The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no con...The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no consensus on whether Pseudosorghum,a small genus in tropical Asia with only two species,should be included.Here,we performed phylogenomic analyses using whole plastomes(69 of them newly sequenced)from 132 individuals,representing 65 species in 19 related genera.We also built trees with nuclear ribosomal DNA sequences.Our results justify the inclusion of Pseudosorghum,likely also the Eulalia Clade III,in Saccharinae.Furthermore,both morphological and molecular analyses support merging the two Pseudosorghum species.The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum.Pseudosorghum is moderately supported as sister to the Miscanthus Clade I,while the remaining Tripidium species could be excluded from the subtribe.Saccharinae is estimated to have originated~3.73 million years ago in East Asia,followed by intercontinental dispersals.Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.展开更多
Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine...Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.展开更多
The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains controversial.Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evi...The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains controversial.Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae.In this study,we used plastome data to determine the phylogenetic position of Parapteropyrum(Fagopyrum)tibeticum.Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae:Parapteropyrum(Fagopyrum)tibeticum,Atraphaxis bracteata and Calligonum ebinuricum.Once assembled,plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae.Phylogenetic analyses of Polygonaceae were performed using whole plastome,all plastome genes,and single-copy genes.Plastomes assembled using different reference plastomes did not differ;however,annotations showed small variation.Plastomes of Parapteropyrum(Fagopyrum)tibeticum,A.bracteata and C.ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp,and a total number of plastome genes of about 130.Plastome microsatellites(SSR)ranged in number from 48 to 77.Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum.Furthermore,our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic.Our study provides strong evidence that the woody Parapteropyrum tibeticum,which is distantly related to woody genera sampled here,should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.展开更多
Panax stipuleanatus(Araliaceae) is an endangered and medicinally important plant endemic to China.However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the compl...Panax stipuleanatus(Araliaceae) is an endangered and medicinally important plant endemic to China.However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax.The plastome of P. stipuleanatus is 156,069 base pairs(bp) in length, consisting of a pair of inverted repeats(IRs, each 25,887 bp) that divide the plastome into a large single copy region(LSC, 86,126 bp) and a small single copy region(SSC, 8169 bp). The plastome contains 114 unigenes(80 protein-coding genes,30 tRNA genes, and 4 r RNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine proteincoding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.展开更多
Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten gen...Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.展开更多
Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylo...Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.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
The wood sorrel family,Oxalidaceae,is mainly composed of annual or perennial herbs,a few shrubs,and trees distributed from temperate to tropical zones.Members of Oxalidaceae are of high medicinal,ornamental,and econom...The wood sorrel family,Oxalidaceae,is mainly composed of annual or perennial herbs,a few shrubs,and trees distributed from temperate to tropical zones.Members of Oxalidaceae are of high medicinal,ornamental,and economic value.Despite the rich diversity and value of Oxalidaceae,few molecular markers or plastomes are available for phylogenetic analysis of the family.Here,we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family,as well as the plastome of Rourea microphylla in the closely related family Connaraceae.The eight plastomes ranged in length from 150,673 bp(Biophytum sensitivum)to 156,609 bp(R.microphylla).Genome annotations revealed a total of 129e131 genes,including 83e84 protein-coding genes,eight rRNA genes,37 tRNA genes,and two to three pseudogenes.Comparative analyses showed that the plastomes of these species have minor variations at the gene level.The smaller plastomes of herbs B.sensitivum and three Oxalis species are associated with variations in IR region sizes,intergenic region variation,and gene or intron loss.We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae.The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae.Our research also supported the monophyly of the COM(Celastrales,Oxalidales,and Malpighiales)clade.展开更多
Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important ge...Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.展开更多
Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and m...Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).展开更多
Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine(TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species ba...Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine(TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants(SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3′trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices(Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system(ARMS).展开更多
Different from the traditional magnetorheological(MR)fluids and elastomers,the magnetic particles in the plastic MR materials are not‘deadly’trapped in the polymer matrix;thus,the MR plastomers exhibit higher MR eff...Different from the traditional magnetorheological(MR)fluids and elastomers,the magnetic particles in the plastic MR materials are not‘deadly’trapped in the polymer matrix;thus,the MR plastomers exhibit higher MR effects and lower sedimentation.The plastic MR materials have attracted increasing attention,and the relevant fundamental mechanisms and practical applications have been intensively studied due to their unique physical and mechanical properties.In this highlight,we have mainly reviewed the preparation and the rheological properties of the MR plastomers.The formation mechanism of the MR plastomers has also been briefly summarized.展开更多
基金supported by Yunnan Fundamental Research Project(202401BC070001)a research project of the Germplasm Bank of Wild Species,Kunming Institute of Botany,CAS,and the Project of Science and Technology Commission of Shanghai Municipality(23DZ1204601).
文摘The sugarcane subtribe Saccharinae(Andropogoneae,Poaceae)was established in 1846,but its delimitation has long been debated.Moreover,the relationships among the genera of Saccharinae remain unclear,and there is no consensus on whether Pseudosorghum,a small genus in tropical Asia with only two species,should be included.Here,we performed phylogenomic analyses using whole plastomes(69 of them newly sequenced)from 132 individuals,representing 65 species in 19 related genera.We also built trees with nuclear ribosomal DNA sequences.Our results justify the inclusion of Pseudosorghum,likely also the Eulalia Clade III,in Saccharinae.Furthermore,both morphological and molecular analyses support merging the two Pseudosorghum species.The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum.Pseudosorghum is moderately supported as sister to the Miscanthus Clade I,while the remaining Tripidium species could be excluded from the subtribe.Saccharinae is estimated to have originated~3.73 million years ago in East Asia,followed by intercontinental dispersals.Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.
基金supported by grants from CAS' Largescale Scientific Facilities (Grant No.2017-LSF-GBOWS-02)the Key R & D Program of Yunnan Province,China (Grant No.20210 3AC100003)Ten Thousand Talent Program of Yunnan Province (Grant No.YNWR-QNBJ-2020-297)。
文摘Fargesia,the largest genus within the temperate bamboo tribe Arundinarieae,has more than 90 species mainly distributed in the mountains of Southwest China.The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals,including the giant panda.However,species-level identification of Fargesia is difficult.Moreover,the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes(rbcL,matK,and ITS) in bamboos.With progress in the sequencing technologies,complete plastid genomes(plastomes) and nuclear ribosomal DNA(nrDNA)sequences have been proposed as organelle barcodes for species identification;however,these have not been tested in bamboos.We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes.Our analysis indicates that complete plastomes have substantially higher discriminatory power(28.6%) than standard barcodes(5.7%),whereas nrDNA sequences show a moderate improvement(65.4%) compared to ITS(47.2%).We also found that nuclear markers performed better than plastid markers,and ITS alone had higher discriminatory power than complete plastomes.The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia.However,neither of these sequences were able to discriminate all the sampled species,and therefore,more nuclear markers need to be identified.
基金This work was funded by the National Natural Science Foundation of China(grant No.31590821).
文摘The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains controversial.Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae.In this study,we used plastome data to determine the phylogenetic position of Parapteropyrum(Fagopyrum)tibeticum.Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae:Parapteropyrum(Fagopyrum)tibeticum,Atraphaxis bracteata and Calligonum ebinuricum.Once assembled,plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae.Phylogenetic analyses of Polygonaceae were performed using whole plastome,all plastome genes,and single-copy genes.Plastomes assembled using different reference plastomes did not differ;however,annotations showed small variation.Plastomes of Parapteropyrum(Fagopyrum)tibeticum,A.bracteata and C.ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp,and a total number of plastome genes of about 130.Plastome microsatellites(SSR)ranged in number from 48 to 77.Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum.Furthermore,our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic.Our study provides strong evidence that the woody Parapteropyrum tibeticum,which is distantly related to woody genera sampled here,should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.
基金financially supported by the Major Program of National Natural Science Foundation of China (No. 31590823)the National Natural Science Foundation of China (No. 31070297)
文摘Panax stipuleanatus(Araliaceae) is an endangered and medicinally important plant endemic to China.However, phylogenetic relationships within the genus Panax have remained unclear. In this study, we sequenced the complete plastome of P. stipuleanatus and included previously reported Panax plastomes to better understand the relationships between species and plastome evolution within the genus Panax.The plastome of P. stipuleanatus is 156,069 base pairs(bp) in length, consisting of a pair of inverted repeats(IRs, each 25,887 bp) that divide the plastome into a large single copy region(LSC, 86,126 bp) and a small single copy region(SSC, 8169 bp). The plastome contains 114 unigenes(80 protein-coding genes,30 tRNA genes, and 4 r RNA genes). Comparative analyses indicated that the plastome gene content and order, as well as the expansion/contraction of the IR regions, are all highly conserved within Panax. No significant positive selection in the plastid protein-coding genes was observed across the eight Panax species, suggesting the Panax plastomes may have undergone a strong purifying selection. Our phylogenomic analyses resulted in a phylogeny with high resolution and supports for Panax. Nine proteincoding genes and 10 non-coding regions presented high sequence divergence, which could be useful for identifying different Panax species.
基金supported by grants from the National Natural Science Foundation of Chinakey international (regional) cooperative research project (31720103903)The Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB0201)
文摘Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.
基金the National Natural Science Foundation of China(31960080,41671052 and 42175139)the Reserve Talents of Young and Middle-aged Academic and Technical Leaders in Yunnan province(202005AC160020)the Program Innovative Research Team in Science and Technology in Yunnan Province(202005AE160004).
文摘Wintergreen oil is a folk medicine widely used in foods,pesticides,cosmetics and drugs.In China,nine out of 47 species within Gaultheria(Ericaceae)are traditionally used as Chinese medicinal wintergreens;however,phylogenetic approaches currently used to discriminating these species remain unsatisfactory.In this study,we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria.Each Gaultheria plastome contained 110 unique genes(76 protein-coding,30 tRNA,and four rRNA genes).Duplication of trnfM,rps14,and rpl23 genes were detected,while all plastomes lacked ycf1 and ycf2 genes.Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene.Moreover,plastomes of Gaultheria leucocarpa var.yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene.Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales.Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species.Additionally,seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens.Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria.In addition,our findings provide important resources for identification of Chinese medicinal wintergreens.
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the Disciplinary Professional Construction Project of College of Art&College of Landscape Architecture,Fujian Agriculture and Forestry University(YSYL-bdpy-2,YSYL-bdpy-1).
文摘The wood sorrel family,Oxalidaceae,is mainly composed of annual or perennial herbs,a few shrubs,and trees distributed from temperate to tropical zones.Members of Oxalidaceae are of high medicinal,ornamental,and economic value.Despite the rich diversity and value of Oxalidaceae,few molecular markers or plastomes are available for phylogenetic analysis of the family.Here,we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family,as well as the plastome of Rourea microphylla in the closely related family Connaraceae.The eight plastomes ranged in length from 150,673 bp(Biophytum sensitivum)to 156,609 bp(R.microphylla).Genome annotations revealed a total of 129e131 genes,including 83e84 protein-coding genes,eight rRNA genes,37 tRNA genes,and two to three pseudogenes.Comparative analyses showed that the plastomes of these species have minor variations at the gene level.The smaller plastomes of herbs B.sensitivum and three Oxalis species are associated with variations in IR region sizes,intergenic region variation,and gene or intron loss.We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae.The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae.Our research also supported the monophyly of the COM(Celastrales,Oxalidales,and Malpighiales)clade.
基金funded by the National Natural Science Foundation of China(42171071,42211540718)Key Research Program of Frontier Sciences,CAS(ZDBS-LY-7001)+3 种基金Yunnan Fundamental Research Projects(202401AT070190,202201BC070001)Top-notch Young Talents Project of Yunnan Provincial“Ten Thousand Talents Program”(YNWR-QNBJ-2018-146,YNWR-QNBJ-2020-293)CAS“Light of West China”Programsupported by the China Scholarship Council(202304910135 and 202304910138)for a one-year study at the University of Toronto.
文摘Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades.Debregeasia(Urticaceae),an economically important genus,presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments.Here,we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia.We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia.Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter-and intra-specific levels.Three Debregeasia species were non-monophyletic and could not be discerned by any barcode;however,ultra-barcodes identified the remaining six(67%),outperforming standard barcodes(56%).Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia,although the placement between Debregeasia hekouensis and Debregeasia libera varied.There was extensive trait overlap in key morphologically diagnostic characters,with reticulation analysis showing potentially pervasive hybridization,likely influenced by speciation patterns and overlaps between species ranges.We inferred that Debregeasia crown diversification began at ca.12.82 Ma(95%HPD:11.54-14.63 Ma)in the mid-Miocene within Australia,followed by vicariance and later longdistance dispersal,mainly out of southern China.Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.
基金supported by the National Natural Science Foundation of China (Grant Nos. 31170300 and 31670330)the Priority Academic Program Development of Jiangsu Higher Education Institutions to Xiaoyu Ding (Grant No. 2015-SWYY-014)
文摘Owing to its great medicinal and ornamental values, Dendrobium officinale is frequently adulterated with other Dendrobium species on the market. Unfortunately, the utilization of the common DNA markers ITS,ITS2, and mat Ktrbc L is unable to distinguish D. officinale from 5 closely related species of it(D. tosaense, D.shixingense, D. flexicaule, D. scoriarum and D. aduncum). Here, we compared 63 Dendrobium plastomes comprising 40 newly sequenced plastomes of the 6 species and 23 previously published plastomes. The plastomes of D. officinale and its closely related species were shown to have conserved genome structure and gene content. Comparative analyses revealed that small single copy region contained higher variation than large single copy and inverted repeat regions, which was mainly attributed to the loss/retention of ndh genes.Furthermore, the intraspecific sequence variability among different Dendrobium species was shown to be diversified, which necessitates a cautious evaluation of genetic markers specific for different Dendrobium species.By evaluating the maximum likelihood trees inferred from different datasets, we found that the complete plastome sequence dataset had the highest discriminatory power for D. officinale and its closely related species,indicating that complete plastome sequences can be used to accurately authenticate Dendrobium species.& 2018 Chinese Pharmaceutical Association and Institute of Materia Medica, Chinese Academy of Medical Sciences. Production and hosting by Elsevier B.V. This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/).
基金supported by the National Natural Science Foundation of China(Grant Nos.31170300 and 31670330)the Priority Academic Program Development of Jiangsu Higher Education Institutions to Xiaoyu Ding
文摘Dendrobium species and their corresponding medicinal slices have been extensively used as traditional Chinese medicine(TCM) in many Asian countries. However, it is extremely difficult to identify Dendrobium species based on their morphological and chemical features. In this study, the plastomes of D. huoshanense were used as a model system to investigate the hypothesis that plastomic mutational hotspot regions could provide a useful single nucleotide variants(SNVs) resource for authentication studies. We surveyed the plastomes of 17 Dendrobium species, including the newly sequenced plastome of D. huoshanense. A total of 19 SNVs that could be used for the authentication of D. huoshanense were detected. On the basis of this comprehensive comparison, we identified the four most informative hotspot regions in the Dendrobium plastome that encompass ccsA to ndhF, matK to 3′trnG, rpoB to psbD, and trnT to rbcL. Furthermore, to established a simple and accurate method for the authentication of D. huoshanense and its medicinal slices, a total of 127 samples from 20 Dendrobium species including their corresponding medicinal slices(Fengdous) were used in this study. Our results suggest that D. huoshanense and its medicinal slices can be rapidly and unequivocally identified using this method that combines real-time PCR with the amplification refractory mutation system(ARMS).
基金supported by the Collaborative Innovation Center of Suzhou Nano Science and Technology.Financial support from the National Natural Science Foundation of China[grant number 11372301],[grant number 11125210]the Anhui Provincial Natural Science Foundation of China[grant number 1408085QA17]the National Basic Research Program of China(973 Program)[grant number 2012CB937500]is gratefully acknowledged.
文摘Different from the traditional magnetorheological(MR)fluids and elastomers,the magnetic particles in the plastic MR materials are not‘deadly’trapped in the polymer matrix;thus,the MR plastomers exhibit higher MR effects and lower sedimentation.The plastic MR materials have attracted increasing attention,and the relevant fundamental mechanisms and practical applications have been intensively studied due to their unique physical and mechanical properties.In this highlight,we have mainly reviewed the preparation and the rheological properties of the MR plastomers.The formation mechanism of the MR plastomers has also been briefly summarized.
