Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus o...Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.展开更多
Rice blast,caused by Magnaporthe oryzae,is a fungal disease that causes devastating damage to rice production worldwide.During infection,pathogens secrete effector proteins that modulate plant immunity.Disulfide bond ...Rice blast,caused by Magnaporthe oryzae,is a fungal disease that causes devastating damage to rice production worldwide.During infection,pathogens secrete effector proteins that modulate plant immunity.Disulfide bond formation catalyzed by protein disulfide isomerases(PDI)is essential for protein folding and maturation.However,the biological function of Pdi1 in M.oryzae has not yet been characterized.In this study,we identified the endoplasmic reticulum(ER)-located protein,MoPdi1,in M.oryzae.MoPdi1 regulates conidiation,cell wall stress,and pathogenicity of M.oryzae.Furthermore,the CGHC active sites in the a and a'redox domain of MoPdi1 were essential for the biological function of MoPDI1.Further tests demonstrated that MoPdi1 was involved in the regulation of ER stress and positively regulated ER phagy.We also found that MoPdi1 interacted with MoHut1.Deletion of MoPDI1 led to the bereft of MoHut1 dimerization,which depends on the formation of disulfide bonds.In addition,MoPdi1 affected the normal secretion of the cytoplasmic effector AVR-Pia.We provided evidence that MoHut1 is important for the vegetative growth,conidiation,and pathogenicity in M.oryzae.Therefore,our findings could provide a suitable target point for designing antifungal agrochemicals against rice blast fungus.展开更多
Background The rapid development of intensive layer breeding has intensified odor pollution that must be paid attention to for the green transformation of the industry. This study used Jingfen No.6 laying hens as the ...Background The rapid development of intensive layer breeding has intensified odor pollution that must be paid attention to for the green transformation of the industry. This study used Jingfen No.6 laying hens as the model to systematically evaluate the regulatory effect of compound microalgal powder(Chlorella vulgaris:Spirulina platensis:Haematococcus pluvialis = 3:1:1, 1:3:1, 1:1:3) on ammonia(NH3) emissions from laying hen manure.Results Through analysis of the static NH3production in manure, it was found that the NH3emissions within 24 h in the experimental group with 0.50% compound microalgal powder added were reduced to 6.27–16.84 mg(vs. control: 28.29 mg), achieving a 40.47%–77.84% reduction. GC/MS and 16S rRNA sequencing analyses indicated that the compound microalgal powder intervened in the remodeling of the microbial community and nitrogen metabolism network in manure, driving the transformation from inorganic nitrogen to organic nitrogen, mitigated the proliferation of NH3-producing bacteria(such as Escherichia coli, Klebsiella pneumoniae, Kurthia, and Proteus), and increased the abundance of acid-producing bacteria(such as Leuconostocaceae and Lactobacillaceae). The Spirulina platensis powder group had the best emission reduction effect(reduced by 77.84%), and its mechanism was closely related to the mitigation of Gram-negative bacteria activity by phycocyanin and increased synthesis of aromatic compounds, such as 2,3,5-trimethyl-6-ethylpyrazine.Conclusions This study revealed the mechanism by which the compound microalgal powder reduces NH3emissions by regulating the proliferation of acid-producing bacteria, reshaping the nitrogen metabolism network, and mitigating the activity of NH3-producing bacteria, while providing theoretical and data support for the development of environmentally friendly feed.展开更多
Plant bacterial diseases have infiicted substantial economic losses in global crop,fruit,and vegetable production.The conventional methods for managing these diseases typically rely on the application of antibiotics.H...Plant bacterial diseases have infiicted substantial economic losses in global crop,fruit,and vegetable production.The conventional methods for managing these diseases typically rely on the application of antibiotics.However,these antibiotics often target the growth factors of the pathogenic bacteria,leading to the accumulation and emergence of drug-resistant strains,which exacerbates antibiotic resistance.Innovative methods are urgently needed to treat and prevent the toxicity caused by these pathogenic bacteria.Targeting virulence mechanisms in pathogens is a globally recognized and effective strategy for mitigating bacterial resistance.TypeⅢsecretion system(T3SS)serves as a crucial virulence determinant in Gram-negative pathogens,and its non-essentials for pathogen growth renders it an ideal target.Targeting the T3SS holds significant potential to alleviate selective pressure for resistance mutations in pathogens.Therefore,targeting T3SS in pathogenic bacteria,while preserving their growth,has emerged as a novel avenue for the development of antimicrobial drugs.In recent years,a multitude of small molecular inhibitors targeting T3SS have been identified.This article offers a comprehensive review of T3SS inhibitors in plant pathogens,while also presenting the latest research advancements in this research direction.展开更多
Rice false smut disease, which is caused by the fungus Ustilaginoidea virens, is currently one of the most devastating rice fungal diseases in the world. Rice false smut disease not only causes severe yield loss and g...Rice false smut disease, which is caused by the fungus Ustilaginoidea virens, is currently one of the most devastating rice fungal diseases in the world. Rice false smut disease not only causes severe yield loss and grain quality reduction, but also threatens food safety due to its production of mycotoxins. In this review, the most recent progresses regarding the life cycle, infection processes, genome and genetic diversity, pathogenic gene and disease resistance in rice were summarized in order to provide theoretical basis for the control of U. virens. We also proposed some future directions and key questions that need to be addressed for a better understanding of the molecular mechanism that leads to rice false smut disease and the prospects for sustainable control of rice false smut.展开更多
The basidiomycetous fungus Sporisorium scitamineum causes sugarcane smut that leads to severe economic losses in the major sugarcane growing areas in China,India and Brazil,etc.Autophagy is a conserved pathway in euka...The basidiomycetous fungus Sporisorium scitamineum causes sugarcane smut that leads to severe economic losses in the major sugarcane growing areas in China,India and Brazil,etc.Autophagy is a conserved pathway in eukaryotes for bulk degradation and cellular recycling,and was shown to be important for fungal cell growth,development,and pathogenicity.However,physiological function of autophagy has not been studied in S.scitamineum.In this study,we identified a conserved Atg8 protein,named as SsAtg8 and characterized its function.Our results showed that autophagy was blocked in the ssatg8Δ mutant,in nitrogen starvation.The ssatg8Δ mutant formed pseudohypha frequently and was hypersensitive to oxidative stress.However,mating or filamenation was unaffected in the ssatg8Δ mutant in vitro.Overall we demonstrate that autophagy is dispensable for S.scitamineum mating/filamentation,while critical for oxidative stress tolerance and proper morphology in sporidial stage.展开更多
A series of photoinduced palladium-catalyzed 1,3-diene-selective fluoroalkylamination derivatives was rationally synthesized based on diversity-oriented synthesis via cross coupling of 1,3-dienes,amines and fluoroalky...A series of photoinduced palladium-catalyzed 1,3-diene-selective fluoroalkylamination derivatives was rationally synthesized based on diversity-oriented synthesis via cross coupling of 1,3-dienes,amines and fluoroalkyl iodides.The reaction featured good function group tolerance and a broad substrate scope,which could be extended to the late-stage modification of bioactive molecules.Bactericidal activity of all the compounds against Xanthomonas oryzae pv.oryzae(Xoo)was evaluated.Among them,compound E14 showed significant activity against Xanthomonas oryzae pv.oryzae(Xoo)with half maximal effective concentration(EC50)value of 6.61μmol/mL.In pot experiments,the results showed that E14 could control rice bacterial blight with protective and curative efficiencies of 37.5%and 63.2%at 200μg/mL,respectively.Additionally,a plausible mechanism for antibacterial behavior of E14 was proposed by electron microscopy,flow cytometry,reactive oxygen species detection,and biofilm assay.In current work,it can promote the development of photoinduced palladium-catalyzed 1,3-diene-selective fluoroalkyl amination compounds as prospective antibacterial agent bearing an intriguing mode of action.展开更多
Natural isoquinolinium alkaloids possess a wide range of biological activities.The design and synthesis of mesoionic isoquinoliniums is of great importance.This paper reports the synthesis of unique mesoionic thiazolo...Natural isoquinolinium alkaloids possess a wide range of biological activities.The design and synthesis of mesoionic isoquinoliniums is of great importance.This paper reports the synthesis of unique mesoionic thiazoloisoquinolinium thiolates stabilized by aromatization and 1,3-dipolarization.Such compounds can be synthesized via the three component [2 + 2 + 1] cycloaddition reaction of isoquinolines with ethyl propionate and elemental sulfur in the absence of any metal catalyst and additives.Importantly,thiazoloisoquinolinium thiolates can be transformed to thioether-containing thiazoloisoquinolinium halides.A selective [4 + 2] cycloaddition can also be used to form S-bridged fused tetracyclic compounds with a thiothiamide ring unit and two quarternary carbon centres.Compound I-1 shows good bioactivity against the chlorophyll of duckweed(Lemna minor) with inhibition rate of 51.5 mg/mL.展开更多
Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monoco...Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.展开更多
Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structur...Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.展开更多
基金supported by the National Key R&D Program of China(2022YFD1401600)the National Science Foundation for Distinguished Young Scholars of Zhejang Province,China(LR23C140001)supported by the Key Area Research and Development Program of Guangdong Province,China(2018B020205003 and 2020B0202090001).
文摘Inferring phylogenetic trees from molecular sequences is a cornerstone of evolutionary biology.Many standard phylogenetic methods(such as maximum-likelihood[ML])rely on explicit models of sequence evolution and thus often suffer from model misspecification or inadequacy.The on-rising deep learning(DL)techniques offer a powerful alternative.Deep learning employs multi-layered artificial neural networks to progressively transform input data into more abstract and complex representations.DL methods can autonomously uncover meaningful patterns from data,thereby bypassing potential biases introduced by predefined features(Franklin,2005;Murphy,2012).Recent efforts have aimed to apply deep neural networks(DNNs)to phylogenetics,with a growing number of applications in tree reconstruction(Suvorov et al.,2020;Zou et al.,2020;Nesterenko et al.,2022;Smith and Hahn,2023;Wang et al.,2023),substitution model selection(Abadi et al.,2020;Burgstaller-Muehlbacher et al.,2023),and diversification rate inference(Voznica et al.,2022;Lajaaiti et al.,2023;Lambert et al.,2023).In phylogenetic tree reconstruction,PhyDL(Zou et al.,2020)and Tree_learning(Suvorov et al.,2020)are two notable DNN-based programs designed to infer unrooted quartet trees directly from alignments of four amino acid(AA)and DNA sequences,respectively.
基金supported by the National Natural Science Foundation of China(32202253)the Natural Science Foundation of Anhui Higher Education Institutions,China(KJ2020A0102)the Talent Research Project of Anhui Agricultural University,China(rc342001)。
文摘Rice blast,caused by Magnaporthe oryzae,is a fungal disease that causes devastating damage to rice production worldwide.During infection,pathogens secrete effector proteins that modulate plant immunity.Disulfide bond formation catalyzed by protein disulfide isomerases(PDI)is essential for protein folding and maturation.However,the biological function of Pdi1 in M.oryzae has not yet been characterized.In this study,we identified the endoplasmic reticulum(ER)-located protein,MoPdi1,in M.oryzae.MoPdi1 regulates conidiation,cell wall stress,and pathogenicity of M.oryzae.Furthermore,the CGHC active sites in the a and a'redox domain of MoPdi1 were essential for the biological function of MoPDI1.Further tests demonstrated that MoPdi1 was involved in the regulation of ER stress and positively regulated ER phagy.We also found that MoPdi1 interacted with MoHut1.Deletion of MoPDI1 led to the bereft of MoHut1 dimerization,which depends on the formation of disulfide bonds.In addition,MoPdi1 affected the normal secretion of the cytoplasmic effector AVR-Pia.We provided evidence that MoHut1 is important for the vegetative growth,conidiation,and pathogenicity in M.oryzae.Therefore,our findings could provide a suitable target point for designing antifungal agrochemicals against rice blast fungus.
基金supported by National Key Research and Development Program of China (Grant No.2023YFD1701700)approved by the Experimental Animal Ethics Committee of South China Agricultural University (Approval Number:2025f014)
文摘Background The rapid development of intensive layer breeding has intensified odor pollution that must be paid attention to for the green transformation of the industry. This study used Jingfen No.6 laying hens as the model to systematically evaluate the regulatory effect of compound microalgal powder(Chlorella vulgaris:Spirulina platensis:Haematococcus pluvialis = 3:1:1, 1:3:1, 1:1:3) on ammonia(NH3) emissions from laying hen manure.Results Through analysis of the static NH3production in manure, it was found that the NH3emissions within 24 h in the experimental group with 0.50% compound microalgal powder added were reduced to 6.27–16.84 mg(vs. control: 28.29 mg), achieving a 40.47%–77.84% reduction. GC/MS and 16S rRNA sequencing analyses indicated that the compound microalgal powder intervened in the remodeling of the microbial community and nitrogen metabolism network in manure, driving the transformation from inorganic nitrogen to organic nitrogen, mitigated the proliferation of NH3-producing bacteria(such as Escherichia coli, Klebsiella pneumoniae, Kurthia, and Proteus), and increased the abundance of acid-producing bacteria(such as Leuconostocaceae and Lactobacillaceae). The Spirulina platensis powder group had the best emission reduction effect(reduced by 77.84%), and its mechanism was closely related to the mitigation of Gram-negative bacteria activity by phycocyanin and increased synthesis of aromatic compounds, such as 2,3,5-trimethyl-6-ethylpyrazine.Conclusions This study revealed the mechanism by which the compound microalgal powder reduces NH3emissions by regulating the proliferation of acid-producing bacteria, reshaping the nitrogen metabolism network, and mitigating the activity of NH3-producing bacteria, while providing theoretical and data support for the development of environmentally friendly feed.
基金the financial support from the National Key Research and Development Program of China(No.2023YFD1701100)the National Natural Science Foundation of China(No.32072450)+2 种基金the National Science Fund for Distinguished Young Scholars of Guangdong Province(No.2021B1515020107)the Opening Foundation of Hubei Key Laboratory of Novel Reactor and Green Chemical Technology(No.NRG202306)the Opening Foundation of Guangdong Province Key Laboratory of Microbial Signals and Disease Control(No.MSDC2023-19)。
文摘Plant bacterial diseases have infiicted substantial economic losses in global crop,fruit,and vegetable production.The conventional methods for managing these diseases typically rely on the application of antibiotics.However,these antibiotics often target the growth factors of the pathogenic bacteria,leading to the accumulation and emergence of drug-resistant strains,which exacerbates antibiotic resistance.Innovative methods are urgently needed to treat and prevent the toxicity caused by these pathogenic bacteria.Targeting virulence mechanisms in pathogens is a globally recognized and effective strategy for mitigating bacterial resistance.TypeⅢsecretion system(T3SS)serves as a crucial virulence determinant in Gram-negative pathogens,and its non-essentials for pathogen growth renders it an ideal target.Targeting the T3SS holds significant potential to alleviate selective pressure for resistance mutations in pathogens.Therefore,targeting T3SS in pathogenic bacteria,while preserving their growth,has emerged as a novel avenue for the development of antimicrobial drugs.In recent years,a multitude of small molecular inhibitors targeting T3SS have been identified.This article offers a comprehensive review of T3SS inhibitors in plant pathogens,while also presenting the latest research advancements in this research direction.
基金funded by the Zhejiang Provincial Natural Science Foundation of China (Grant Nos. LQ19C140004 and LQ19C130007)the Chinese Academy of Agricultural Sciences under the ’Elite Youth’ Programthe Agricultural Sciences and Technologies Innovation Program of China (CAAS-ASTIP-2016-CNRRI)
文摘Rice false smut disease, which is caused by the fungus Ustilaginoidea virens, is currently one of the most devastating rice fungal diseases in the world. Rice false smut disease not only causes severe yield loss and grain quality reduction, but also threatens food safety due to its production of mycotoxins. In this review, the most recent progresses regarding the life cycle, infection processes, genome and genetic diversity, pathogenic gene and disease resistance in rice were summarized in order to provide theoretical basis for the control of U. virens. We also proposed some future directions and key questions that need to be addressed for a better understanding of the molecular mechanism that leads to rice false smut disease and the prospects for sustainable control of rice false smut.
基金supported by the National 973 Program of China(2015CB150600)the Natural Science Foundation of Guangdong Province,China(2017A030310144)
文摘The basidiomycetous fungus Sporisorium scitamineum causes sugarcane smut that leads to severe economic losses in the major sugarcane growing areas in China,India and Brazil,etc.Autophagy is a conserved pathway in eukaryotes for bulk degradation and cellular recycling,and was shown to be important for fungal cell growth,development,and pathogenicity.However,physiological function of autophagy has not been studied in S.scitamineum.In this study,we identified a conserved Atg8 protein,named as SsAtg8 and characterized its function.Our results showed that autophagy was blocked in the ssatg8Δ mutant,in nitrogen starvation.The ssatg8Δ mutant formed pseudohypha frequently and was hypersensitive to oxidative stress.However,mating or filamenation was unaffected in the ssatg8Δ mutant in vitro.Overall we demonstrate that autophagy is dispensable for S.scitamineum mating/filamentation,while critical for oxidative stress tolerance and proper morphology in sporidial stage.
基金the National Natural Science Foundation of China(No.32072450)the National Science Fund for Distinguished Young Scholars of Guangdong Province(No.2021B1515020107)the International Science and Technology Cooperation Program in Guangdong(Nos.2020A0505100048 and 2022A0505050060).
文摘A series of photoinduced palladium-catalyzed 1,3-diene-selective fluoroalkylamination derivatives was rationally synthesized based on diversity-oriented synthesis via cross coupling of 1,3-dienes,amines and fluoroalkyl iodides.The reaction featured good function group tolerance and a broad substrate scope,which could be extended to the late-stage modification of bioactive molecules.Bactericidal activity of all the compounds against Xanthomonas oryzae pv.oryzae(Xoo)was evaluated.Among them,compound E14 showed significant activity against Xanthomonas oryzae pv.oryzae(Xoo)with half maximal effective concentration(EC50)value of 6.61μmol/mL.In pot experiments,the results showed that E14 could control rice bacterial blight with protective and curative efficiencies of 37.5%and 63.2%at 200μg/mL,respectively.Additionally,a plausible mechanism for antibacterial behavior of E14 was proposed by electron microscopy,flow cytometry,reactive oxygen species detection,and biofilm assay.In current work,it can promote the development of photoinduced palladium-catalyzed 1,3-diene-selective fluoroalkyl amination compounds as prospective antibacterial agent bearing an intriguing mode of action.
基金financially supported by Natural Science Foundation of Guangdong Province for Distinguished Young Scholars (Nos.2019B151502052, 2021B1515020107)the programs of National Natural Science Foundation of China (No.32072450)+2 种基金the International Science and Technology Cooperation Program in Guangdong (No.2020A0505100048)the Program of Science and Technology of Guangzhou (No.202002030295)the open Project of the State Key Laboratory of Crop Stress Biology for Arid Areas (No.CSBAAKF2021009)。
文摘Natural isoquinolinium alkaloids possess a wide range of biological activities.The design and synthesis of mesoionic isoquinoliniums is of great importance.This paper reports the synthesis of unique mesoionic thiazoloisoquinolinium thiolates stabilized by aromatization and 1,3-dipolarization.Such compounds can be synthesized via the three component [2 + 2 + 1] cycloaddition reaction of isoquinolines with ethyl propionate and elemental sulfur in the absence of any metal catalyst and additives.Importantly,thiazoloisoquinolinium thiolates can be transformed to thioether-containing thiazoloisoquinolinium halides.A selective [4 + 2] cycloaddition can also be used to form S-bridged fused tetracyclic compounds with a thiothiamide ring unit and two quarternary carbon centres.Compound I-1 shows good bioactivity against the chlorophyll of duckweed(Lemna minor) with inhibition rate of 51.5 mg/mL.
基金This study is supported by the National Natural Science Foundation of China(no.31970229,no.31570219,and no.91531301)the Young Elite Scientists Sponsorship Program of Jiangsu Province,the State Key Laboratory of Paleobiology and Stratigraphy(Nanjing Institute of Geology and Paleontology,CAS)and the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Angiosperms(flowering plants)are the most diverse and species-rich group of plants.The vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and Ceratophyllales.The relationships among these Mesangiospermae groups have been the subject of long debate.In this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased methods.We dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm phylogeny.We further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister lineages.Similar frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm phylogeny.Our analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of angiosperms.Meanwhile,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.
基金supported by the National Key R&D Program of China(2019YFE0119000)the National Science Fund for Distinguished Young Scholars(32225049)+1 种基金the National Natural Science Foundation of China(31872561)the Alliance of International Science Organizations(ANSO-CR-PP-2021-03).
文摘Hybridization and polyploidization have made great contributions to speciation,heterosis,and agricultural production within plants,but there is still limited understanding and utilization in animals.Subgenome structure and expression reorganization and cooperation post hybridization and polyploidization are essential for speciation and allopolyploid success.However,the mechanisms have not yet been comprehensively assessed in animals.Here,we produced a high-fidelity reference genome sequence for common carp,a typical allotetraploid fish species cultured worldwide.This genome enabled in-depth analysis of the evolution of subgenome architecture and expression responses.Most genes were expressed with subgenome biases,with a trend of transition from the expression of subgenome A during the early stages to that of subgenome B during the late stages of embryonic development.While subgenome A evolved more rapidly,subgenome B contributed to a greater level of expression during development and under stressful conditions.Stable dominant patterns for homoeologous gene pairs both during development and under thermal stress suggest a potential fixed heterosis in the allotetraploid genome.Preferentially expressing either copy of a homoeologous gene at higher levels to confer development and response to stress indicates the dominant effect of heterosis.The plasticity of subgenomes and their shifting of dominant expression during early development,and in response to stressful conditions,provide novel insights into the molecular basis of the successful speciation,evolution,and heterosis of the allotetraploid common carp.
