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Article
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Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.
- Xiao Feng
- , Qipian Chen
- & Ziwen He
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Article
| Open Access
Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery
Cepharanthine is a secondary metabolite isolated from Stephania with a variety of medicinal properties. Here, the authors assembled three Stephania genomes, propose cepharanthine biosynthetic pathway, and assess the antiviral potential of cepharanthine-related metabolites.
- Liang Leng
- , Zhichao Xu
- & Shilin Chen
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Article
| Open Access
Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats
Telomeres protect the extremities of linear chromosomes and are involved in ageing, senescence and genome stability. Here, the authors have identified peculiar and specific telomeric DNA repeats in the genomes of devastating plant-parasitic nematodes, opening new perspectives for their control.
- Ana Paula Zotta Mota
- , Georgios D. Koutsovoulos
- & Etienne G. J. Danchin
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Article
| Open Access
Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae
Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. Here the authors present an engineered yeast strain with 83 sparsely distributed loxPsym sites across the genome can genrerate large-scale genomic rearrangements, which benefits cell fitness under stress and boosts the SCRaMbLE system when combined with synthetic chromosomes.
- Li Cheng
- , Shijun Zhao
- & Junbiao Dai
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Article
| Open Access
A chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.
- Simone Scalabrin
- , Gabriele Magris
- & Michele Morgante
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Article
| Open Access
Multiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family
Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.
- Jiao Yang
- , Ying Wu
- & Jianquan Liu
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Article
| Open Access
Topological structures and syntenic conservation in sea anemone genomes
Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.
- Bob Zimmermann
- , Juan D. Montenegro
- & Ulrich Technau
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Article
| Open Access
Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome
The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.
- Youjie Zhao
- , Chengyong Su
- & Jiasheng Hao
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Article
| Open Access
The rate of epigenetic drift scales with maximum lifespan across mammals
Epigenetic drift has been hypothesized to contribute to epigenetic clock signals and variation in lifespan across species. Here, the authors show that an empirical measure of epigenetic drift scales with maximum lifespan across four mammal species and accumulates in non-random genomic locations.
- Emily M. Bertucci-Richter
- & Benjamin B. Parrott
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Article
| Open Access
Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years
Bacteria usually have at least one rRNA operon on the chromosome, suggesting that the exclusive presence of rRNA operons on a plasmid is rare and unlikely to be stably maintained. Here, Anda et al. find that at least four bacterial clades in different phyla lost their chromosomal rRNA operons independently, and one of the clades has maintained this peculiar genome organization for hundreds of millions of years.
- Mizue Anda
- , Shun Yamanouchi
- & Wataru Iwasaki
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Article
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Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi
In the absence of recombination, the number of transposable elements (TEs) increases, but their accumulation dynamics are not well characterized. This study shows that TEs rapidly accumulated in non-recombining fungal mating-type chromosomes before reaching a plateau, possibly forming a TE reservoir.
- Marine Duhamel
- , Michael E. Hood
- & Tatiana Giraud
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Article
| Open Access
Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation
Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population differentiation.
- Feng Liu
- , Jiantao Zhao
- & Xuexiao Zou
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Article
| Open Access
Genomic insight into domestication of rubber tree
Understanding the genetic basis of rubber tree domestication is critical for improving natural rubber production. Here, the authors assemble the genome of the rubber tree clone CATAS8-79 and conduct population and genetic association analyses to reveal the function of phytosulfokine in regulating number of laticifer rings.
- Jinquan Chao
- , Shaohua Wu
- & Wei-Min Tian
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Article
| Open Access
Rapid gene content turnover on the germline-restricted chromosome in songbirds
Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function.
- Stephen A. Schlebusch
- , Jakub Rídl
- & Radka Reifová
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Article
| Open Access
Origin of minicircular mitochondrial genomes in red algae
While the organelle genome is commonly considered to be a single circular DNA molecule, extensive variation exists. Here, the authors report multipartite minicircular genomes in red algae and indicate an origin driven by recombination due to loss of DNA replication, recombination, and repair genes.
- Yongsung Lee
- , Chung Hyun Cho
- & Hwan Su Yoon
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Article
| Open Access
Transposon signatures of allopolyploid genome evolution
Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.
- Adam M. Session
- & Daniel S. Rokhsar
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Article
| Open Access
Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms
Annelid worms have colonised extreme ecological niches, such as hydrothermal vents and whale falls thanks to symbiotic bacteria. This study finds that Osedax worms and the related Vestimentifera have evolved different genomic adaptations to sustain their bacterial symbioses and exploit different resources, such as decaying bone.
- Giacomo Moggioli
- , Balig Panossian
- & José M. Martín-Durán
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Matters Arising
| Open AccessReply to “Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes”
- Xiaofei Yang
- , Shenghan Gao
- & Kai Ye
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Matters Arising
| Open Access
Subgenome-aware analyses suggest a reticulate allopolyploidization origin in three Papaver genomes
- Ren-Gang Zhang
- , Chaoxia Lu
- & Wei Zhao
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Article
| Open Access
Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum
Chrysanthemum is an important ornamental species with great economic value. Here, the authors assemble the haploid genome of C. morifolium, reveal its segmental allopolyploid genomic composition (AA’B), and identify candidate genes associated with flower development, petal shape, and flower colour.
- Aiping Song
- , Jiangshuo Su
- & Fadi Chen
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Article
| Open Access
Revealing evolution of tropane alkaloid biosynthesis by analyzing two genomes in the Solanaceae family
Tropane alkaloids (TAs) are synthesized by some species in Solanaceae. Here, the authors assemble the genomes of two representative TAs producing species, show that gene loss shapes uneven distribution of TAs in Solanaceae, and identify a cytochrome P450 gene catalyzing N-demethylation of hyoscyamine to generate norhyoscyamine.
- Fangyuan Zhang
- , Fei Qiu
- & Zhihua Liao
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Article
| Open Access
The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis
Torreya grandis is a gymnosperm species that produces edible seeds with high level of sciadonic acid (SCA). Here, the authors assemble the genome of this species, preform methylone analysis of seeds at different developmental stages, and reveal two key genes involved in SCA biosynthesis.
- Heqiang Lou
- , Lili Song
- & Jiasheng Wu
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Article
| Open Access
Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes
The phylogenetic relationship among genera within the walnut family Juglandaceae remains unclear. Here, the authors assemble the genomes of Rhoiptelea chiliantha and Engelhardia roxburghiana, resolve the topology of this family, and propose a hybrid origin of the family from progenitors nested within or sister to Myricaceae.
- Ya-Mei Ding
- , Xiao-Xu Pang
- & Wei-Ning Bai
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Article
| Open Access
Uncovering 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
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Article
| Open Access
Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species
DNA methylation is involved in regulatory processes throughout the animal kingdom. Here, the authors map DNA methylation in 535 vertebrates and 45 invertebrates, establishing a reference dataset for cross-species analysis and exploring epigenetic variation across vertebrate evolution.
- Johanna Klughammer
- , Daria Romanovskaia
- & Christoph Bock
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Article
| Open Access
Micro and macroevolution of sea anemone venom phenotype
Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.
- Edward G. Smith
- , Joachim M. Surm
- & Yehu Moran
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Article
| Open Access
Genome-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
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Article
| Open Access
A method to build extended sequence context models of point mutations and indels
The mutation rate at any specific position in the human genome depends on sequence context. Here, the authors develop a method for predicting mutation rates of point mutations and indels based on sequence context; the results can be used to find genes where de novo mutations cause disease and genes under strong selective constraint.
- Jörn Bethune
- , April Kleppe
- & Søren Besenbacher
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Article
| Open Access
Primate-specific transposable elements shape transcriptional networks during human development
The human genome harbors more than 4.5 million transposable element (TE)-derived insertions, the result of recurrent waves of invasion and internal propagation. Here they show that TEs belonging to evolutionarily recent subfamilies go on to regulate later stages of human embryonic development, notably conditioning the expression of genes involved in gastrulation and early organogenesis.
- Julien Pontis
- , Cyril Pulver
- & Didier Trono
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Article
| Open Access
Genomic signatures of recent convergent transitions to social life in spiders
Sociality has evolved repeatedly in arthropods. Tong et al. compare the genomes of 22 spider species with a range of social complexity and eight independent origins of sociality, and identify specific genetic changes associated with the evolution of sociality in spiders.
- Chao Tong
- , Leticia Avilés
- & Timothy A. Linksvayer
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Article
| Open Access
Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer
Evolutionary principles could help distinguish driver from passenger mutations in cancer. Here, the authors develop SEISMIC, a method to identify cancer driver genes based on their deviation from expected mutation status patterns across a cohort under neutral evolution, and find potential drivers in melanoma and other cancer types.
- Martin Boström
- & Erik Larsson
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Article
| Open Access
Translation and natural selection of micropeptides from long non-canonical RNAs
Translation of 100 to 300 micropeptides from small ORFs within lncRNA was detected by Ribosomal Profiling in Drosophila embryos. These translated small ORFs showed natural selection conserving micropeptide sequence and function.
- Pedro Patraquim
- , Emile G. Magny
- & Juan Pablo Couso
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Article
| Open Access
Arctic 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
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Article
| Open Access
Genomic 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
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Article
| Open Access
Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches
Endogenous retroviruses (ERV) are inherited remains of retroviruses that have colonized host genomes during evolution. Here the authors observe considerable species-specific ERV variation among Darwin’s finches, reflecting historic retrovirus-host interactions.
- Jason Hill
- , Mette Lillie
- & Patric Jern
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Article
| Open Access
High-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
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Article
| Open Access
Equilibrated 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
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Article
| Open Access
Dispersed 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
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Article
| Open Access
The 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
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Article
| Open Access
Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli
The ploidy level of patchouli, an aromatic plant in the Lamiaceae family, remain unclear. Here, the authors assemble a chromosome-level and haplotype-resolved genome for patchouli and reveal that it is tetraploid hybrid as well as compensated aneuploidy.
- Yanting Shen
- , Wanying Li
- & Hong-bin Wang
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Article
| Open Access
Evolution of sexual systems, sex chromosomes and sex-linked gene transcription in flatworms and roundworms
Transitions between hermaphroditic and separate sexes are relatively understudied in animals compared to pants. Here, Wang et al. reconstruct the evolution of separate sexes in the flatworms and complex changes of sex chromosomes in the roundworms.
- Yifeng Wang
- , Robin B. Gasser
- & Qi Zhou
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Article
| Open Access
A functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago
The STORR gene fusion event is a key step in the evolution of benzylisoquinoline alkaloid metabolism in opium poppy. Here, the authors combine phylogenetic, transcriptomic, metabolomic, biochemical and genomic analyses to show the STORR gene fusion occurred only once between 16.8-24.1 million years ago in Papaver species.
- Theresa Catania
- , Yi Li
- & Ian A. Graham
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Matters Arising
| Open Access
Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes
- Houra Merrikh
- & Christopher Merrikh
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Matters Arising
| Open AccessTesting the adaptive hypothesis of lagging-strand encoding in bacterial genomes
- Haoxuan Liu
- & Jianzhi Zhang
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Article
| Open Access
Genome and transcriptome mechanisms driving cephalopod evolution
“Cephalopods are known for their large nervous systems, complex behaviors, and morphological innovations. Here, the authors find that soft-bodied cephalopod genomes are more rearranged than other extant molluscs and that mRNA editing patterns are associated with the nervous system and repetitive elements”.
- Caroline B. Albertin
- , Sofia Medina-Ruiz
- & Daniel S. Rokhsar
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Article
| Open Access
Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression
Barrett’s esophagus is a pre-malignant condition that can progress to esophageal cancer. Here, the authors carry out whole genome sequencing of samples from patients who did or did not progress to cancer and find that mutations in many genes occur regardless of progression status, but also find features associated with progressive disease.
- Thomas G. Paulson
- , Patricia C. Galipeau
- & Xiaohong Li
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Article
| Open Access
Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata
Unlike Panax species, which can produce dammarane-type saponins, Aralia elata can only synthesize oleananetype saponins. Here, the authors reveal that the loss of the dammaranediol synthase-encoding gene and tandem duplication of triterpene biosynthetic genes drive structural divergences of saponins between the two genera.
- Yu Wang
- , He Zhang
- & Yuhua Li
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Article
| Open Access
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks
The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features relevant to its evolutionary success.
- Victoria L. Sork
- , Shawn J. Cokus
- & Steven L. Salzberg
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Article
| Open Access
Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations
‘Pre-contact era humans from coastal South America were infected by Mycobacterium pinnipedii, most likely, through contact with infected pinnipeds. Here, the authors investigate the presence of M. pinnipedii in pre-contact era humans from inland South America and explore potential scenarios of human-to-human or animal-mediated transmission.’
- Åshild J. Vågene
- , Tanvi P. Honap
- & Kirsten I. Bos
Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks