Featured
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| Open AccessHaplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations
Moso bamboo is a critical species for carbon sequestration and mitigating climate change. This study presents a haplotype-based pangenome that uncovers substantial genetic diversity associated with climate adaptation and enables predictions of genetic vulnerability under future emission scenarios.
- Yinguang Hou
- , Junwei Gan
- & Hansheng Zhao
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Article
| Open AccessBaTwa populations from Zambia retain ancestry of past hunter-gatherer groups
Few genetic studies have focused on BaTwa populations in southern Africa. Here, the authors have examined the genetic ancestry of 80 individuals from two isolated BaTwa communities in Zambia, finding evidence of hunter gatherer and Western African ancestry.
- Gwenna Breton
- , Lawrence Barham
- & Mattias Jakobsson
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Article
| Open AccessPan-genome and phylogenomic analyses highlight Hevea species delineation and rubber trait evolution
The para rubber tree is the world’s sole commercial source of natural rubber. Here, the authors assemble the pangenome based on five genomes of H. brasiliensis and three genomes of other Hevea species, and reveal species delineation and rubber trait evolution through phylogenomic analyses.
- Yongjun Fang
- , Xiaohu Xiao
- & Chaorong Tang
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Article
| Open AccessAllopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes
How different parental sex chromosome systems affect allopolyploidization is yet unknown. Here, the authors assemble the genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid S. dunnii, and explore the transition from XY system to ZW system following allopolyploidization.
- Li He
- , Yuàn Wang
- & Ray Ming
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Article
| Open AccessLoss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution
Cold tolerance has lost during tomato natural evolution. Here, the authors report that absence of a 60 bp promoter fragment in the WRKY34 gene results in loss of cold tolerance in domesticated tomato varieties, and reveal how this natural variation can affect cold tolerance.
- Mingyue Guo
- , Fengjun Yang
- & Jie Zhou
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Article
| Open AccessPhylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation
The phylogenetic and hybridization history of Xiphophorus fish remains contentious, despite their long-standing role as models in evolutionary biology and human disease research. This study presents a complete genome resource that resolves the previously conflicting phylogeny and evolutionary history of the group, revealing that hybridizations preceded speciation.
- Kang Du
- , Juliana Morena Bonita Ricci
- & Manfred Schartl
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Article
| Open AccessEcological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
Marine life depends on zooplankton like krill, but it’s uncertain how these species will respond to a warming ocean. This study of genome variation in the Northern krill uncovered many gene variants that could be crucial for environmental adaptation and support stock assessment under climate change.
- Per Unneberg
- , Mårten Larsson
- & Andreas Wallberg
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Article
| Open AccessCentury-old chromatin architecture revealed in formalin-fixed vertebrates
Formaldehyde-preserved museum specimens have produced genetic data. Here, the authors generate chromatin profiles from museum specimens 117 years old and experimentally demonstrate chromatin profile presence in formalin-fixed mouse and yeast models.
- Erin E. Hahn
- , Jiri Stiller
- & Clare E. Holleley
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Article
| Open AccessGenome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation
Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Here, the authors assemble the chromosome-scale genome of the sexually deceptive orchid Ophrys sphegodes and reveal insights into sexual deception and pollinator adaptation.
- Alessia Russo
- , Mattia Alessandrini
- & Philipp M. Schlüter
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Article
| Open AccessSubfunctionalisation and self-repression of duplicated E1 homologues finetunes soybean flowering and adaptation
Unlike cultivated soybean, the genetic basis for high latitude adaptation for wild soybean accessions is largely unknown. Here, the authors reveal how the subfunctionalization of E1 family genes and gene introgression have driven adaptation to higher latitudes in wild soybean accessions.
- Chao Fang
- , Zhihui Sun
- & Sijia Lu
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Article
| Open AccessHow antisense transcripts can evolve to encode novel proteins
New protein coding genes can emerge de novo overlapping existing protein genes but in the opposite orientation. Here, the authors investigate the possibility of such events using mathematical modelling and data analysis, and find that emergence of a protein coding region is generally most likely in one frame of overlap (frame 1).
- Bharat Ravi Iyengar
- , Anna Grandchamp
- & Erich Bornberg-Bauer
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Article
| Open AccessBdelloid rotifers deploy horizontally acquired biosynthetic genes against a fungal pathogen
Fungi and bacteria fight coevolutionary wars using antimicrobial compounds that animal cells cannot usually produce. This study finds that bdelloid rotifers attacked by a fungal pathogen express genes acquired horizontally from bacteria, including some resembling antibiotic synthesis clusters.
- Reuben W. Nowell
- , Fernando Rodriguez
- & Christopher G. Wilson
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Article
| Open AccessReplication timing alterations are associated with mutation acquisition during breast and lung cancer evolution
The role of altered replication timing (ART) during malignant transformation requires further exploration. Here, analysis of replication-timing sequencing and whole genome sequencing reveals a significant association of ART with the genomic and transcriptomic landscape during cancer evolution in lung and breast tumours.
- Michelle Dietzen
- , Haoran Zhai
- & Nnennaya Kanu
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Article
| Open AccessDivergent evolution of male-determining loci on proto-Y chromosomes of the housefly
For sexually reproducing organisms, experimental models to study the evolution of primary sex-determining loci are scarce. This study shows male-determining loci on proto-Y chromosomes of the housefly, containing the same gene, can genomically diverge into regions of various complexity.
- Xuan Li
- , Sander Visser
- & Leo W. Beukeboom
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Article
| Open AccessGenomic and single-cell analyses reveal genetic signatures of swimming pattern and diapause strategy in jellyfish
Jellyfish represent a critical step in the evolution of early animal movement systems. Here, the authors identify adaptive genetic bases explaining the loss of statocysts in Turritopsis rubra and its ability for reverse development.
- Zhijun Dong
- , Fanghan Wang
- & Qiang Lin
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Article
| Open AccessEvolution and subfunctionalization of CIPK6 homologous genes in regulating cotton drought resistance
Functional differentiation of homologous genes are usually followed by polyploidization in plants, which may contribute to adaptation. Here, the authors report the negative and positive synergistic regulation of GhCBL1A1-GhCIPK6D1 and GhCBL2A1-GhCIPK6D3, respectively, on drought resistance in cotton.
- Weinan Sun
- , Linjie Xia
- & Xiyan Yang
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Article
| Open AccessCopy number variation introduced by a massive mobile element facilitates global thermal adaptation in a fungal wheat pathogen
The deletion and duplication of genes can be major facilitators of evolution. Here, the role of such variation was investigated in over a thousand genomes characterizing the global spread of a major fungal pathogen of wheat. The study suggests that gene loss likely facilitated the pathogen’s colonization of new continents by modulating climate tolerance and metabolic capabilities.
- Sabina Moser Tralamazza
- , Emile Gluck-Thaler
- & Daniel Croll
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Article
| Open AccessThe loci of environmental adaptation in a model eukaryote
Systematic studies are needed to form a general understanding of the genomic basis of adaptation. In this work, authors perform laboratory evolution of 3360 yeast populations in 252 environments of varying levels of stress to uncover the genomic principles of environmental adaptation.
- Piaopiao Chen
- & Jianzhi Zhang
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Article
| Open AccessLow-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes
Pacific Biosciences (PacBio) High Fidelity (HiFi) long-read sequencing usually requires a relatively high amount of DNA input ( > 1 µg). Here the authors develop LILAP, a Low-Input (100 ng), Low-cost, and Amplification-free library-generation method for PacBio sequencing, enabling the generation of two high-quality individual fly genomes.
- Hangxing Jia
- , Shengjun Tan
- & Yong E. Zhang
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Article
| Open AccessSirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria
Sirenians are aquatic mammals that originated in Africa ~60 million years ago. Using comparative genomics of a new dugong genome, this study finds genetic adaptations shared by extant sirenians and assessed the diversity of dugongs in Australian waters and the functionally extinct Okinawan dugong.
- Ran Tian
- , Yaolei Zhang
- & Inge Seim
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Article
| Open AccessImpact of whole-genome duplications on structural variant evolution in Cochlearia
Cochlearia is an evolutionarily dynamic genus with different base chromosome numbers and ploidal levels. Here, the authors construct a graph-based pangenome for Cochlearia and reveal that whole-genome duplication associated with greater diversity of genomic structural variation and their possible function in adaptation.
- Tuomas Hämälä
- , Christopher Moore
- & Levi Yant
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Article
| Open AccessBiotic interactions promote local adaptation to soil in plants
Little is known about the interaction of different ecological factors in shaping adaptive evolution in natural habitats. This study found that plants evolved local adaption to different soils, but only when they interacted with aphid- herbivores and bumblebee-pollinators.
- Thomas Dorey
- , Léa Frachon
- & Florian P. Schiestl
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Article
| Open AccessMapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color
Here, the authors perform a large GWAS for objectively quantified skin color in an East Asian population (N = 48,433), identifying potential causal genes, polygenic adaptations, and interaction between genetic variants and sun-exposure at polygenic level.
- Beomsu Kim
- , Dan Say Kim
- & Hong-Hee Won
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Article
| Open AccessMicrobiome and epigenetic variation in wild fish with low genetic diversity
Species with low genetic diversity have limited capacity to adapt to environmental change. This study finds that the skin microbiome and non-genetic (epigenetic) modifications of the DNA represent additional sources of variation that could help low diversity fish survive environmental challenges.
- Ishrat Z. Anka
- , Tamsyn M. Uren Webster
- & Sofia Consuegra
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Article
| Open AccessA multidimensional selective landscape drives adaptive divergence between and within closely related Phlox species
Selection drives divergence between species, contributing to speciation, while simultaneously favoring extensive diversity that is maintained across populations within a species. This study demonstrates how the selection landscape is complex and multidimensional across three species of Phlox flowers.
- Benjamin E. Goulet-Scott
- , Matthew C. Farnitano
- & Robin Hopkins
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Article
| Open AccessEnvironment-induced heritable variations are common in Arabidopsis thaliana
Ancestral environments can induce heritable phenotypic changes, but whether it is a common phenomenon remains unknown. This long-term experiment in Arabidopsis thaliana reveals that environment-induced heritable changes that are common, reproducible, and predictable.
- Xiaohe Lin
- , Junjie Yin
- & Yuan-Ye Zhang
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Article
| Open AccessPhylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae
Lichen symbiosis between chlorophyte algae and fungi is a key player in ecosystems but our understanding of its evolution and genetic regulation in algae remains limited. This study finds that lichen symbiosis evolved at least three times in algae through gene family expansion and horizontal gene transfers
- Camille Puginier
- , Cyril Libourel
- & Jean Keller
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Article
| Open AccessUnveiling the A-to-I mRNA editing machinery and its regulation and evolution in fungi
A-to-I editing in animals is catalyzed by enzymes of the Adenosine Deaminase Acting on RNA family, orthologues of which do not exist in fungi. Here, Feng et al. characterise the enzymes involved in A-to-I mRNA editing in Fusarium graminearum.
- Chanjing Feng
- , Kaiyun Xin
- & Huiquan Liu
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Article
| Open AccessMutation characteristics and molecular evolution of ovarian metastasis from gastric cancer and potential biomarkers for paclitaxel treatment
‘Gastric cancer metastasis to the ovary is difficult to treat and is not fully understood. Here, the authors characterized mutations in a cohort of matched primary and metastatic disease, and found mutations, including in CLDN18, could predict treatment response to paclitaxel.
- Pengfei Yu
- , Can Hu
- & Xiangdong Cheng
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Article
| Open AccessPositive selection in the genomes of two Papua New Guinean populations at distinct altitude levels
This study explores selection signals of Papua New Guinean highlanders and lowlanders using 128 new whole genome sequences. It highlights two genetic variants associated with blood traits that also influence the heart rate of these populations.
- Mathilde André
- , Nicolas Brucato
- & François-Xavier Ricaut
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Article
| Open AccessEmergence of enhancers at late DNA replicating regions
Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.
- Paola Cornejo-Páramo
- , Veronika Petrova
- & Emily S. Wong
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Article
| Open AccessA genomic basis of vocal rhythm in birds
Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.
- Matteo Sebastianelli
- , Sifiso M. Lukhele
- & Alexander N. G. Kirschel
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Matters Arising
| Open AccessReply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Chase W. Nelson
- , Leo L. M. Poon
- & Haogao Gu
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Matters Arising
| Open AccessPopulation genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data
- Vivak Soni
- , John W. Terbot II
- & Jeffrey D. Jensen
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Article
| Open AccessIntrogression and disruption of migration routes have shaped the genetic integrity of wildebeest populations
The evolutionary genetics of a keystone savannah species the blue wildebeest, and the related black wildebeest, remain largely unexplored. This study finds evidence for archaic introgression of black wildebeest to blue wildebeest and detrimental effects of human activities on migratory populations.
- Xiaodong Liu
- , Long Lin
- & Rasmus Heller
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Article
| Open AccessEvolution of T cells in the cancer-resistant naked mole-rat
Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.
- Tzuhua D. Lin
- , Nimrod D. Rubinstein
- & Rochelle Buffenstein
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Article
| Open AccessAdaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events
Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.
- Guangji Chen
- , Dan Yu
- & Shaohong Feng
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Article
| Open AccessA chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution
Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.
- Yixue Bao
- , Qing Zhang
- & Muqing Zhang
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Article
| Open AccessNaked mole-rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles
The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.
- Chris G. Faulkes
- , Thomas R. Eykyn
- & Dunja Aksentijevic
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Article
| Open AccessMacroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages
Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.
- Mirjana Domazet-Lošo
- , Tin Široki
- & Tomislav Domazet-Lošo
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Article
| Open AccessThe Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal
The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.
- Leonardo Vallini
- , Carlo Zampieri
- & Luca Pagani
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Article
| Open AccessDynamics 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 AccessClearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation
There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.
- Farina Karim
- , Catherine Riou
- & Alex Sigal
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Article
| Open AccessInter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection closely related to Streptococcus pyogenes. Here the authors investigate the degree of genomic similarity between the two species and assess implications for development of vaccines.
- Ouli Xie
- , Jacqueline M. Morris
- & Mark R. Davies
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Article
| Open AccessDependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos et al show that the virulence of Mycobacterium tuberculosis is dependent on sufficient uptake of exogenous vitamin B12 from host serum and this phenotype is not conserved in environmental, opportunistic and ancestral lineages.
- Elena Campos-Pardos
- , Santiago Uranga
- & Jesús Gonzalo-Asensio
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Article
| Open AccessThe evolutionary impact of childhood cancer on the human gene pool
Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.
- Ulrik Kristoffer Stoltze
- , Jon Foss-Skiftesvik
- & Kjeld Schmiegelow
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Article
| Open AccessDipterocarpoidae genomics reveal their demography and adaptations to Asian rainforests
Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.
- Rong Wang
- , Chao-Nan Liu
- & Xiao-Yong Chen
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Article
| Open AccessEvolution and expression patterns of the neo-sex chromosomes of the crested ibis
The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.
- Lulu Xu
- , Yandong Ren
- & Gang Li
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Article
| Open AccessGenomic 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