Dear Editor,Pinellia Tenore,a small genus of the monocot family Araceae,consists of only nine perennial herbaceous species and is mainly distributed in East Asia[1].Pinellia plants have been widely used as herbal medi...Dear Editor,Pinellia Tenore,a small genus of the monocot family Araceae,consists of only nine perennial herbaceous species and is mainly distributed in East Asia[1].Pinellia plants have been widely used as herbal medicines in Asia for over 2000 years.Among these species,P.ternata and P.pedatisecta are most widely used as traditional medicinal herbs[2].In China,the medicinal utilization of P.ternata and P.pedatisecta was first documented in the Divine Farmer’s Materia Medica(Chinese name:‘Shennong Bencao Jing’)during the Eastern Han dynasty(25–250 AD).Tubers produced by these plants have been traditionally utilized to treat vomiting,infection,and inf lammation[3].Modern pharmacological studies have indicated that the pharmacological effects of Pinellia plants are closely related to endogenous components,such as plant lectins,alkaloids,amino acids,nucleosides,and polysaccharides[2].P.ternata has been listed in the Chinese Pharmacopoeia as a common traditional Chinese medicine.However,to date no genomic resources have been reported in the genus Pinellia,which greatly limits further studies on this valuable resource.展开更多
Histone H3 lysine 27 trimethylation(H3K27me3) is a histone modification associated with transcriptional repression. However, insights into the genome-wide pattern of H3K27me3 in grapevines are limited. Here, anti-H3K2...Histone H3 lysine 27 trimethylation(H3K27me3) is a histone modification associated with transcriptional repression. However, insights into the genome-wide pattern of H3K27me3 in grapevines are limited. Here, anti-H3K27 chromatin immunoprecipitation(ChIP), high-throughput sequencing, and transcriptome analysis were performed using leaves of Vitis amurensis. The leaves were treated at 4°C for 2 h and 24 h and used to investigate changes in H3K27me3 under chilling treatment. The results show that H3K27me3 is well-distributed both in gene regions(-50%) and in the intergenic region(-50%) in the grapevine genome(Vitis vinifera ‘Pinot Noir PN40024'). H3K27me3 was found to be localized in8 368 annotated gene regions in all detected samples(leaves at normal temperature and under chilling treatments) and mainly enriched in gene bodies with the adjacent promoter and downstream areas. The short-term chilling treatments(4°C for 2 h) induced 2 793 gains and 305losses in H3K27me3 modification. Subsequently, 97.3% of the alterations were restored to original levels after 24 h treatment. The ChIP-qPCR for five differential peaks showed similar results to the data for ChIP-seq, indicating that the chilling-induced H3K27me3 modification is reliable.Integrative analysis of transcriptome and ChIP-seq results showed that the expression of H3K27me3 target genes was significantly lower than those of non-target genes, indicating transcriptional repression of H3K27me3 in grapevine leaves. Furthermore, histone methylation alterations were detected in 82 genes and were related to either repression or activation of their expression during chilling stress. The findings provide the genome-wide H3K27me3 patterns in grapevines and shed light on uncovering its regulation in chilling stress responses.展开更多
Although auxin is known to induce ethylene biosynthesis in some Rosaceae fruit crops,the mechanisms underlying the auxin–ethylene interaction during fruit ripening remain largely unknown.Here,the regulatory role of a...Although auxin is known to induce ethylene biosynthesis in some Rosaceae fruit crops,the mechanisms underlying the auxin–ethylene interaction during fruit ripening remain largely unknown.Here,the regulatory role of an auxin response factor,PpARF6,in fruit ripening was investigated in peach.Peach fruits showed accelerated ripening after treatment with auxin and PpARF6 was found to be significantly induced.PpARF6 not only could induce ethylene synthesis by directly activating the transcription of ethylene biosynthetic genes,but also competed with EIN3-binding F-box proteins PpEBF1/2 for binding to ethylene-insensitive3-like proteins PpEIL2/3,thereby keeping PpEIL2/3 active.Moreover,PpARF6 showed an interaction with PpEIL2/3 to enhance the PpEIL2/3-activated transcription of ethylene biosynthetic genes.Additionally,ectopic overexpression of PpARF6 in tomato accelerated fruit ripening by promoting the expression of genes involved in ethylene synthesis and fruit texture.In summary,our results revealed a positive regulatory role of PpARF6 in peach fruit ripening via integrating auxin and ethylene signaling.展开更多
A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates.Actinidia eriantha is a shade-tolerant species,widely distributed in the s...A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates.Actinidia eriantha is a shade-tolerant species,widely distributed in the southern tropical region of China,occurring in spatially heterogeneous environments.In the present study we combined population genomic,epigenomic,and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient,and to assess genomic offset to climatic change for A.eriantha.The population structure is strongly shaped by geography and influenced by restricted gene f low resulting from isolation by distance due to habitat fragmentation.In total,we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation,which were enriched in functional categories related to development processes and stress response;both temperature and precipitation are important factors driving adaptive variation.In addition to single-nucleotide polymorphisms(SNPs),a total of 27 single-methylation variants(SMVs)had significant correlation with at least one of four climatic variables and 16 SMVswere located in or adjacent to genes,several of whichwere predicted to be involved in plant response to abiotic or biotic stress.Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change.Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation.Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.展开更多
Rural communities in Kenya largely depend on plant resources for their livelihood.The utilization of these resources depends on the availability of plant resources and the level of knowledge of the residents.We conduc...Rural communities in Kenya largely depend on plant resources for their livelihood.The utilization of these resources depends on the availability of plant resources and the level of knowledge of the residents.We conducted an ethnobotanical study in Tharaka-Nithi County in Kenya to determine the knowledge and utilization of various plant species by the local communities.The study was conducted in four major administrative regions from June 2018 to February 2019,involving interview schedules using semi-structured open-ended questionnaires and guided field collections with 48 informants.A total of 214 plant species distributed in 73 families and 169 genera with 616 Use Reports(URs)were documented.Fabaceae was the highest family cited by the informants(31 species)followed by Lamiaceae and Euphorbiaceae(each with 11 species).Trees(49%)and shrubs(32%)were the top life forms of the plants frequently utilized by the local residents.The general plant uses reported were medicinal,food,fodder,construction,fuel,pesticidal,religious,live fencing,and making crafts.Zanthoxylum gilletii,Prunus africana,and Solanum incanum were found to be highly valued by the local communities.Plant utilization as food and medicinal uses against snake-bite related problems had the highest Informant Consensus Factor(ICF).Only 29(13.6%)of the species reported had their status assessed by the International Union for Conservation of Nature(IUCN).Conservation measures,alongside awareness creation in this region,are highly recommended for the species endemic to the region,highly depended on by the community,and those threatened according to IUCN standards.展开更多
The upsurge of multiple drug resistance(MDR)bacteria substantially diminishes the effectiveness of antibiotic arsenal and therefore intensifies the rate of therapeutic failure.The major factor in MDR is efflux pump-me...The upsurge of multiple drug resistance(MDR)bacteria substantially diminishes the effectiveness of antibiotic arsenal and therefore intensifies the rate of therapeutic failure.The major factor in MDR is efflux pump-mediated resistance.A unique pump can make bacteria withstand a wide range of structurally diverse compounds.Therefore,their inhibition is a promising route to eliminate resistance phenomenon in bacteria.Phytochemicals are excellent alternatives as resistance-modifying agents.They can directly kill bacteria or interact with the crucial events of pathogenicity,thereby decreasing the ability of bacteria to develop resistance.Numerous botanicals display noteworthy efflux pumps inhibitory activities.Edible plants are of growing interest.Likewise,some plant families would be excellent sources of efflux pump inhibitors(EPIs)including Apocynaceae,Berberidaceae,Convolvulaceae,Cucurbitaceae,Fabaceae,Lamiaceae,and Zingiberaceae.Easily applicable methods for screening plant-derived EPIs include checkerboard synergy test,berberine uptake assay and ethidium bromide test.In silico highthroughput virtual detection can be evaluated as a criterion of excluding compounds with efflux substrate-like characteristics,thereby improving the selection process and extending the identification of EPIs.To ascertain the efflux activity inhibition,real-time PCR and quantitative mass spectrometry can be applied.This review emphasizes on efflux pumps and their roles in transmitting bacterial resistance and an update plant-derived EPIs and strategies for identification.展开更多
Dear Editor,Understanding the evolution and survival mechanisms of endangered wild medicinal herbs is crucial for their cultivation,utilization,and conservation.The snow lotus species Saussurea involucrata(Kar.&Ki...Dear Editor,Understanding the evolution and survival mechanisms of endangered wild medicinal herbs is crucial for their cultivation,utilization,and conservation.The snow lotus species Saussurea involucrata(Kar.&Kir.)Sch.Bip.(2n=32)(i.e.the well-known Tianshan snow lotus)which belongs to the eudicot family Asteraceae,is a famous traditional Chinese medicinal herb having anti-inflammatory.展开更多
Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,A...Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,AABB),i.e.,diploid T.natans(2x,AA)and Trapa incisa(2x,BB).In conjunction with four published(sub)genomes of Trapa,we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element(TE)library to develop Trapa genomic resources.The pangenome displayed substantial gene-content variationwith dispensable and private gene clusters occupying a large proportion(51.95%)of the total cluster sets in the six(sub)genomes.Genotyping of presence-absence variation(PAVs)identified 40453 PAVs associated with 2570 genes specific to A-or B-lineages,of which 1428were differentially expressed,andwere enriched in organ development process,organic substancemetabolic process and response to stimulus.Comparative genome analyses showed that the allotetraploid T.natans underwent asymmetric subgenome divergence,with the B-subgenome being more dominant than the A-subgenome.Multiple factors,including PAVs,asymmetrical amplification of TEs,homeologous exchanges(HEs),and homeolog expression divergence,together affected genome evolution after polyploidization.Overall,this study sheds lights on the genome architecture and evolution of Trapa,and facilitates its functional genomic studies and breeding program.展开更多
Climate change poses a serious long-term threat to biodiversity.To effectively reduce biodiversity loss,conservationists need to have a thorough understanding of the preferred habitats of species and the variables tha...Climate change poses a serious long-term threat to biodiversity.To effectively reduce biodiversity loss,conservationists need to have a thorough understanding of the preferred habitats of species and the variables that affect their distribution.Therefore,predicting the impact of climate change on speciesappropriate habitats may help mitigate the potential threats to biodiversity distribution.Xerophyta,a monocotyledonous genus of the family Velloziaceae is native to mainland Africa,Madagascar,and the Arabian Peninsula.The key drivers of Xerophyta habitat distribution and preference are unknown.Using 308 species occurrence data and eight environmental variables,the MaxEnt model was used to determine the potential distribution of six Xerophyta species in Africa under past,current and future climate change scenarios.The results showed that the models had a good predictive ability(Area Under the Curve and True Skill Statistics values for all SDMs were more than 0.902),indicating high accuracy in forecasting the potential geographic distribution of Xerophyta species.The main bioclimatic variables that impacted potential distributions of most Xerophyta species were mean temperature of the driest quarter(Bio9)and precipitation of the warmest quarter(Bio18).According to our models,tropical Africa has zones of moderate and high suitability for Xerophyta taxa,which is consistent with the majority of documented species localities.The habitat suitability of the existing range of the Xerophyta species varied based on the climate scenario,with most species experiencing a range loss greater than the range gain regardless of the climate scenario.The projected spatiotemporal patterns of Xerophyta species help guide recommendations for conservation efforts.展开更多
Water management is an important practice that affects fruit size and quality.Effective implementation of irrigation scheduling requires knowledge of the appropriate indicators and thresholds,which are established man...Water management is an important practice that affects fruit size and quality.Effective implementation of irrigation scheduling requires knowledge of the appropriate indicators and thresholds,which are established manly based on the effects of water deficits on final fruit quality.Few studies have focused on the real-time effects of water status on fruit and shoot growth.To establish soil water potential (ψ_(soil)) thresholds to trigger irrigation of peach at pivotal fruit developmental stages,photogrammetry,^(13)C labelling,and other techniques were used in this study to investigate real-time changes in stem diameter,fruit projected area,net leaf photosynthetic rate (P_(n)),and allocation of photoassimilates to fruit under soil water potential conditions ranging from saturation to stress in 6-year-old Shimizu hakuto’peach.Stem growth,fruit growth,and P_n exhibited gradually decreasing sensitivity to water deficits during fruit developmental stages I,II,and III.Stem diameter growth was significantly inhibited whenψ_(soil)dropped to-8.5,-7.6,and-5.4 k Pa,respectively.Fruit growth rate was low,reaching zero when theψ_(soil)was-9.0 to-23.1,-14.9 to-21.4,and-16.5 to-23.3 k Pa,respectively,and P_ndecreased significantly when theψ_(soil)reached-24.2,-22.7,and-20.4 kPa,respectively.In addition,more photoassimilates were allocated to fruit under moderateψ_(soil)conditions (-10.1 to-17.0 k Pa) than under otherψ_(soil)values.Our results revealed threeψ_(soil)thresholds,-10.0,-15.0,and-15.0 kPa,suitable for triggering irrigation during stages I,II,and III,respectively.These thresholds can be helpful for controlling excessive tree vigor,maintaining rapid fruit growth and leaf photosynthesis,and promoting the allocation of more photoassimilates to fruit.展开更多
The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we d...The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.展开更多
English grain aphid （EGA） is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistanc...English grain aphid （EGA） is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistance and tolerance traits at two locations, and genotyped with 51 SSR markers. Totally, three accessions showed high or moderate levels resistance and 17 genotypes displayed highly or moderately tolerate to EGA. Genetic diversity of these lines was investigated also. After 97 SSR loci which evenly covered all wheat chromosomes were scanned for association, four SSR loci were significantly associated with EGA resistance and four with EGA tolerance. After association analysis was conducted with dynamic aphid densities, we found four loci Xgwm192b, Xgwm391, Xbarc98, and Xgwm613b were detected continuously at different growing stages of wheat. In addition, the loci of EGA resistance/tolerance and Russian wheat aphid resistance were compared. The results generated in this study would be helpful for utilization of the EGA resistance/tolerance germplasm, and for development of mapping populations in EGA resistance breeding programs.展开更多
Lotus predominantly accumulates benzylisoquinoline alkaloids(BIAs),but their biosynthesis and regulation remain unclear.Here,we investigated structural and regulatory genes involved in BIA accumulation in lotus.Two cl...Lotus predominantly accumulates benzylisoquinoline alkaloids(BIAs),but their biosynthesis and regulation remain unclear.Here,we investigated structural and regulatory genes involved in BIA accumulation in lotus.Two clustered CYP80 genes were identified to be responsible for the biosynthesis of bis-BIAs and aporphine-type BIAs,respectively,and their tissue-specific expression causes divergence in alkaloid component between leaf and embryo.In contrast with the common(S)-reticuline precursor for most BIAs,aporphine alkaloids in lotus leaf may result from the(S)-N-methylcoclaurine precursor.Structural diversity of BIA alkaloids in the leaf is attributed to enzymatic modifications,including intramolecular C–C phenol coupling on ring A and methylation and demethylation at certain positions.Additionally,most BIA biosynthetic pathway genes show higher levels of expression in the leaf of high-BIA cultivar compared with low-BIA cultivar,suggesting transcriptional regulation of BIA accumulation in lotus.Five transcription factors,including three MYBs,one ethylene-responsive factor,and one basic helix–loop–helix(bHLH),were identified to be candidate regulators of BIA biosynthesis in lotus.Our study reveals a BIA biosynthetic pathway and its transcriptional regulation in lotus,which will enable a deeper understanding of BIA biosynthesis in plants.展开更多
Corallorhiza sinensis,a new species of mycoheterotrophic orchid from western Sichuan,China,is described and illustrated based on molecular and morphological evidence.It is morphologically similar to Corallorhiza trifi...Corallorhiza sinensis,a new species of mycoheterotrophic orchid from western Sichuan,China,is described and illustrated based on molecular and morphological evidence.It is morphologically similar to Corallorhiza trifida,but can be distinguished by bigger flowers,both sepals and petals with 3 veins,and longer lateral lobes of lip.To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae,this study employed sequences of the nuclear ribosomal DNA(nrDNA)and whole plastome assembled from the genome skimming approach.The plastome is 148,124 bp in length,including a pair of inverted repeats(IRs)of 26,165 bp,a large single-copy region(LSC)of 82,207 bp,and a small single-copy region(SSC)of 13,587 bp.Further,phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences(CDSs)from 26 complete plastomes of subtribe Calypsoinae.The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group,and strongly support C.sinensis as sister to the rest species of Corallorhiza.The plastid tree showed that 10 Corallorhiza species grouped into two clades and C.sinensis is most closely related to the North American C.striata and C.bentleyi instead of Oreorchis foliosa and O.angustata in the same clade.The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic.Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C.sinensis,it is still the most closely related to Corallorhiza.Comparative analysis showed that C.sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis.The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.展开更多
Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures.However,the accumulation of metabolites during cold acclimation(CA)in V.amurensis remains largely unknown.In this study,plantlets of V...Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures.However,the accumulation of metabolites during cold acclimation(CA)in V.amurensis remains largely unknown.In this study,plantlets of V.amurensis and V.vinifera cv.Muscat of Hamburg were treated at 4℃ for 24 and 72 h,and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry.Most of the identified metabolites,including carbohydrates,amino acids,and organic acids,accumulated in the two types of grape after CA.Galactinol,raffinose,fructose,mannose,glycine,and ascorbate were continuously induced by cold in V.amurensis,but not in Muscat of Hamburg.Twelve metabolites,including isoleucine,valine,proline,2-oxoglutarate,and putrescine,increased in V.amurensis during CA.More galactinol,ascorbate,2-oxoglutarate,and putrescine,accumulated in V.amurensis,but not in Muscat of Hamburg,during CA,which may be responsible for the excellent cold tolerance in V.amurensis.The expression levels of the genes encodingβ-amylase(BAMY),galactinol synthase(GolS),and raffinose synthase(RafS)were evaluated by quantitative reverse transcription-PCR.The expression BAMY(VIT_02s0012 g00170)and RafS(VIT_05s0077 g00840)were primarily responsible for the accumulation of maltose and raffinose,respectively.The accumulation of galactinol was attributed to different members of GolS in the two grapes.In conclusion,these results show the inherent differences in metabolites between V.amurensis and V.vinifera under CA.展开更多
Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In t...Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In the present study,we sequenced the complete plastome of M.dioica,generating the first plastome sequences of the subfamily Pertyoideae.The plastome of M.dioica has a typical quadripartite circular structure.A large^20-kb and a small^3-kb inversion were detected in the large single copy(LSC)region and shared by other Asteraceae species.Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups,corresponding to four Asteraceae subfamilies:Asteroideae,Cichorioideae,Pertyoideae and Carduoideae.Among these four subfamilies,Pertyoideae is sister to Asteroideae+Cichorioideae;Carduoideae is the most basal clade.In addition,we characterized 13 simple sequence repeats(SSRs)that may be useful in future studies on population genetics.展开更多
Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xin...Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.展开更多
Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research.Although many efforts have been made to compare different reproductive strategies,the association b...Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research.Although many efforts have been made to compare different reproductive strategies,the association between reproductive strategies and lineage divergence is largely unknown.To explore the impact of different reproductive strategies on lineage divergence,we investigated the evolution of clonality in Saxifraga sect.Irregulares+Heterisia.By integrating several lines of evidence,we found that the loss of clonality in Irregulares+Heterisia was associated with a progressive increase in diversification rate and intraspecific morphological diversity but with a reduction in species distribution range.Our findings provide insights into the ecological and evolutionary effects of different reproductive strategies,suggesting the necessity of integrating clonality into ecological and evolutional research.展开更多
Actinidia arguta,the most widely distributed Actinidia species and the second cultivated species in the genus,can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth...Actinidia arguta,the most widely distributed Actinidia species and the second cultivated species in the genus,can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit,rapid softening,and excellent cold tolerance.Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear.Here,we generated a chromosome-scale genome assembly of an autotetraploid male A.arguta accession.The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes.Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups,Southern and Northern,which first diverged 12.9 million years ago.A.arguta underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late Pleistocene.Population genomics studies using paleoclimate data enabled us to discern the evolution of the species’adaptation to different historical environments.Three genes(AaCEL1,AaPME1,and AaDOF1)related to flesh softening were identified by multi-omics analysis,and their ability to accelerate flesh softening was verified through transient expression assays.A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome(Chr3)or autosomal chromosomes showed biased expression during stamen or carpel development.This chromosome-level assembly of the autotetraploid A.arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A.arguta.展开更多
In this paper,we investigated the effects of temperature,oxygen,antioxidants,and corn germ oil on the stability of astaxanthin from Haematococcus pluvialis under different storage conditions,and changes in the composi...In this paper,we investigated the effects of temperature,oxygen,antioxidants,and corn germ oil on the stability of astaxanthin from Haematococcus pluvialis under different storage conditions,and changes in the composition of astaxanthin esters during storage using high performance liquid chromatography and spectrophotometry.Oxygen and high temperatures(22–25°C) significantly reduced the stability of astaxanthin esters.Corn germ oil and antioxidants(ascorbic acid and vitamin E)failed to protect astaxanthin from oxidation,and actually significantly increased the instability of astaxanthin.A change in the relative composition of astaxanthin esters was observed after 96 weeks of long-term storage.During storage,the relative amounts of free astaxanthin and astaxanthin monoesters declined,while the relative amount of astaxanthin diesters increased.Thus,the ratio of astaxanthin diester to monoester increased,and this ratio could be used to indicate if astaxanthin esters have been properly preserved.If the ratio is greater than 0.2,it suggests that the decrease in astaxanthin content could be higher than 20%.Our results show that storing algal powder from H.pluvialis or other natural astaxanthin products under vacuum and in the dark below 4°C is the most economical and applicable storage method for the large-scale production of astaxanthin from H.pluvialis.This storage method can produce an astaxanthin preservation rate of at least 80%after 96 weeks of storage.展开更多
基金supported by grants from the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDB31000000).
文摘Dear Editor,Pinellia Tenore,a small genus of the monocot family Araceae,consists of only nine perennial herbaceous species and is mainly distributed in East Asia[1].Pinellia plants have been widely used as herbal medicines in Asia for over 2000 years.Among these species,P.ternata and P.pedatisecta are most widely used as traditional medicinal herbs[2].In China,the medicinal utilization of P.ternata and P.pedatisecta was first documented in the Divine Farmer’s Materia Medica(Chinese name:‘Shennong Bencao Jing’)during the Eastern Han dynasty(25–250 AD).Tubers produced by these plants have been traditionally utilized to treat vomiting,infection,and inf lammation[3].Modern pharmacological studies have indicated that the pharmacological effects of Pinellia plants are closely related to endogenous components,such as plant lectins,alkaloids,amino acids,nucleosides,and polysaccharides[2].P.ternata has been listed in the Chinese Pharmacopoeia as a common traditional Chinese medicine.However,to date no genomic resources have been reported in the genus Pinellia,which greatly limits further studies on this valuable resource.
基金supported by the National Key Research and Development Program of China (Grant No. 2018YFD1000300)the National Natural Science Foundation of China (Grant No. 32025032)+1 种基金the Grape Breeding Project of Ningxia (Grant No. NXNYYZ202101-04)Major Program of Technological Innovation in Hubei Province (Grant No. 2019ABA093).
文摘Histone H3 lysine 27 trimethylation(H3K27me3) is a histone modification associated with transcriptional repression. However, insights into the genome-wide pattern of H3K27me3 in grapevines are limited. Here, anti-H3K27 chromatin immunoprecipitation(ChIP), high-throughput sequencing, and transcriptome analysis were performed using leaves of Vitis amurensis. The leaves were treated at 4°C for 2 h and 24 h and used to investigate changes in H3K27me3 under chilling treatment. The results show that H3K27me3 is well-distributed both in gene regions(-50%) and in the intergenic region(-50%) in the grapevine genome(Vitis vinifera ‘Pinot Noir PN40024'). H3K27me3 was found to be localized in8 368 annotated gene regions in all detected samples(leaves at normal temperature and under chilling treatments) and mainly enriched in gene bodies with the adjacent promoter and downstream areas. The short-term chilling treatments(4°C for 2 h) induced 2 793 gains and 305losses in H3K27me3 modification. Subsequently, 97.3% of the alterations were restored to original levels after 24 h treatment. The ChIP-qPCR for five differential peaks showed similar results to the data for ChIP-seq, indicating that the chilling-induced H3K27me3 modification is reliable.Integrative analysis of transcriptome and ChIP-seq results showed that the expression of H3K27me3 target genes was significantly lower than those of non-target genes, indicating transcriptional repression of H3K27me3 in grapevine leaves. Furthermore, histone methylation alterations were detected in 82 genes and were related to either repression or activation of their expression during chilling stress. The findings provide the genome-wide H3K27me3 patterns in grapevines and shed light on uncovering its regulation in chilling stress responses.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(Precision Seed Design and Breeding,XDA24030404)the National Natural Science Foundation of China(32102363 and 32272687)+1 种基金the China Agriculture Research System(CARS-30)Hubei Hongshan Laboratory(2021hszd017).
文摘Although auxin is known to induce ethylene biosynthesis in some Rosaceae fruit crops,the mechanisms underlying the auxin–ethylene interaction during fruit ripening remain largely unknown.Here,the regulatory role of an auxin response factor,PpARF6,in fruit ripening was investigated in peach.Peach fruits showed accelerated ripening after treatment with auxin and PpARF6 was found to be significantly induced.PpARF6 not only could induce ethylene synthesis by directly activating the transcription of ethylene biosynthetic genes,but also competed with EIN3-binding F-box proteins PpEBF1/2 for binding to ethylene-insensitive3-like proteins PpEIL2/3,thereby keeping PpEIL2/3 active.Moreover,PpARF6 showed an interaction with PpEIL2/3 to enhance the PpEIL2/3-activated transcription of ethylene biosynthetic genes.Additionally,ectopic overexpression of PpARF6 in tomato accelerated fruit ripening by promoting the expression of genes involved in ethylene synthesis and fruit texture.In summary,our results revealed a positive regulatory role of PpARF6 in peach fruit ripening via integrating auxin and ethylene signaling.
基金funded by the National Natural Science Foundation of China(grants 31770374 and 32070377)the Key Projects of the Joint Fund of the National Natural Science Foundation of China(grant U1802232).
文摘A full understanding of adaptive genetic variation at the genomic level will help address questions of how organisms adapt to diverse climates.Actinidia eriantha is a shade-tolerant species,widely distributed in the southern tropical region of China,occurring in spatially heterogeneous environments.In the present study we combined population genomic,epigenomic,and environmental association analyses to infer population genetic structure and positive selection across a climatic gradient,and to assess genomic offset to climatic change for A.eriantha.The population structure is strongly shaped by geography and influenced by restricted gene f low resulting from isolation by distance due to habitat fragmentation.In total,we identified 102 outlier loci and annotated 455 candidate genes associated with the genomic basis of climate adaptation,which were enriched in functional categories related to development processes and stress response;both temperature and precipitation are important factors driving adaptive variation.In addition to single-nucleotide polymorphisms(SNPs),a total of 27 single-methylation variants(SMVs)had significant correlation with at least one of four climatic variables and 16 SMVswere located in or adjacent to genes,several of whichwere predicted to be involved in plant response to abiotic or biotic stress.Gradient forest analysis indicated that the central/east populations were predicted to be at higher risk of future population maladaptation under climate change.Our results demonstrate that local climate factors impose strong selection pressures and lead to local adaptation.Such information adds to our understanding of adaptive mechanisms to variable climates revealed by both population genome and epigenome analysis.
基金We acknowledge the support of the foresters,rangers,area chiefs,sub-chiefs and residents of Tharaka-Nithi county accorded to this study.The Kenya Forest Service for the fieldwork permits and the scientist Mr.Ken Wambua of National Museums of Kenya for help with specimen identification.Dr.Emily Wabuyele who gave helpful insights in the development of this manuscript.This research was supported by grants of the National Natural Science Foundation of China(31970211)from the Sino-Africa Joint Research Centre,CAS(SAJC201614).
文摘Rural communities in Kenya largely depend on plant resources for their livelihood.The utilization of these resources depends on the availability of plant resources and the level of knowledge of the residents.We conducted an ethnobotanical study in Tharaka-Nithi County in Kenya to determine the knowledge and utilization of various plant species by the local communities.The study was conducted in four major administrative regions from June 2018 to February 2019,involving interview schedules using semi-structured open-ended questionnaires and guided field collections with 48 informants.A total of 214 plant species distributed in 73 families and 169 genera with 616 Use Reports(URs)were documented.Fabaceae was the highest family cited by the informants(31 species)followed by Lamiaceae and Euphorbiaceae(each with 11 species).Trees(49%)and shrubs(32%)were the top life forms of the plants frequently utilized by the local residents.The general plant uses reported were medicinal,food,fodder,construction,fuel,pesticidal,religious,live fencing,and making crafts.Zanthoxylum gilletii,Prunus africana,and Solanum incanum were found to be highly valued by the local communities.Plant utilization as food and medicinal uses against snake-bite related problems had the highest Informant Consensus Factor(ICF).Only 29(13.6%)of the species reported had their status assessed by the International Union for Conservation of Nature(IUCN).Conservation measures,alongside awareness creation in this region,are highly recommended for the species endemic to the region,highly depended on by the community,and those threatened according to IUCN standards.
基金We are grateful to Chinese Academy of Sciences(CAS)for jointly supports(project No.2018PB0089 to AJS and project No.2019VBA0026 to SDS)under CAS President’s International Fellowship Initiative(CAS-PIFI)projectsthe Major Project for Special Technology Innovation of Hubei Province(Grant No.2017AHB054 to MG).
文摘The upsurge of multiple drug resistance(MDR)bacteria substantially diminishes the effectiveness of antibiotic arsenal and therefore intensifies the rate of therapeutic failure.The major factor in MDR is efflux pump-mediated resistance.A unique pump can make bacteria withstand a wide range of structurally diverse compounds.Therefore,their inhibition is a promising route to eliminate resistance phenomenon in bacteria.Phytochemicals are excellent alternatives as resistance-modifying agents.They can directly kill bacteria or interact with the crucial events of pathogenicity,thereby decreasing the ability of bacteria to develop resistance.Numerous botanicals display noteworthy efflux pumps inhibitory activities.Edible plants are of growing interest.Likewise,some plant families would be excellent sources of efflux pump inhibitors(EPIs)including Apocynaceae,Berberidaceae,Convolvulaceae,Cucurbitaceae,Fabaceae,Lamiaceae,and Zingiberaceae.Easily applicable methods for screening plant-derived EPIs include checkerboard synergy test,berberine uptake assay and ethidium bromide test.In silico highthroughput virtual detection can be evaluated as a criterion of excluding compounds with efflux substrate-like characteristics,thereby improving the selection process and extending the identification of EPIs.To ascertain the efflux activity inhibition,real-time PCR and quantitative mass spectrometry can be applied.This review emphasizes on efflux pumps and their roles in transmitting bacterial resistance and an update plant-derived EPIs and strategies for identification.
基金This work was supported by grants from the National Natural Science Foundation of China(U2003122)the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502).Sequencing service was provided by Bioyi Biotechnology Co.,Ltd.Wuhan,China。
文摘Dear Editor,Understanding the evolution and survival mechanisms of endangered wild medicinal herbs is crucial for their cultivation,utilization,and conservation.The snow lotus species Saussurea involucrata(Kar.&Kir.)Sch.Bip.(2n=32)(i.e.the well-known Tianshan snow lotus)which belongs to the eudicot family Asteraceae,is a famous traditional Chinese medicinal herb having anti-inflammatory.
基金supported by the collaborative program of Chinese Academy of Agricultural Sciences(CAAS)-Jinhua Academy of Agricultural Sciences,funded by Jinhua City of Zhejiang Province,and the Research Grant fromWuhan Botanic Garden(E1559901)。
文摘Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,AABB),i.e.,diploid T.natans(2x,AA)and Trapa incisa(2x,BB).In conjunction with four published(sub)genomes of Trapa,we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element(TE)library to develop Trapa genomic resources.The pangenome displayed substantial gene-content variationwith dispensable and private gene clusters occupying a large proportion(51.95%)of the total cluster sets in the six(sub)genomes.Genotyping of presence-absence variation(PAVs)identified 40453 PAVs associated with 2570 genes specific to A-or B-lineages,of which 1428were differentially expressed,andwere enriched in organ development process,organic substancemetabolic process and response to stimulus.Comparative genome analyses showed that the allotetraploid T.natans underwent asymmetric subgenome divergence,with the B-subgenome being more dominant than the A-subgenome.Multiple factors,including PAVs,asymmetrical amplification of TEs,homeologous exchanges(HEs),and homeolog expression divergence,together affected genome evolution after polyploidization.Overall,this study sheds lights on the genome architecture and evolution of Trapa,and facilitates its functional genomic studies and breeding program.
基金supported by grants from the International Partnership Program of Chinese Academy of Sciences (151853KYSB20190027)Sino-Africa Joint Research Center, CAS (SAJC202101)The ANSO Scholarship for Young Talents, PhD Fellowship Program University of Chinese Academy of Sciences, China
文摘Climate change poses a serious long-term threat to biodiversity.To effectively reduce biodiversity loss,conservationists need to have a thorough understanding of the preferred habitats of species and the variables that affect their distribution.Therefore,predicting the impact of climate change on speciesappropriate habitats may help mitigate the potential threats to biodiversity distribution.Xerophyta,a monocotyledonous genus of the family Velloziaceae is native to mainland Africa,Madagascar,and the Arabian Peninsula.The key drivers of Xerophyta habitat distribution and preference are unknown.Using 308 species occurrence data and eight environmental variables,the MaxEnt model was used to determine the potential distribution of six Xerophyta species in Africa under past,current and future climate change scenarios.The results showed that the models had a good predictive ability(Area Under the Curve and True Skill Statistics values for all SDMs were more than 0.902),indicating high accuracy in forecasting the potential geographic distribution of Xerophyta species.The main bioclimatic variables that impacted potential distributions of most Xerophyta species were mean temperature of the driest quarter(Bio9)and precipitation of the warmest quarter(Bio18).According to our models,tropical Africa has zones of moderate and high suitability for Xerophyta taxa,which is consistent with the majority of documented species localities.The habitat suitability of the existing range of the Xerophyta species varied based on the climate scenario,with most species experiencing a range loss greater than the range gain regardless of the climate scenario.The projected spatiotemporal patterns of Xerophyta species help guide recommendations for conservation efforts.
基金supported by the projects of China Agriculture Research System of MOF and MARA (Grant No.CARS-29-ZP-7)Outstanding Youth Science and Technology Fund of Henan Academy of Agricultural Sciences (Grant No.2022YQ08)。
文摘Water management is an important practice that affects fruit size and quality.Effective implementation of irrigation scheduling requires knowledge of the appropriate indicators and thresholds,which are established manly based on the effects of water deficits on final fruit quality.Few studies have focused on the real-time effects of water status on fruit and shoot growth.To establish soil water potential (ψ_(soil)) thresholds to trigger irrigation of peach at pivotal fruit developmental stages,photogrammetry,^(13)C labelling,and other techniques were used in this study to investigate real-time changes in stem diameter,fruit projected area,net leaf photosynthetic rate (P_(n)),and allocation of photoassimilates to fruit under soil water potential conditions ranging from saturation to stress in 6-year-old Shimizu hakuto’peach.Stem growth,fruit growth,and P_n exhibited gradually decreasing sensitivity to water deficits during fruit developmental stages I,II,and III.Stem diameter growth was significantly inhibited whenψ_(soil)dropped to-8.5,-7.6,and-5.4 k Pa,respectively.Fruit growth rate was low,reaching zero when theψ_(soil)was-9.0 to-23.1,-14.9 to-21.4,and-16.5 to-23.3 k Pa,respectively,and P_ndecreased significantly when theψ_(soil)reached-24.2,-22.7,and-20.4 kPa,respectively.In addition,more photoassimilates were allocated to fruit under moderateψ_(soil)conditions (-10.1 to-17.0 k Pa) than under otherψ_(soil)values.Our results revealed threeψ_(soil)thresholds,-10.0,-15.0,and-15.0 kPa,suitable for triggering irrigation during stages I,II,and III,respectively.These thresholds can be helpful for controlling excessive tree vigor,maintaining rapid fruit growth and leaf photosynthesis,and promoting the allocation of more photoassimilates to fruit.
基金supported by the National Natural Science Foundation of China(Grant No.32102364)the General Program of Shandong Natural Science Foundation(Grant No.ZR2022MC064)+3 种基金the Shanxi Province Postdoctoral Research Activity Fund(Grant No.K462101001)the Doctoral Research Initiation Fund of Shanxi Datong University(Grant No.2023-B-15)the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.2023CYJSTX07)the Shanxi Province Excellent Doctoral Work Award Project(Grant No.606-02010609)。
文摘The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.
基金supported by the National Basic Research Program of China(2009CB118300)
文摘English grain aphid （EGA） is a destructive insect pest of wheat. To identify the loci associated with EGA resistance and tolerance, 70 bread wheat accessions mainly from central Asia were evaluated for EGA resistance and tolerance traits at two locations, and genotyped with 51 SSR markers. Totally, three accessions showed high or moderate levels resistance and 17 genotypes displayed highly or moderately tolerate to EGA. Genetic diversity of these lines was investigated also. After 97 SSR loci which evenly covered all wheat chromosomes were scanned for association, four SSR loci were significantly associated with EGA resistance and four with EGA tolerance. After association analysis was conducted with dynamic aphid densities, we found four loci Xgwm192b, Xgwm391, Xbarc98, and Xgwm613b were detected continuously at different growing stages of wheat. In addition, the loci of EGA resistance/tolerance and Russian wheat aphid resistance were compared. The results generated in this study would be helpful for utilization of the EGA resistance/tolerance germplasm, and for development of mapping populations in EGA resistance breeding programs.
基金This project was supported by funds received from the National Natural Science Foundation of China(Grants 31450110420 and 31272195)the Overseas Construction Plan for Science and Education Base,China-Africa Center for Research and Education,Chinese Academy of Sciences(Grant No.SAJC201327).
文摘Lotus predominantly accumulates benzylisoquinoline alkaloids(BIAs),but their biosynthesis and regulation remain unclear.Here,we investigated structural and regulatory genes involved in BIA accumulation in lotus.Two clustered CYP80 genes were identified to be responsible for the biosynthesis of bis-BIAs and aporphine-type BIAs,respectively,and their tissue-specific expression causes divergence in alkaloid component between leaf and embryo.In contrast with the common(S)-reticuline precursor for most BIAs,aporphine alkaloids in lotus leaf may result from the(S)-N-methylcoclaurine precursor.Structural diversity of BIA alkaloids in the leaf is attributed to enzymatic modifications,including intramolecular C–C phenol coupling on ring A and methylation and demethylation at certain positions.Additionally,most BIA biosynthetic pathway genes show higher levels of expression in the leaf of high-BIA cultivar compared with low-BIA cultivar,suggesting transcriptional regulation of BIA accumulation in lotus.Five transcription factors,including three MYBs,one ethylene-responsive factor,and one basic helix–loop–helix(bHLH),were identified to be candidate regulators of BIA biosynthesis in lotus.Our study reveals a BIA biosynthetic pathway and its transcriptional regulation in lotus,which will enable a deeper understanding of BIA biosynthesis in plants.
基金Project of Orchid Biodiversity Survey of China from National Forestry and Grassland AdministrationNational Wild Plant Germplasm Resource Center for all kinds of support+1 种基金supported by the grants from the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)the National Natural Science Foundation of China(31970211)。
文摘Corallorhiza sinensis,a new species of mycoheterotrophic orchid from western Sichuan,China,is described and illustrated based on molecular and morphological evidence.It is morphologically similar to Corallorhiza trifida,but can be distinguished by bigger flowers,both sepals and petals with 3 veins,and longer lateral lobes of lip.To distinguish the new Corallorhiza species and explore its phylogenetic position within subtribe Calypsoinae,this study employed sequences of the nuclear ribosomal DNA(nrDNA)and whole plastome assembled from the genome skimming approach.The plastome is 148,124 bp in length,including a pair of inverted repeats(IRs)of 26,165 bp,a large single-copy region(LSC)of 82,207 bp,and a small single-copy region(SSC)of 13,587 bp.Further,phylogenetic analyses were performed using nrDNA sequence and 79 coding sequences(CDSs)from 26 complete plastomes of subtribe Calypsoinae.The phylogenetic tree based on nrDNA sequence suggested that Corallorhiza is a monophyletic group,and strongly support C.sinensis as sister to the rest species of Corallorhiza.The plastid tree showed that 10 Corallorhiza species grouped into two clades and C.sinensis is most closely related to the North American C.striata and C.bentleyi instead of Oreorchis foliosa and O.angustata in the same clade.The plastid tree and nrDNA tree indicate Oreorchis is a paraphyletic.Although the topological conflicts are displayed between plastome and nrDNA phylogenies of C.sinensis,it is still the most closely related to Corallorhiza.Comparative analysis showed that C.sinensis populations are characteristic of the intermediate morphological traits between Corallorhiza and Oreorchis.The finding of this new species from China shed new light on the phylogeny of Oreorchis and Corallorhiza.
基金The Youth Innovation Promotion Association of CAS(2015281)National Natural Science Foundation of China(NSFC Accession No.31471857 and 31672132)+1 种基金Science and Technology Service Network Initiative of CAS(KFJ-STSZDTP-025)Grape Breeding Project of Ningxia(NXNYYZ201502)supported this work.
文摘Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures.However,the accumulation of metabolites during cold acclimation(CA)in V.amurensis remains largely unknown.In this study,plantlets of V.amurensis and V.vinifera cv.Muscat of Hamburg were treated at 4℃ for 24 and 72 h,and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry.Most of the identified metabolites,including carbohydrates,amino acids,and organic acids,accumulated in the two types of grape after CA.Galactinol,raffinose,fructose,mannose,glycine,and ascorbate were continuously induced by cold in V.amurensis,but not in Muscat of Hamburg.Twelve metabolites,including isoleucine,valine,proline,2-oxoglutarate,and putrescine,increased in V.amurensis during CA.More galactinol,ascorbate,2-oxoglutarate,and putrescine,accumulated in V.amurensis,but not in Muscat of Hamburg,during CA,which may be responsible for the excellent cold tolerance in V.amurensis.The expression levels of the genes encodingβ-amylase(BAMY),galactinol synthase(GolS),and raffinose synthase(RafS)were evaluated by quantitative reverse transcription-PCR.The expression BAMY(VIT_02s0012 g00170)and RafS(VIT_05s0077 g00840)were primarily responsible for the accumulation of maltose and raffinose,respectively.The accumulation of galactinol was attributed to different members of GolS in the two grapes.In conclusion,these results show the inherent differences in metabolites between V.amurensis and V.vinifera under CA.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDA20050203)the National Key R&D Program of China (2017YFC0505200)+1 种基金the Major Program of the National Natural Science Foundation of China (31590823)the National Natural Science Foundation of China (31570213)
文摘Myripnois is a monotypic shrub genus in the daisy family constricted to northern China.Although wild populations of Myripnois dioica are relatively rare,this plant may potentially be cultured as a fine ornamental.In the present study,we sequenced the complete plastome of M.dioica,generating the first plastome sequences of the subfamily Pertyoideae.The plastome of M.dioica has a typical quadripartite circular structure.A large^20-kb and a small^3-kb inversion were detected in the large single copy(LSC)region and shared by other Asteraceae species.Plastome phylogenomic analyses based on 78 Asteraceae species and three outgroups revealed four groups,corresponding to four Asteraceae subfamilies:Asteroideae,Cichorioideae,Pertyoideae and Carduoideae.Among these four subfamilies,Pertyoideae is sister to Asteroideae+Cichorioideae;Carduoideae is the most basal clade.In addition,we characterized 13 simple sequence repeats(SSRs)that may be useful in future studies on population genetics.
基金This work was supported by National R&D Project of Transgenic Crops of Ministry of Science and Technology of China(2016ZX08005–004-002).
文摘Background:Soil salt stress seriously restricts the yield and quality of cotton worldwide.To investigate the molecular mechanism of cotton response to salt stress,a main cultivated variety Gossypium hirsutum L.acc.Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis.Results:Through transcriptome analysis in cotton leaves under salt stress for 0 h(T0),3 h(T3)and 12 h(T12),we identified 8436,11628 and 6311 differentially expressed genes(DEGs)in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.A total of 459 differentially expressed proteins(DEPs)were identified by proteomic analysis,of which 273,99 and 260 DEPs were identified in T3 vs.T0,T12 vs.T0 and T12 vs.T3,respectively.Metabolic pathways,biosynthesis of secondary metabolites,photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs.Detail analysis of the DEGs or DEPs revealed that complex signaling pathways,such as abscisic acid(ABA)and jasmonic acid(JA)signaling,calcium signaling,mitogen-activated protein kinase(MAPK)signaling cascade,transcription factors,activation of antioxidant and ion transporters,were participated in regulating salt response in cotton.Conclusions:Our research not only contributed to understand the mechanism of cotton response to salt stress,but also identified nine candidate genes,which might be useful for molecular breeding to improve salt-toleranee in cotton.
基金supported by the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK0502)the National Natural Science Foundation of China(32322006)+4 种基金the Key Projects of the Joint Fund of the National Natural Science Foundation of China(U1802232)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2019382)the International Partnership Program of Chinese Academy of Sciences(151853KYSB20180009)Yunnan Science and Technology Project(YNWR-QNBJ-2019-033,202103AF140005,202305AM070005)Project of Background Resources Survey in Shennongjia National Park(SNJNP2022003).
文摘Understanding the maintenance and shift in reproductive strategies is a fundamental question in evolutionary research.Although many efforts have been made to compare different reproductive strategies,the association between reproductive strategies and lineage divergence is largely unknown.To explore the impact of different reproductive strategies on lineage divergence,we investigated the evolution of clonality in Saxifraga sect.Irregulares+Heterisia.By integrating several lines of evidence,we found that the loss of clonality in Irregulares+Heterisia was associated with a progressive increase in diversification rate and intraspecific morphological diversity but with a reduction in species distribution range.Our findings provide insights into the ecological and evolutionary effects of different reproductive strategies,suggesting the necessity of integrating clonality into ecological and evolutional research.
基金funded by the Chinese National Key Research And Development Program(2019YFD1000202)the Biodiversity Survey,Observation and Assessment Program awarded by the Ministry of Ecology and Environment,The People’s Republic of China(2019HJ2096001006)+2 种基金the International Partnership Program of the Chinese Academy of Sciences(151542KYSB20210004)the Regional Key Projects of Science and Technology Service Network Initiative granted by the Chinese Academy of Sciences(KFJ-STS-QYZD-192)the Natural Science Foundation of China(NSFC)(31372031).
文摘Actinidia arguta,the most widely distributed Actinidia species and the second cultivated species in the genus,can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit,rapid softening,and excellent cold tolerance.Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear.Here,we generated a chromosome-scale genome assembly of an autotetraploid male A.arguta accession.The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes.Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups,Southern and Northern,which first diverged 12.9 million years ago.A.arguta underwent two prominent expansions and one demographic bottleneck from the midPleistocene climate transition to the late Pleistocene.Population genomics studies using paleoclimate data enabled us to discern the evolution of the species’adaptation to different historical environments.Three genes(AaCEL1,AaPME1,and AaDOF1)related to flesh softening were identified by multi-omics analysis,and their ability to accelerate flesh softening was verified through transient expression assays.A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome(Chr3)or autosomal chromosomes showed biased expression during stamen or carpel development.This chromosome-level assembly of the autotetraploid A.arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A.arguta.
基金Supported by the Yunnan Provincial Sciences and Technology Department,China(No.2007AD009)the National Natural Science Foundation of China(No.31272680)the Ministry of Science and Technology of China(No.2013AA065805)
文摘In this paper,we investigated the effects of temperature,oxygen,antioxidants,and corn germ oil on the stability of astaxanthin from Haematococcus pluvialis under different storage conditions,and changes in the composition of astaxanthin esters during storage using high performance liquid chromatography and spectrophotometry.Oxygen and high temperatures(22–25°C) significantly reduced the stability of astaxanthin esters.Corn germ oil and antioxidants(ascorbic acid and vitamin E)failed to protect astaxanthin from oxidation,and actually significantly increased the instability of astaxanthin.A change in the relative composition of astaxanthin esters was observed after 96 weeks of long-term storage.During storage,the relative amounts of free astaxanthin and astaxanthin monoesters declined,while the relative amount of astaxanthin diesters increased.Thus,the ratio of astaxanthin diester to monoester increased,and this ratio could be used to indicate if astaxanthin esters have been properly preserved.If the ratio is greater than 0.2,it suggests that the decrease in astaxanthin content could be higher than 20%.Our results show that storing algal powder from H.pluvialis or other natural astaxanthin products under vacuum and in the dark below 4°C is the most economical and applicable storage method for the large-scale production of astaxanthin from H.pluvialis.This storage method can produce an astaxanthin preservation rate of at least 80%after 96 weeks of storage.
