Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are...Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are highly prized for their ornamental beauty and enjoy widespread admiration.For instance,H.syriacus serves as the national flower of South Korea,H.rosa-sinensis is favored as the floral emblem of Malaysia,and Chengdu city has earned the moniker"City of H.mutabilis"owing to its substantial cultivation.展开更多
Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploi...Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.展开更多
Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression ...Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.展开更多
The sugarcane genome polyploidization can reduce the pressure of gene evolution selection,promote the fixation of fine traits,and increase the biomass and economic value of sugarcane.This paper mainly introduced the o...The sugarcane genome polyploidization can reduce the pressure of gene evolution selection,promote the fixation of fine traits,and increase the biomass and economic value of sugarcane.This paper mainly introduced the origin of the sugarcane genome,the chromosome composition,the research progress of polyploidization genetic mechanism,in the hope of providing theoretical reference for sugarcane polyploidization breeding.展开更多
Polyploidization is recognized as a powerful driver of plant evolution and domestication.In the genus Gossypium,the natural hybridization of an A-genome ancestor and a D-genome ancestor gave rise to allopolyploid cott...Polyploidization is recognized as a powerful driver of plant evolution and domestication.In the genus Gossypium,the natural hybridization of an A-genome ancestor and a D-genome ancestor gave rise to allopolyploid cottons(Huang et al.,2024),such as Gossypium hirsutum and Gossypium barbadense.Previous cotton reference genomes(Du et al.,2018;Hu et al.,2019;Huang et al.,2020;Li et al.,2015;Wang et al.,2019;Yang et al.,2019;Zhang et al.,2015),although instrumental to cotton genetics and breeding,contained large assembly gaps,especially repetitive regions like centromeres.展开更多
As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,w...As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.展开更多
Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants i...Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants illustrates the immediate changes that follow WGDs and the mechanisms behind in both genetic and epigenetic consequences. Unfortunately, equivalent questions remain to be explored in animals. Enlightened by botanical research, the study of polyploidization in vertebrates involves the identification of model animals and the establishment of strategies. Here we review and compare the research on plants and vertebrates while considering intrageneric or intraspecific variation in genome size. Suitable research methods on recently established poly- ploidy systems could provide important clues for under- standing what happens after WGDs in vertebrates. The approach yields insights into survival and the rarity of polyploidization in vertebrates. The species of Carassius and the allopolyploid system of goldfish × common carp hybridization appear to be suitable models for unraveling the evolution and adaptation of polyploid vertebrates.展开更多
Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a pote...Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.展开更多
Whole-genome duplication(WGD or polyploidization)has been suggested as a genetic contributor to angiosperm adaptation to environmental changes.However,many eudicot lineages did not undergo recent WGD(R-WGD)around and/...Whole-genome duplication(WGD or polyploidization)has been suggested as a genetic contributor to angiosperm adaptation to environmental changes.However,many eudicot lineages did not undergo recent WGD(R-WGD)around and/or after the Cretaceous-Paleogene(K-Pg)boundary,times of severe environmental changes;how those plants survived has been largely ignored.Here,we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD:12 R-WGD-containing plants(R-WGD-Y)and 10 R-WGD-lacking plants(R-WGD-N).Subsequently,we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation.The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF Ⅲ and IX subfamilies through recurrent independent WGDs and tandem duplications(TDs)after the radiation of the plants.The expansions showed coincident enrichments in-times around and/or after the K-Pg boundary,when global cooling was a major environmental stressor.Consequently,convergent expansions and co-retentions of AP2/ERF Ⅲ C-repeat binding factor(CBF)duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks.Moreover,promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code(G-box:CACGTG).We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF Ⅲ and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes,and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.展开更多
Wild peanut(Arachis)species are promising sources of disease resistance for improving peanut cultivars.The objective of this study was to assess cross-compatibility among cultivated and wild peanuts in crosses between...Wild peanut(Arachis)species are promising sources of disease resistance for improving peanut cultivars.The objective of this study was to assess cross-compatibility among cultivated and wild peanuts in crosses between eight peanut cultivars and 27 wild species carrying the A,B,E,Ex,F,K,P,and H genomes.Embryo culture and chromosome doubling led to polyploids representing hybrids between cultivated peanut and A.stenosperma,A.macedoi,A.duranensis,A.villosa,and A.diogoi.The first two showed greater resistance to bacterial wilt than their cultivated parents.DNA markers were developed for verifying the hybrids and for identifying translocation or introgression lines with alien chromosome fragments.展开更多
Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wil...Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.展开更多
Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study a...Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study aimed to identify the underlying genetic basis of fruit quality traits in A.arguta,using a single nucleotide polymorphism(SNP)genetic linkage map previously developed in a tetraploid F1 population of‘Ruby-3’בKuiLv-M’.The F1 population was phenotyped over three years(2020–2022)for fruit quality traits,including skin color,flesh color,fruit weight,fruit diameter,total soluble solids,fruit longitudinal diameter and fruit shape index.A total of nine QTLs were detected for five traits,explaining 10%–32%of the trait variation.For fruit color,the support interval of a major QTL on LG9 contained an MYB transcription factor MYB110,which was previously demonstrated to control color regulation in kiwifruit,thus suggesting that the MYB110 is the candidate gene for fruit color in kiwiberry.The linked marker for fruit color was validated in an F1 population and 25 kiwiberry cultivars.In conclusion,the knowledge obtained through the QTL mapping is applicable to improve the efficiency and cost-effectiveness in kiwiberry breeding.展开更多
Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids.A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type(AABBCC)by combinin...Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids.A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type(AABBCC)by combining different diploid and allotetraploid crop species.However,early-generation allohexaploids often face challenges like unstable meiosis and low fertility,and the phenotypic performance of these synthetic lines has rarely been assessed.This study analyzes agronomic traits,fertility,and genome stability in ArArBcBcCcCc lines derived from four crosses between B.carinata and B.rapa after 9–11 selfing generations.Our results demonstrate polyploid advantage in vigor and seed traits,considerable phenotypic variation,and high fertility and genome stability.Meanwhile,parental genotypes significantly influence outcomes in advanced allohexaploids.Structural variants,largely resulting from A–C homoeologous exchanges,contribute to genomic variation and influence hexaploid genome stability,with the A sub-genome showing the highest variability.Both positive and negative impacts of SVs on fertility and seed weight are observed.Pseudo-euploids,frequently appearing,do not significantly affect fertility or other agronomic traits compared to euploids,indicating a potential pathway toward a stable allohexaploid species.These findings provide insights into the challenge and potential for developing an adaptable and stable Brassica hexaploid through selection.展开更多
Polyploidization is a commonly employed strategy in crop breeding to augment genetic diversity,particularly leveraging the distinctive benefits of additional progressive heterosis or multi-generation heterosis unique ...Polyploidization is a commonly employed strategy in crop breeding to augment genetic diversity,particularly leveraging the distinctive benefits of additional progressive heterosis or multi-generation heterosis unique to polyploidy.Despite genetic disparities between polyploids and diploids,challenges stem from reproductive anomalies,complicating genetic investigations in polyploid systems.Through nearly two decades of intensive research,our team has effectively generated a series of fertile tetraploid lines known as neo-tetraploid rice(NTR),facilitating comparative genetic studies between diploid and tetraploid rice.In this study,we identified diploid counterparts(H3d and H8d)for two NTR lines[Huaduo 3(H3)and Huaduo 8(H8)]and utilized them to create diploid and tetraploid fertile F_(2) populations to assess genotype segregation ratios,recombination rates,and their impact on QTL mapping via bulked segregant analysis combined with sequencing(BSA-seq).Additionally,we assessed yield heterosis in F_(1) and F_(2) generations of two tetraploid populations(H3×H8 and T449×H1),revealing evidence of multi-generation heterosis in polyploid rice.These findings provide valuable insights into the advantages and challenges of polyploid rice breeding.展开更多
Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber develo...Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution.展开更多
Plant polyploidy often occurs in conjunction with higher yield and superior quality.Therefore,obtaining polyploid germplasms is a significant part of breeding.The oil-tea Camellia tree is an important native woody pla...Plant polyploidy often occurs in conjunction with higher yield and superior quality.Therefore,obtaining polyploid germplasms is a significant part of breeding.The oil-tea Camellia tree is an important native woody plant that produces high-quality edible oil and includes many species of Camellia with different ploidies.However,whether higher ploidy levels in oil-tea Camellia trees are related to better traits remains unclear.In this study,the ploidy levels of 30 different oil-tea Camellia strains in three different species in the Sect.Paracamellia were determined by flow cytometry and chromosome preparation,and the phenotypic characteristics and fatty acid compositions of the fruits were examined by field observations and laboratory analyses.The correlations between the ploidy level of oil-tea Camellia and the main traits of the fruit were investigated.Our results showed that 10 Camellia lanceoleosa strains were diploid,10 Camellia meiocarpa strains were tetraploid and 10 Camellia oleifera strains were hexaploid.Hexaploid C.oleifera had larger fruit size and weight,more seeds per fruit,greater seed weight per fruit,higher oil content and greater yield per crown width than tetraploid C.meiocarpa and diploid C.lanceoleosa,but their fruit peel thickness and fresh seed rate were significantly lower,and these traits were significantly correlated with ploidy level.In addition,in terms of fatty acid composition,hexaploid C.oleifera had a higher oleic acid content than tetraploid C.meiocarpa and diploid C.lanceoleosa,but their linoleic acid,linolenic acid and arachidonic acid contents were lower.The contents of palmitic acid,stearic acid and total unsaturated fatty acids were not significantly correlated with ploidy level.In conclusion,certain correlations exist between the main characteristics of oil-tea Camellia fruit and the ploidy level,and increasing the ploidy level led to an increase in fruit yield with no effect on oil composition.The discovery of variations in the main characteristics of oil-tea Camellia fruit with different ploidies will facilitate germplasm innovation and lay a foundation for ploidy breeding and mechanistic research on fruit traits.展开更多
Polyploidization in plants often leads to increased cell size and grain size,which may be affected by the increased genome dosage and transcription abundance.The synthesized Triticum durum(AABB)-Hay-naldia villosa(WM)...Polyploidization in plants often leads to increased cell size and grain size,which may be affected by the increased genome dosage and transcription abundance.The synthesized Triticum durum(AABB)-Hay-naldia villosa(WM)amphiploid(AABBM)has significantly increased grain size,especially grain length,than the tetraploid and diploid parents.To investigate how polyploidization affects grain development at the transcriptional level,we perform transcriptome analysis using the immature seeds of T.durum,H.villosa,and the amphiploid.The dosage effect genes are contributed more by differentially expressed genes from genome V of H.villosa.The dosage effect genes overrepresent grain development-related genes.Inter-estingly,the vernalization gene TaVRN1 is among the positive dosage effect genes in the T.durum-H.villosa and T.turgidum-Ae.tauschii amphiploids.The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight.The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence,decreased cell size,grain size,and grain yield.These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development.The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improvingwheat yield.展开更多
Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by usin...Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.cgrpoee.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of early eudicots.展开更多
文摘Hibiscus Linn.,an angiosperm genus belonging to Malvaceae,Malvales,is mainly distributed in tropic and subtropic regions.Numerous species within the Hibiscus genus exhibit large and visually appealing flowers that are highly prized for their ornamental beauty and enjoy widespread admiration.For instance,H.syriacus serves as the national flower of South Korea,H.rosa-sinensis is favored as the floral emblem of Malaysia,and Chengdu city has earned the moniker"City of H.mutabilis"owing to its substantial cultivation.
基金funded by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA19050404)National Natural Science Foundation of China(No.31800174).
文摘Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.
基金supported by the National Natural Science Foundation of China(31922069,32170645)the Fundamental Research Funds for the Central Universities(2662020ZKPY017)。
文摘Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits.
基金Supported by National High-tech R&D Program of China(863 Program)Project of Natural Science Foundation of Hainan Province(20163124)Special Project of Fundamental Research Funds for Central Public Welfare Research Institutes(ITBB2015RC04 & ITBB2015ZY12)
文摘The sugarcane genome polyploidization can reduce the pressure of gene evolution selection,promote the fixation of fine traits,and increase the biomass and economic value of sugarcane.This paper mainly introduced the origin of the sugarcane genome,the chromosome composition,the research progress of polyploidization genetic mechanism,in the hope of providing theoretical reference for sugarcane polyploidization breeding.
基金supported by the National Key Research and Development Program of China(2023YFD2301201)the Key Research and Development Project of Henan Province(231111110400)+1 种基金Major Science and Technology Projects of Xinjiang Uygur Autonomous Region(2023A02001)the Fundamental Research Funds of State Key Laboratory of Cotton Bio-breeding and Integrated Utilization(CB202406)。
文摘Polyploidization is recognized as a powerful driver of plant evolution and domestication.In the genus Gossypium,the natural hybridization of an A-genome ancestor and a D-genome ancestor gave rise to allopolyploid cottons(Huang et al.,2024),such as Gossypium hirsutum and Gossypium barbadense.Previous cotton reference genomes(Du et al.,2018;Hu et al.,2019;Huang et al.,2020;Li et al.,2015;Wang et al.,2019;Yang et al.,2019;Zhang et al.,2015),although instrumental to cotton genetics and breeding,contained large assembly gaps,especially repetitive regions like centromeres.
基金supported by the National Natural Science Foundation of China(32470676 and 32170236)Central Guidance on Local Science and Technology Development Fund of Hebei Province(246Z2508G)+2 种基金Hebei Natural Science Foundation(C2020209064)Tangshan Science and Technology Program Project(21130217C)Key research project of North China University of Science and Technology(ZD-YG-202313-23).
文摘As a high-value eudicot family,many famous horticultural crop genomes have been deciphered in Oleaceae.However,there are currently no bioinformatics platforms focused on empowering genome research in Oleaceae.Herein,we developed the first comprehensive Oleaceae Genome Research Platform(OGRP,https://oleaceae.cgrpoee.top/).In OGRP,70 genomes of 10 Oleaceae species and 46 eudicots and 366 transcriptomes involving 18 Oleaceae plant tissues can be obtained.We built 34 window-operated bioinformatics tools,collected 38 professional practical software programs,and proposed 3 new pipelines,namely ancient polyploidization identification,ancestral karyotype reconstruction,and gene family evolution.Employing these pipelines to reanalyze the Oleaceae genomes,we clarified the polyploidization,reconstructed the ancestral karyotypes,and explored the effects of paleogenome evolution on genes with specific biological regulatory roles.Significantly,we generated a series of comparative genomic resources focusing on the Oleaceae,comprising 108 genomic synteny dot plots,1952225 collinear gene pairs,multiple genome alignments,and imprints of paleochromosome rearrangements.Moreover,in Oleaceae genomes,researchers can efficiently search for 1785987 functional annotations,22584 orthogroups,29582 important trait genes from 74 gene families,12664 transcription factor-related genes,9178872 transposable elements,and all involved regulatory pathways.In addition,we provided downloads and usage instructions for the tools,a species encyclopedia,ecological resources,relevant literatures,and external database links.In short,ORGP integrates rich data resources and powerful analytical tools with the characteristic of continuous updating,which can efficiently empower genome research and agricultural breeding in Oleaceae and other plants.
基金supported by the National Natural Science Foundation of China(91331105,31360514)
文摘Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants illustrates the immediate changes that follow WGDs and the mechanisms behind in both genetic and epigenetic consequences. Unfortunately, equivalent questions remain to be explored in animals. Enlightened by botanical research, the study of polyploidization in vertebrates involves the identification of model animals and the establishment of strategies. Here we review and compare the research on plants and vertebrates while considering intrageneric or intraspecific variation in genome size. Suitable research methods on recently established poly- ploidy systems could provide important clues for under- standing what happens after WGDs in vertebrates. The approach yields insights into survival and the rarity of polyploidization in vertebrates. The species of Carassius and the allopolyploid system of goldfish × common carp hybridization appear to be suitable models for unraveling the evolution and adaptation of polyploid vertebrates.
基金supported by the National Natural Science Foundation of China(NSFC grants 31722048 and 31972411)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences,and the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,P.R.Chinasupported by the China Agricultural Research System—Green Manure(CARS-22).
文摘Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.
基金supported by the National Natural Science Foundation of China(grant number 31871233)the National Key R&D Program of China(2018YFD1000604).
文摘Whole-genome duplication(WGD or polyploidization)has been suggested as a genetic contributor to angiosperm adaptation to environmental changes.However,many eudicot lineages did not undergo recent WGD(R-WGD)around and/or after the Cretaceous-Paleogene(K-Pg)boundary,times of severe environmental changes;how those plants survived has been largely ignored.Here,we collected 22 plants from major branches of the eudicot phylogeny and classified them into two groups according to the occurrence or absence of R-WGD:12 R-WGD-containing plants(R-WGD-Y)and 10 R-WGD-lacking plants(R-WGD-N).Subsequently,we identified 496 gene-rich families in R-WGD-Y and revealed that members of the AP2/ERF transcription factor family were convergently over-retained after R-WGDs and showed exceptional cold stimulation.The evolutionary trajectories of the AP2/ERF family were then compared between R-WGD-Y and R-WGD-N to reveal convergent expansions of the AP2/ERF Ⅲ and IX subfamilies through recurrent independent WGDs and tandem duplications(TDs)after the radiation of the plants.The expansions showed coincident enrichments in-times around and/or after the K-Pg boundary,when global cooling was a major environmental stressor.Consequently,convergent expansions and co-retentions of AP2/ERF Ⅲ C-repeat binding factor(CBF)duplicates and their regulons in different eudicot lineages contributed to the rewiring of cold-specific regulatory networks.Moreover,promoter analysis of cold-responsive AP2/ERF genes revealed an underlying cis-regulatory code(G-box:CACGTG).We propose a seesaw model of WGDs and TDs in the convergent expansion of AP2/ERF Ⅲ and IX genes that has contributed to eudicot adaptation during paleoenvironmental changes,and we suggest that TD may be a reciprocal/alternative mechanism for genetic innovation in plants that lack WGD.
基金supported by National Natural Science Foundation of China(32272153)Henan Province Science and Technology R&D Joint Fund(232301420025)+4 种基金National Key Research and Development Program of China(2023YFD1200200)the Key Research Project of the Shennong Laboratory(SN01-2022-03)Independent Innovation Foundation of Henan Academy of Agricultural Sciences(2024ZC024)China Agriculture Research System(CARS-13)Henan Provincial Agriculture Research System(S2012-5).
文摘Wild peanut(Arachis)species are promising sources of disease resistance for improving peanut cultivars.The objective of this study was to assess cross-compatibility among cultivated and wild peanuts in crosses between eight peanut cultivars and 27 wild species carrying the A,B,E,Ex,F,K,P,and H genomes.Embryo culture and chromosome doubling led to polyploids representing hybrids between cultivated peanut and A.stenosperma,A.macedoi,A.duranensis,A.villosa,and A.diogoi.The first two showed greater resistance to bacterial wilt than their cultivated parents.DNA markers were developed for verifying the hybrids and for identifying translocation or introgression lines with alien chromosome fragments.
基金funded by the National Natural Science Foundation of China(grant no.32270238 and 31870311).
文摘Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress,while hexaploid wild Camellia oleifera shows strong freezing tolerance.As a valuable genetic resource of woody oil crop C.oleifera,wild C.oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress.Here,47 wild C.oleifera from 11 natural distribution sites in China and 4 relative species of C.oleifera were selected for genome sequencing.“Min Temperature of Coldest Month”(BIO6)had the highest comprehensive contribution to wild C.oleifera distribution.The population genetic structure of wild C.oleifera could be divided into two groups:in cold winter(BIO6≤0℃)and warm winter(BIO6>0℃)areas.Wild C.oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_(e) than those in warm winter areas.155 singlenucleotide polymorphisms(SNPs)were significantly correlated with the key bioclimatic variables(106 SNPs significantly correlated with BIO6).Twenty key SNPs and 15 key copy number variation regions(CNVRs)were found with genotype differentiation>50%between the two groups of wild C.oleifera.Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance,and they were also found within a CNVR suggesting interactions between them.Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress.The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.
基金support from the National Natural Science Foundation of China(Grant No.32001995)the Major Science and Technology Project of Henan Province(Grant No.221100110400)+3 种基金the China Agriculture Research System of MOF and MARA(Grant No.CARS-26)the Special Engineering Science and Technology Innovation,CAAS(Grant No.CAAS-ASTIP-2024-ZFRI).Part of this research was funded under the TKI project:“Novel genetic and genomic tools for polyploid crops”(KV 1605-020BO 26.03009004,BO 50002022)and USDA's National Institute of Food and Agriculture(NIFA)Specialty Crop Research Initiative project“Tools for genomics assisted breeding in polyploids:Development of a community resource”(Grant No.2020-51181-32156/SCRI)received a scholarship from China Scholarship Council(Grant No.202303250034).
文摘Fruit quality traits play an important role in consumption of kiwiberry(Actinidia arguta).The genetic basis of fruit quality traits in this woody,perennial and dioecious fruit crop remains largely unknown.This study aimed to identify the underlying genetic basis of fruit quality traits in A.arguta,using a single nucleotide polymorphism(SNP)genetic linkage map previously developed in a tetraploid F1 population of‘Ruby-3’בKuiLv-M’.The F1 population was phenotyped over three years(2020–2022)for fruit quality traits,including skin color,flesh color,fruit weight,fruit diameter,total soluble solids,fruit longitudinal diameter and fruit shape index.A total of nine QTLs were detected for five traits,explaining 10%–32%of the trait variation.For fruit color,the support interval of a major QTL on LG9 contained an MYB transcription factor MYB110,which was previously demonstrated to control color regulation in kiwifruit,thus suggesting that the MYB110 is the candidate gene for fruit color in kiwiberry.The linked marker for fruit color was validated in an F1 population and 25 kiwiberry cultivars.In conclusion,the knowledge obtained through the QTL mapping is applicable to improve the efficiency and cost-effectiveness in kiwiberry breeding.
基金supported by the Sino-German Research Project(GZ 1362)Grains Research and Development Corporation International Visiting Fellowship(UWA2406-010BGX)+1 种基金the National Natural Science Foundation of China(32171982)the Fundamental Research Funds for the Central Universities of the Chinese Government(2662023PY004).
文摘Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids.A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type(AABBCC)by combining different diploid and allotetraploid crop species.However,early-generation allohexaploids often face challenges like unstable meiosis and low fertility,and the phenotypic performance of these synthetic lines has rarely been assessed.This study analyzes agronomic traits,fertility,and genome stability in ArArBcBcCcCc lines derived from four crosses between B.carinata and B.rapa after 9–11 selfing generations.Our results demonstrate polyploid advantage in vigor and seed traits,considerable phenotypic variation,and high fertility and genome stability.Meanwhile,parental genotypes significantly influence outcomes in advanced allohexaploids.Structural variants,largely resulting from A–C homoeologous exchanges,contribute to genomic variation and influence hexaploid genome stability,with the A sub-genome showing the highest variability.Both positive and negative impacts of SVs on fertility and seed weight are observed.Pseudo-euploids,frequently appearing,do not significantly affect fertility or other agronomic traits compared to euploids,indicating a potential pathway toward a stable allohexaploid species.These findings provide insights into the challenge and potential for developing an adaptable and stable Brassica hexaploid through selection.
基金supported by the National Key Resarch and Development Program of China(Grant No.2023YFD1200802)the Base Bank of Lingnan Rice Germplasm Resources Project,China(Grant No.2024B1212060009).
文摘Polyploidization is a commonly employed strategy in crop breeding to augment genetic diversity,particularly leveraging the distinctive benefits of additional progressive heterosis or multi-generation heterosis unique to polyploidy.Despite genetic disparities between polyploids and diploids,challenges stem from reproductive anomalies,complicating genetic investigations in polyploid systems.Through nearly two decades of intensive research,our team has effectively generated a series of fertile tetraploid lines known as neo-tetraploid rice(NTR),facilitating comparative genetic studies between diploid and tetraploid rice.In this study,we identified diploid counterparts(H3d and H8d)for two NTR lines[Huaduo 3(H3)and Huaduo 8(H8)]and utilized them to create diploid and tetraploid fertile F_(2) populations to assess genotype segregation ratios,recombination rates,and their impact on QTL mapping via bulked segregant analysis combined with sequencing(BSA-seq).Additionally,we assessed yield heterosis in F_(1) and F_(2) generations of two tetraploid populations(H3×H8 and T449×H1),revealing evidence of multi-generation heterosis in polyploid rice.These findings provide valuable insights into the advantages and challenges of polyploid rice breeding.
基金Funded by the National Key Research and Development Program of China(2016YFD0100203 and 2016YFD0100306)the Foundation and Frontier Research Grant of Henan Provincial Science and Technology Bureau(162300410171).
文摘Naturally allotetraploid cotton has been widely used as an ideal model to investigate gene expression remodeling as a consequence of polyploidization.However,the global gene pattern variation during early fiber development was unknown.In this study,through RNA-seq technology,we comprehensively investigated the expression patterns of homologous genes between allotetraploid cotton(G.hirsutum)and its diploid progenitors(G.arboreum and G.raimondii)at the fiber early development stage.In tetraploid cotton,genes showed expression level dominance(ELD)bias toward the A genome.This phenomenon was explained by the up-/downregulation of the homologs from the nondominant progenitor(D genome).Gene ontology(GO)enrichment results indicated that the ELD-A genes might be a prominent cause responsible for fiber property change through regulating the fatty acid biosynthesis/metabolism and microtubule procession,and the ELD-D genes might be involved in transcription regulation and stress inducement.In addition,the number and proportion of completely A-and D-subfunctionalized gene were similar at different fiber development stages.However,for neofunctionalization,the number and proportion of reactivated D-derived genes were greater than those of A at 3 and 5 DPA.Eventually,we found that some homologous genes belonging to several specific pathways might create novel asymmetric transcripts between two subgenomes during polyploidization and domestication process,further making the fiber property meet the human demands.Our study identified determinate pathways and their involved genes between allotetraploid cotton and their progenitors at early fiber development stages,providing new insights into the mechanism of cotton fiber evolution.
基金supported by the Special Funds for Construction of Innovative Provinces in Hunan Province,China(2021NK1007)the Hunan Provincial Innovation Foundation for Postgraduate,China(CX20230779)the Scientific Innovation Fund for Post-graduates of Central South University of Forestry and Technology,China(2023CX01009)。
文摘Plant polyploidy often occurs in conjunction with higher yield and superior quality.Therefore,obtaining polyploid germplasms is a significant part of breeding.The oil-tea Camellia tree is an important native woody plant that produces high-quality edible oil and includes many species of Camellia with different ploidies.However,whether higher ploidy levels in oil-tea Camellia trees are related to better traits remains unclear.In this study,the ploidy levels of 30 different oil-tea Camellia strains in three different species in the Sect.Paracamellia were determined by flow cytometry and chromosome preparation,and the phenotypic characteristics and fatty acid compositions of the fruits were examined by field observations and laboratory analyses.The correlations between the ploidy level of oil-tea Camellia and the main traits of the fruit were investigated.Our results showed that 10 Camellia lanceoleosa strains were diploid,10 Camellia meiocarpa strains were tetraploid and 10 Camellia oleifera strains were hexaploid.Hexaploid C.oleifera had larger fruit size and weight,more seeds per fruit,greater seed weight per fruit,higher oil content and greater yield per crown width than tetraploid C.meiocarpa and diploid C.lanceoleosa,but their fruit peel thickness and fresh seed rate were significantly lower,and these traits were significantly correlated with ploidy level.In addition,in terms of fatty acid composition,hexaploid C.oleifera had a higher oleic acid content than tetraploid C.meiocarpa and diploid C.lanceoleosa,but their linoleic acid,linolenic acid and arachidonic acid contents were lower.The contents of palmitic acid,stearic acid and total unsaturated fatty acids were not significantly correlated with ploidy level.In conclusion,certain correlations exist between the main characteristics of oil-tea Camellia fruit and the ploidy level,and increasing the ploidy level led to an increase in fruit yield with no effect on oil composition.The discovery of variations in the main characteristics of oil-tea Camellia fruit with different ploidies will facilitate germplasm innovation and lay a foundation for ploidy breeding and mechanistic research on fruit traits.
基金This work was financially supported by the National Key Research and Development Program of China(Grant No.2022YFF1002900 and 2020YFE0202900)the National Natural Science Foundation of China(32270576)+4 种基金Jiangsu Provincial Key Research and Development Program(BE2022346)Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]006 and JBGS[2021]013)the Jiangsu Agricultural Technology System(JATS[2023]422)the Joint Research of Wheat Variety Improvement of AnhuiZhongshan Biological Breeding Laboratory(ZSBBL)(ZSBBL-KY2023-02-2)。
文摘Polyploidization in plants often leads to increased cell size and grain size,which may be affected by the increased genome dosage and transcription abundance.The synthesized Triticum durum(AABB)-Hay-naldia villosa(WM)amphiploid(AABBM)has significantly increased grain size,especially grain length,than the tetraploid and diploid parents.To investigate how polyploidization affects grain development at the transcriptional level,we perform transcriptome analysis using the immature seeds of T.durum,H.villosa,and the amphiploid.The dosage effect genes are contributed more by differentially expressed genes from genome V of H.villosa.The dosage effect genes overrepresent grain development-related genes.Inter-estingly,the vernalization gene TaVRN1 is among the positive dosage effect genes in the T.durum-H.villosa and T.turgidum-Ae.tauschii amphiploids.The expression levels of TaVRN1 homologs are positively correlated with the grain size and weight.The TaVRN1-B1 or TaVRN1-D1 mutation shows delayed florescence,decreased cell size,grain size,and grain yield.These data indicate that dosage effect genes could be one of the important explanations for increased grain size by regulating grain development.The identification and functional validation of dosage effect genes may facilitate the finding of valuable genes for improvingwheat yield.
基金funded by the National Natural Science Foundation of China(Grant Nos.32170236 and 31501333)the Natural Science Foundation of Hebei Province(Grant No.C2020209064)the Youth Foundation of Educational Committee of Hebei Province(Grant No.QN2020139)。
文摘Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal value.In our study,by using syntenic analysis combined with phylogenomic analysis of C.chinensis and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in C.chinensis was shared by Aquilegia coerulea and Papaver somniferum L.and quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the P.somniferum genome is faster than that of the C.chinensis genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 MYA.Moreover,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference genomes.Notably,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron sinense.In addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST events.We constructed a new platform for Early Eudicot Comparative Genomic Research(http://www.cgrpoee.top/index.html)to store more information.In summary,our findings support the WGD of C.chinensis shared by Ranunculales,which is likely an allotetraploidization event.This present effort offered new insights into the evolution of key polyploidization events and the genes related to secondary metabolites during the diversification of early eudicots.
