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Article
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Allopolyploid origin and diversification of the Hawaiian endemic mints
Hawaiian endemic mints represent the second largest plant radiation in the archipelago. Here, the authors present a reference genome and numerous resequenced individuals to uncover evidence for polyploidy, geographic speciation and localized hybridization underlying diversification in this lineage
- Crystal M. Tomlin
- , Sitaram Rajaraman
- & Charlotte Lindqvist
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Article
| Open Access
Bee-pollination promotes rapid divergent evolution in plants growing in different soils
In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.
- Thomas Dorey
- & Florian P. Schiestl
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Article
| Open Access
Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open Access
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
Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.
- Lin-Feng Li
- , Tonapha Pusadee
- & Kenneth M. Olsen
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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
Repeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling
The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.
- Tom Carruthers
- , Michelangelo S. Moerland
- & Wolf L. Eiserhardt
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| Open Access
Plastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway
The Enter-Doudoroff (ED) pathway is an alternative to glycolysis present in some prokaryotes. Evans et al. show that its dehydratase enzyme, evolved from a branched chain amino acid pathway paralog, acquired a new function through mutations in its active site.
- Sonia E. Evans
- , Anya E. Franks
- & Michael A. Phillips
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| Open Access
Evolutionary trajectory of pattern recognition receptors in plants
Plant cell-surface receptors perceive both self- and nonself-molecules to regulate biological processes. Here the authors show that a subclass of phytohormone and immune receptors share a common origin, which have diverged to perceive distinct ligands and activate differential downstream responses.
- Bruno Pok Man Ngou
- , Michele Wyler
- & Ken Shirasu
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Article
| Open Access
Cell geometry regulates tissue fracture
The epidermal surface of leaves and flower petals often display cells with wavy geometries. Here the authors provide evidence that this pattern represents an energy-efficient mechanism to protect plants from deleterious surface fissures and toughen the plants’ protective surface.
- Amir J. Bidhendi
- , Olivier Lampron
- & Anja Geitmann
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Article
| Open Access
LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat
The regulation of genetic diversity resulting from polyploidization and its impact on environmental adaptability remain unclear. Here, the authors show that LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat.
- Zijuan Li
- , Yuyun Zhang
- & Yijing Zhang
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Article
| Open Access
A toxin-antidote system contributes to interspecific reproductive isolation in rice
Orzya meridionalis is a wild rice species that has reproductive isolation with Asian cultivated rice. Here, the authors report the cloning of the second locus controlling hybrid male sterility between the two species and show the encoded toxin-antidote system provides stacked reproductive isolation for maintaining species identity.
- Shimin You
- , Zhigang Zhao
- & Jianmin Wan
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Article
| Open Access
Discovery of isoflavone phytoalexins in wheat reveals an alternative route to isoflavonoid biosynthesis
Isoflavones are mostly found in the legumes, and little is known about their formation outside of this family. Here, the authors discover an isoflavone synthase gene in wheat, found in a pathogen-induced gene cluster encoding isoflavone biosynthesis.
- Guy Polturak
- , Rajesh Chandra Misra
- & Anne Osbourn
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| Open Access
The pan-genome and local adaptation of Arabidopsis thaliana
Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.
- Minghui Kang
- , Haolin Wu
- & Jianquan Liu
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Article
| Open Access
A de novo evolved gene contributes to rice grain shape difference between indica and japonica
Genetic bases of grain shape differentiation between the two subspecies of Asian cultivated rice have not been fully elucidated. Here, the authors report GSE9, a de novo gene evolved from a non-coding region of wild rice through acquisition of start codon, contributes to the grain shape difference between the two subspecies.
- Rujia Chen
- , Ning Xiao
- & Zefeng Yang
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Article
| Open Access
Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation
Long-term monitoring of plants in field fluctuating environments remains challenging. Here, the authors develop PlantServation, a machine learning-based phenotyping method, and estimate environmental and genotypic effects on the pigment anthocyanin content of diploid and polyploid Arabidopsis.
- Reiko Akiyama
- , Takao Goto
- & Kentaro K. Shimizu
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Article
| Open Access
Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae
Evolutionary relationships among green plants are unresolved and, in particular, the phylogenetic position of Prasinodermophyta remains controversial. Here, the authors conduct phylogenomic analyses to resolve relationships within Viridiplantae, suggesting that this group diverged between the Great Oxidation Event and the Neoproterozoic Oxygenation Event.
- Zhiping Yang
- , Xiaoya Ma
- & Bojian Zhong
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Article
| Open Access
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase copy number variation confers glyphosate resistance in Eleusine indica
Resistance to herbicide glyphosate can be evolved trough copy number variation (CNV) of its target gene EPSPS in goosegrass. Here, the authors assemble the genomes of glyphosate susceptible and resistance lines and provide evidence of sub-telomeric-repeat driven CNV of EPSPS could lead to glyphosate resistance.
- Chun Zhang
- , Nicholas A. Johnson
- & Eric L. Patterson
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Article
| Open Access
Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Functional divergence of CYP76AK subfamily, accompanied by oxidation variations at C-20, leads to diverse abietane-type diterpenoids in Salvia species. Enzyme activity loss contributes to this unique chemical diversity within the lineage.
- Jiadong Hu
- , Shi Qiu
- & Wansheng Chen
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Article
| Open Access
Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice
The mechanisms of the partial reproductive isolation between the two subspecies of rice remains obscure. Here, the authors show that the two adjacent genes form a killer-protector system to induce hybrid male sterility and reproductive isolation between indica and japonica.
- Daiqi Wang
- , Hongru Wang
- & Ziqiang Liu
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Article
| Open Access
The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits
Horseradish is a spicy root vegetable and it also produces horseradish peroxidase, an enzyme widely used in biochemistry applications. Here, the authors report its telomere-to-telomere reference genome, reveal subgenome diversification and the effect on the biosynthesis of glucosinolates and horseradish peroxidases.
- Fei Shen
- , Shixiao Xu
- & Martin A. Lysak
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Article
| Open Access
Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae
Asteraceae is the largest family of flowering plants. Here, the authors assemble the genomes of stem lettuce (within Asteraceae) and beach cabbage (within Goodeniaceae) for evolutionary genomics analyses and reveal the absence of the core regulatory gene of nitrogen and carbon assimilation in Asteraceae.
- Fei Shen
- , Yajuan Qin
- & Xiaozeng Yang
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Article
| Open Access
Evolutionary history of the Arctic flora
The Arctic tundra is a relatively young biome. Here, the authors sample 32 angiosperm clades encompassing 3600+ species and find that both long-term dispersal and in situ speciation may have contributed to Arctic flora assembly, in association with landscape, climate and sea-level changes since the early Late Miocene.
- Jun Zhang
- , Xiao-Qian Li
- & Wei Wang
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Article
| Open Access
Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet
Finger millet is an orphan crop key to food security of people living in eastern Africa, India and Nepal. Here, the authors assemble its genome, conduct population genetics analyses to infer the diversification history, and reveal a candidate gene for purple coloration of anthers and stigma.
- Katrien M. Devos
- , Peng Qi
- & Damaris A. Odeny
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Article
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Diploid and tetraploid genomes of Acorus and the evolution of monocots
Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.
- Liang Ma
- , Ke-Wei Liu
- & Zhong-Jian Liu
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Article
| Open Access
The genome of Acorus deciphers insights into early monocot evolution
Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.
- Xing Guo
- , Fang Wang
- & Huan Liu
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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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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
Selection and adaptive introgression guided the complex evolutionary history of the European common bean
Common bean has two distinct domestication centers in Mesoamerica and in the Andes. The authors show that the Andean is the first gene pool successfully introduced in Europe and identify signature of pervasive introgression among gene pools and of selection for flowering underlying adaptation.
- Elisa Bellucci
- , Andrea Benazzo
- & Roberto Papa
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Bacterial detoxification of plant defence secondary metabolites mediates the interaction between a shrub and frugivorous birds
The interactions between plants and frugivores are mediated by plants’ secondary metabolites. Here the authors demonstrate that specific bacteria, capable of consuming these metabolites, can alter these interactions, benefiting both plants and fruit consumers.
- Beny Trabelcy
- , Nimrod Shteindel
- & Yoram Gerchman
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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
Cross-stress gene expression atlas of Marchantia polymorpha reveals the hierarchy and regulatory principles of abiotic stress responses
How plants respond to multiple stresses occurring simultaneously is poorly understood. Here the authors describe how gene expression in Marchantia polymorpha responds to different combinations of seven abiotic stresses and provide online resources to facilitate data visualization and usability.
- Qiao Wen Tan
- , Peng Ken Lim
- & Marek Mutwil
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| 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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| Open Access
Limited 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
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| Open Access
Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis
Parapatric speciation occurs when reproductive isolation arises without full geographic isolation. Here, the authors combine genomic and phylogeographic analyses to illustrate a case of parapatric speciation attributed to climate change, range expansion and mating system shift.
- Yvonne Willi
- , Kay Lucek
- & Nora Walden
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Article
| Open Access
Transposable elements maintain genome-wide heterozygosity in inbred populations
How highly inbred populations generate novel genetic variations upon which natural selection can act is unclear. Here, the authors reveal the effect of transposable elements on the genome-wide heterozygosity landscape across a natural inbreeding gradient of Arabidopsis lyrata and reducing the probability of inbreeding depression.
- Hanne De Kort
- , Sylvain Legrand
- & James Buckley
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Article
| Open Access
Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
How subgenome-divergent and -convergent transcription is mediated and harmonized in hexaploid common wheat genome remains unclear. Here, via characterizing the cistrome maps, the authors reveal that transposon elements with transcription factor binding ability have the potential to make the contribution.
- Yuyun Zhang
- , Zijuan Li
- & Yijing Zhang
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Article
| Open Access
Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia
Assessment of population vulnerability and adaptive capacity under climate change is crucial for informing conservation strategies. Sang et al. assemble a reference genome for Populus koreana and combine population genomics and modelling to predict spatiotemporal responses to climate change.
- Yupeng Sang
- , Zhiqin Long
- & Jing Wang
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Article
| Open Access
Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding
Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.
- Jiantao Guan
- , Jintao Zhang
- & Lixia Wang
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Article
| Open Access
Climate windows of opportunity for plant expansion during the Phanerozoic
Climatic variables have played a significant role in plant evolution across the Phanerozoic. Here, the authors link climate with a new dynamic vegetation model to identify two windows of opportunity for plant biomass expansion, corresponding with the expansion of land plants and the angiosperm radiation.
- Khushboo Gurung
- , Katie J. Field
- & Benjamin J. W. Mills
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Article
| Open Access
An ancestral function of strigolactones as symbiotic rhizosphere signals
Strigolactones (SLs) regulate angiosperm development and promote symbiosis with arbuscular mycorrhizae. Here the authors show that bryosymbiol, an SL present in bryophytes and angiosperms, promotes AM symbiosis in Marchantia paleacea suggesting an ancestral function of SLs as rhizosphere signals.
- Kyoichi Kodama
- , Mélanie K. Rich
- & Junko Kyozuka
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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
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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Article
| Open Access
Chromosome evolution and the genetic basis of agronomically important traits in greater yam
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci associated with anthracnose resistance and tuber traits.
- Jessen V. Bredeson
- , Jessica B. Lyons
- & Daniel S. Rokhsar
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Article
| Open Access
Genomic 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
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Article
| Open Access
Reshuffling 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
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Article
| Open Access
Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
- Guotai Yu
- , Oadi Matny
- & Brande B. H. Wulff
Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages