover a mammalian HAPSTR1 paralog, called HAPSTR2, which formed via retro-transposition and operates to augment and buffer cellular stress signaling.
- David R. Amici
- , Harun Cingoz
- & Marc L. Mendillo
-
Article
| Open AccessGenome-wide signatures of adaptation to extreme environments in red algae
Extremophilic red algae have thrived in hot springs for more than a billion years. Here, the authors analyze chromosome-level assemblies from three red algal species, finding that horizontal gene transfer, subtelomeric gene duplication, and loss of genes or reduction in gene family size have supported key extremophilic adaptations.
- Chung Hyun Cho
- , Seung In Park
- & Hwan Su Yoon
-
Article
| Open AccessImmunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia
Seahorses may have required adaptations to avoid immunological rejection of allogenic embryos by males. The authors show that a single substitution in tlx1 is associated with loss of the spleen in seahorses, and that across the clade, degree of male pregnancy is negatively correlated with immune gene repertoire complexity.
- Yali Liu
- , Meng Qu
- & Qiang Lin
-
Article
| Open AccessLimited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence
Unlike microbes and mammals, cistrome dynamics in plants remains unclear. Here, using GOLDEN2-LIKE (GLK) transcription factor as an example, the authors find that most GLK binding sites are species-specific and the binding divergence is caused by cis-variations through inter-species transformation experiment.
- Xiaoyu Tu
- , Sibo Ren
- & Silin Zhong
-
Article
| Open AccessPrioritizing autoimmunity risk variants for functional analyses by fine-mapping mutations under natural selection
Immune genes under selection can shed light on phenotypes contributing to survival and modern inflammatory conditions. Here, the authors prioritize adaptive disease variants in 535 risk loci for 21 inflammatory conditions and report promising SNPs for functional studies with predictions of cell context and function.
- Vasili Pankratov
- , Milyausha Yunusbaeva
- & Bayazit Yunusbayev
-
Article
| Open AccessChromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops
Genome evolution of Allium genus and genomic basis underlying the pungency flavor formation remain poorly understood. Here, the authors assemble the genome of bunching onion and conduct population genetics analyses to reveal Allium genome evolution, flavor formation and domestication history.
- Nanqiao Liao
- , Zhongyuan Hu
- & Jing-Quan Yu
-
Article
| Open AccessArctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator
The Qinghai-Tibet Plateau is as cold as the Arctic, but presents unique hypoxia and high ultraviolet conditions. Here the authors find that gene flow from Arctic gyrfalcons aids plateau saker falcons’ cold adaptation, and independent non-coding genomic changes underlie hypoxic and ultraviolet responses.
- Li Hu
- , Juan Long
- & Xiangjiang Zhan
-
Article
| Open AccessGenomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps
Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here, the authors analyze the genomes of two Anastatus wasps, revealing genomic innovations related to maintenance of genomic stability, and rapid turnover of venom genes.
- Xinhai Ye
- , Yi Yang
- & Gongyin Ye
-
Article
| Open AccessIncorporating evolutionary and threat processes into crop wild relatives conservation
Crop wild relatives’ genetic diversity is usually not considered in conservation planning. Here, the authors introduce an approach to identify conservation areas based on evolutionary and threat processes, by developing proxies of genetic differentiation, and including taxa’s habitat preferences.
- Wolke Tobón-Niedfeldt
- , Alicia Mastretta-Yanes
- & Patricia Koleff
-
Article
| Open AccessEarly stages of sympatric homoploid hybrid speciation in crater lake cichlid fishes
Here, the authors present a rare example of sympatric homoploid hybrid speciation, without ploidy changes, in the Midas cichlid fishes from Nicaragua. Midas cichlid hybrids occupy a different ecological niche, likely facilitated by body shape adaptations.
- Melisa Olave
- , Alexander Nater
- & Axel Meyer
-
Article
| Open AccessTissue-specific impacts of aging and genetics on gene expression patterns in humans
Age is a risk factor for many diseases, but the impact of aging on molecular phenotypes is not fully understood. Here, the authors quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues in humans, showing that age and genetics each play distinct roles in shaping expression phenotypes.
- Ryo Yamamoto
- , Ryan Chung
- & Peter H. Sudmant
-
Article
| Open AccessRegain flood adaptation in rice through a 14-3-3 protein OsGF14h
Waterlogging tolerance is important in direct seeding rice cultivation practice. Here, the authors identify a 14-3-3 protein-coding gene OsGF14h in weedy rice that confers anaerobic germination and anaerobic seedling development tolerance by balancing ABA signaling and GA biosynthesis.
- Jian Sun
- , Guangchen Zhang
- & Wenfu Chen
-
Article
| Open AccessHigh-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation
Tong et al. describe a super pangenome assembled from long-read sequences of 545 wild and domesticated silkworms. Naturally selected (diapause, aposemantic coloration) or artificially selected (silk yield and fineness) sets of genes are delineated.
- Xiaoling Tong
- , Min-Jin Han
- & Fangyin Dai
-
Article
| Open AccessGenomic insights into rapid speciation within the world’s largest tree genus Syzygium
The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium.
- Yee Wen Low
- , Sitaram Rajaraman
- & Victor A. Albert
-
Article
| Open AccessRapid evolution of mutation rate and spectrum in response to environmental and population-genetic challenges
How rapidly the mutation rate responds evolutionarily to ecological and population-genetic factors over time is unclear. Here, the authors show that the evolution of mutation rates in E. coli proceeds rapidly in response to these factors with substantial bidirectional shifts.
- Wen Wei
- , Wei-Chin Ho
- & Michael Lynch
-
Article
| Open AccessRepeated genetic adaptation to altitude in two tropical butterflies
Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
- Gabriela Montejo-Kovacevich
- , Joana I. Meier
- & Chris D. Jiggins
-
Article
| Open AccessGenomic architecture of adaptive radiation and hybridization in Alpine whitefish
In this genomic study on Alpine whitefish radiations, the authors reveal details on the genetic architecture underlying the repeated eco-morphological diversification and the role of hybridization in the evolution of endemic whitefish species.
- Rishi De-Kayne
- , Oliver M. Selz
- & Philine G. D. Feulner
-
Article
| Open AccessExtreme purifying selection against point mutations in the human genome
Previous work has investigated selection in the coding genome, but it is not as well characterized in the non-coding genome. By analyzing rare variants in 70k genome sequences from gnomAD, the authors detect very strong purifying selection ("ultraselection”) across the human genome, finding it in some microRNAs and coding sequences but generally rare in regulatory sequences.
- Noah Dukler
- , Mehreen R. Mughal
- & Adam Siepel
-
Article
| Open AccessGenomic insights into the secondary aquatic transition of penguins
This study examines the tempo and drivers of penguin diversification by combining genomes from all extant and recently extinct penguin lineages, stratigraphic data from fossil penguins and morphological and biogeographic data from all extant and extinct species. Together, these datasets provide new insights into the genetic basis and evolution of adaptations in penguins.
- Theresa L. Cole
- , Chengran Zhou
- & Guojie Zhang
-
Article
| Open AccessEquilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp
The haplotype-resolved assembly of the asexual invasive Prussian carp shows six genome copies (AAABBB), evolved from two ancestral species by a recent self-addition (AB) to its hybrid-tetraploid (AABB) goldfish ancestor. Equilibrated gene loss led to subgenome dominance.
- Heiner Kuhl
- , Kang Du
- & Dunja K. Lamatsch
-
Article
| Open AccessDeciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes
Predicting the effects of mutations in a species is a major challenge in genetics. Here, the authors investigate protein sequence landscapes using diverged E. coli sequences, to predict tolerated mutations and capture interactions between mutations.
- Lucile Vigué
- , Giancarlo Croce
- & Martin Weigt
-
Article
| Open AccessGenome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod
Using time-series whole-genome sequencing data from a laboratory evolution experiment, along with extensive computer simulations, the authors show that synergistic epistasis could drive rapid parallel freshwater adaptation in a saline copepod.
- David B. Stern
- , Nathan W. Anderson
- & Carol Eunmi Lee
-
Article
| Open AccessDispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference
The contribution of ancient haplotypes to domestication is largely unknown. Here, the authors develop an ancestral genomic haploblock dissection method to generate a mosaic pan-ancestry genomic map and reveal that the domesticated polyploidy wheat emerged from the admixture of six founder wild emmer linages.
- Zihao Wang
- , Wenxi Wang
- & Weilong Guo
-
Article
| Open AccessAn essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea
Trace metals have been an important ingredient for life throughout Earth’s history. Here, the authors show that a member of an elusive archaeal lineage (Caldarchaeales or Aigarchaeota) requires tungsten for growth, and provide evidence that tungsten-dependent metabolism played a role in the origin and evolution of this lineage.
- Steffen Buessecker
- , Marike Palmer
- & Jeremy A. Dodsworth
-
Matters Arising
| Open AccessReply to: “Steller’s sea cow uncertain history illustrates importance of ecological context when interpreting demographic histories from genomes”
- Fedor S. Sharko
- , Sergey M. Rastorguev
- & Artem V. Nedoluzhko
-
Article
| Open AccessThe genomic basis of the plant island syndrome in Darwin’s giant daisies
Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.
- José Cerca
- , Bent Petersen
- & Michael D. Martin
-
Article
| Open AccessBifurcation drives the evolution of assembly-line biosynthesis
Reprogramming biosynthetic assembly-lines is a topic of interest for antibiotics. Here, the authors explore the evolutionary biosynthesis of anti-tubercular wollamides, show gene duplication and neo-functionalisation results in bifurcation allowing for testing of new structures with the ability to recover old structures by gene loss.
- Thomas J. Booth
- , Kenan A. J. Bozhüyük
- & Barrie Wilkinson
-
Article
| Open AccessThe 3D architecture of the pepper genome and its relationship to function and evolution
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
- Yi Liao
- , Juntao Wang
- & Changming Chen
-
Matters Arising
| Open AccessReply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes
- Houra Merrikh
- & Christopher Merrikh
-
Matters Arising
| Open AccessTesting the adaptive hypothesis of lagging-strand encoding in bacterial genomes
- Haoxuan Liu
- & Jianzhi Zhang
-
Article
| Open AccessPossible stochastic sex determination in Bursaphelenchus nematodes
In most species, sex is determined by genetic or environmental factors. Here, the authors present evidence that sex determination in Bursaphelenchus nematodes is instead likely to be regulated by a random, epigenetic mechanism.
- Ryoji Shinya
- , Simo Sun
- & Paul W. Sternberg
-
Article
| Open Access3D chromatin remodelling in the germ line modulates genome evolutionary plasticity
The role of genome folding in the heritability and evolvability of structural variations is not well understood. Here the authors investigate the impact of the three-dimensional genome topology of germ cells in the formation and transmission of gross structural genomic changes detected from comparing whole-genome sequences of 14 rodent species.
- Lucía Álvarez-González
- , Frances Burden
- & Aurora Ruiz-Herrera
-
Article
| Open AccessThe evolution of trait variance creates a tension between species diversity and functional diversity
The positive relationship between species diversity and functional diversity has been shown to vary. Here, the authors use theoretical models and data from Galápagos land snail communities to show how eco-evolutionary processes can force species to evolve narrower trait breadths in more species-rich communities to avoid competition, creating a negative relationship.
- György Barabás
- , Christine Parent
- & Frederik De Laender
-
Article
| Open AccessEmergence of novel cephalopod gene regulation and expression through large-scale genome reorganization
Cephalopods are an enigmatic animal group with complex and adaptive behaviors such as camouflage; however the genetic basis for these traits is not well understood. Here the authors reveal a set of cephalopod-restricted rearranged genomic loci, involving known neuronal regulators but also unexpected gene families, that confer topological organization and gene regulation.
- Hannah Schmidbaur
- , Akane Kawaguchi
- & Oleg Simakov
-
Article
| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
-
Article
| Open AccessPopulation-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
Even in well-studied species, there is still substantial natural genetic variation that has not been characterized. Here, the authors use long read sequencing to discover transposable elements in the Drosophila genome not detected by short read sequencing, and link them to gene expression.
- Gabriel E. Rech
- , Santiago Radío
- & Josefa González
-
Article
| Open AccessCongruent evolutionary responses of European steppe biota to late Quaternary climate change
Quaternary climatic oscillations had a large impact on European biogeography. Using genomic data, machine learning, and approximate Bayesian computation, this study outlines a general scenario in which Quaternary climatic oscillations shaped the evolution of European steppe biota in a congruent way, emphasizing the role of climate underlying patterns of genetic variance at the biome level.
- Philipp Kirschner
- , Manolo F. Perez
- & Peter Schönswetter
-
Article
| Open AccessReshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax
The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
- Zhen-Hui Wang
- , Xin-Feng Wang
- & Lin-Feng Li
-
Article
| Open AccessPredictive models for the selection of thermally tolerant corals based on offspring survival
Finding coral reefs resilient to climate warming is challenging. This study combines Great Barrier Reef remote sensing with breeding experiments that estimate coral survival under exposure to high temperatures to develop forecasting models that locate reefs with increased heat tolerance. These reefs represent targets for protection and potential sources of corals for reef restoration.
- K. M. Quigley
- & M. J. H. van Oppen
-
Article
| Open AccessTransposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms
Epistasis can lead to different phenotypic consequences from the same mutation. Here the authors carry out a genome-wide analysis of conditionally essential genes in yeast, finding that gene essentiality changes tend to occur concordantly among components of the same protein complex or metabolic pathway.
- Piaopiao Chen
- , Agnès H. Michel
- & Jianzhi Zhang
-
Article
| Open AccessParallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
- Andrea Fulgione
- , Célia Neto
- & Angela M. Hancock
-
Article
| Open AccessRecurring adaptive introgression of a supergene variant that determines social organization
Solenopsis fire ants have a polymorphic social system in which some colonies have multiple queens. Here, Stolle, Pracana et al. show that the supergene that produces the multiple-queen phenotype has spread repeatedly between Solenopsis species by introgression.
- Eckart Stolle
- , Rodrigo Pracana
- & Yannick Wurm
-
Article
| Open AccessBacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA
Eukaryotic DNA can be methylated as 5-methylcytosine and N6-methyladenine, but whether other forms of DNA methylation occur has been controversial. Here the authors show that a bacterial DNA methyltransferase was acquired >60 Mya in bdelloid rotifers that catalyzes N4-methylcytosine addition and is involved in suppression of transposon proliferation.
- Fernando Rodriguez
- , Irina A. Yushenova
- & Irina R. Arkhipova
-
Article
| Open AccessAlternative splicing in seasonal plasticity and the potential for adaptation to environmental change
Little is known about how alternative splicing and other post-transcriptional molecular mechanisms impact plasticity. Steward et al. use transcriptomic and genomic data from the butterfly Bicyclus anynana, finding that splicing plasticity is likely to experience genetic constraints.
- Rachel A. Steward
- , Maaike A. de Jong
- & Christopher W. Wheat
-
Article
| Open AccessThe genetic architecture underlying prey-dependent performance in a microbial predator
What prevents a generalist predator from evolving and outperforming specialist predators? By combing analyses of natural variation with experimental evolution, Stewart et al. suggest that predator variation persists because most mutations have prey-specific effects, which results in relaxed selection
- Balint Stewart
- , Nicole Gruenheit
- & Christopher R. L. Thompson