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
Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative ...Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels,we integrated morphological,physiological,and transcriptomic datasets to investigate rapid growth.In particular,these bamboos include two large-sized and a small-sized woody species,compared with a diploid herbaceous species.Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo,Dendrocalamus sinicus,and indicated that two gibberellins(GAs)-related genes,KAO and SLRL1,were key to the rapid shoot growth and culm size in woody bamboos.The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species.The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure,particularly UTRs and core promoters.Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos,particularly via subgenome asymmetry.These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.展开更多
BACKGROUND Epigenetic involvement of methyltransferase-like factor 14(METTL14)in tumor development has not been clearly defined.AIM To investigate METTL14 expression and its relationship with pathological stage in pat...BACKGROUND Epigenetic involvement of methyltransferase-like factor 14(METTL14)in tumor development has not been clearly defined.AIM To investigate METTL14 expression and its relationship with pathological stage in patients undergoing radical surgery for colorectal cancer(CRC).METHODS This retrospective study included 80 patients with CRC who were admitted to the Third Hospital of Hefei and the Western District of the First Affiliated Hospital of Anhui Medical University between June 2021 and June 2024.These patients were selected for treatment.Lesions and adjacent tissues were collected from these patients,and METTL14 expression was assessed using immunohistochemistry.Expression levels of METTL14 were compared across different tissue samples.Additionally,we evaluated METTL14 expression in patients with varying pa-thological characteristics using statistical methods such asχ2 tests and analysis of variance to identify significant differences.RESULTS The positivity rate of METTL14 in tumor tissues was significantly lower than that in adjacent tissues(30%vs 60%,P<0.05).Conversely,the negative expression rate of METTL14 was higher in tumor tissues compared to adjacent tissues(P<0.05).The positive expression of METTL14 mRNA did not differ by age,sex,tumor tissue classification,tumor diameter,or tumor location(P>0.05).However,the positive expression rate of METTL14 was significantly lower in patients with lymph node metastasis,invasion depth T3+T4,and tumor,node,and metastasis(TNM)stage III/IV compared to those without lymph node metastasis,invasion depth T1+T2,and TNM stage I(P<0.05).Specifically,METTL14 mRNA expression was significantly lower in patients with lymph node metastasis(0.51±0.12 vs 1.23±0.25,P<0.001),invasion depth T3+T4(0.48±0.15 vs 1.18±0.21,P<0.001),and TNM stage III/IV(0.45±0.13 vs 1.20±0.22,P<0.001)compared to those with no lymph node metastasis,invasion depth T1+T2,and TNM stage I,respectively.CONCLUSION In CRC,low positive METTL14 expression is closely correlated with lymph node metastasis,invasion depth T3+T4,and TNM stage,indicating the malignant biological behavior of rectal cancer.展开更多
Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.Ho...Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.However,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied.In the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes.Gene content,gene order,and GC content were highly similar in these plastomes.The inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and S.rosmarinus).In Salvia,sequence divergence was higher in non-coding regions than in coding regions.We found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research.This study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia subg.Glutinaria.The newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.展开更多
Binder jetting 3D printing is a rapid,cost effective,and efficient moulding/core making process,which can be applied to a large variety of materials.However,it exhibits a relatively low green-part strength.This may ca...Binder jetting 3D printing is a rapid,cost effective,and efficient moulding/core making process,which can be applied to a large variety of materials.However,it exhibits a relatively low green-part strength.This may cause the collapse of the printed parts during de-caking and the pick-up procedure,especially in the case of small-scale structures,such as thin walls,tips,and channels.In this work,polyvinyl alcohol(PVA)was used as the additive in coated sand powder.By exploiting the binding effect between the two composites(thermoplastic phenolic resin and PVA)triggered by the binder,bonding necks firmly form among the sand particles,improving the green-part strength of the coated sand printed parts.Experiments based on the Taguchi method were used to investigate the relationship between the process parameters and the green-part tensile strength.The following set of optimal process parameters was identified:50wt.%alcoholicity of the binder,75%binder saturation,0.36 mm layer thickness and 4.5wt.%PVA content.Further,the effect of such parameters on the green-part tensile strength was determined via statistical analysis.The green part of an engine cylinder head sand pattern with complex cavity structures was printed,and the green-part tensile strength reached 2.31 MPa.Moreover,the ZL301 aluminum alloy impeller shape casting was prepared using sand molds printed with the optimal process parameters.The results confirm that the proposed binder jetting 3D printing process can guarantee the integrity of the printed green parts and of small-size structures during de-caking and the pick-up procedure.Furthermore,the casting made from the printed sand molds exhibits a relatively high quality.展开更多
Objective Conflicting data have been generated from previous studies to determine which kind of relationship exists between HIV-1 specific CD8 Tcell responses and HIV-1 viral load or CD4 count over the course of infec...Objective Conflicting data have been generated from previous studies to determine which kind of relationship exists between HIV-1 specific CD8 Tcell responses and HIV-1 viral load or CD4 count over the course of infection.In this study,153 HIV-1 infected LTNPs were enrolled to investigate the role of HIV-1 specific CD8 T-cell responses in chronic HIV-1 infection among HIV-1 infected former blood donors.Methods The patients were stratified into three groups according to CD4 count：CD4≥500 cells/μL;350 cells/μL≤CD4〈500 cells/μL;CD4〈350 cells/μL.PBMCs were isolated from the patients＇ anticoagulated blood samples.IL-2 and IFN-γ secretions of CD 8 T cells against 17 HIV-1 consensus B full peptide pools were analyzed by using ICS assay.Results An overall inverse correlation were observed between CD4 count and plasma viral load.Although no significant difference was observed during the comparisons of frequency/breadth of HIV-1 specific CD8 T cell responses,CD4 count stratification analysis showed that different correlation pattern existed in three strata：as for patients whose CD4 counts were less than 350 cells/μL,no significant correlations were identified between frequency/breadth of HIV-1 specific CD8 T cell responses and CD4 count/viral load;as for patients whose CD4 counts ranged from 350 cells /μL to 500 cells/μL,significant correlation was only observed between the response breadth of IL-2＋IFN-γ＋ CD8 T cells and CD4 count;however,as for patients whose CD4 counts were more than 500 cells/μL,direct correlations were identified between IL-2＋IFN-γ＋/IL-2＋/IFN-γ＋ CD8 T cells and viral load or CD4 count.Conclusions Universal consistent inverse correlation was only indentified between CD4 count and viral load.The relationship between HIV-1 specific CD8 T cell responses and CD4 count/viral load varied in different CD4 strata,which showed that better preserved CD4 T cells were correlated with better CD8 T cell functions.展开更多
Rates of protein evolution(d_(N)/d_(S))vary widely across the tree of life.In plants,both life-history traits and GC-biased gene conversion(gBGC)are thought to contribute to this variation,although disentangling their...Rates of protein evolution(d_(N)/d_(S))vary widely across the tree of life.In plants,both life-history traits and GC-biased gene conversion(gBGC)are thought to contribute to this variation,although disentangling their individual contributions remains a challenge.Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae(mostly woody)and Pooideae(exclusively herbaceous),we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies.Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size.Although g BGC slightly reduced protein evolutionary rates in both subfamilies,its contribution had only a limited effect on molecular divergence between the groups.Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC.Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and lifehistory traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.展开更多
Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon f...Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(Peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;Ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso bamboo.What is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic investigations.Here,we present BambooBase(https://bamboo.genobank.org/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.展开更多
Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized.Bamboos comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only ma...Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized.Bamboos comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified culm.In this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels(diploid,tetraploid,and hexaploid).We also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids.Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos.Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found.Taken together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.展开更多
The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkab...The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos(PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos.However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and timecalibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing,and explored the evolutionary trends of habit,inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae,Racemobambosinae s.l.(comprising Dinochloinae,Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l.(comprising Bambusinae s.str. plus Holttumochloinae).The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.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supported by the Key Project of Natural Science Foundation of Yunnan Province (202401AS070082)the National Natural Science Foundation of China (grants 32120103003 and 31970355)
文摘Rapid growth is an innovative trait of woody bamboos that has been widely studied.However,the genetic basis and evolution of this trait are poorly understood.Taking advantage of genomic resources of 11 representative bamboos at different ploidal levels,we integrated morphological,physiological,and transcriptomic datasets to investigate rapid growth.In particular,these bamboos include two large-sized and a small-sized woody species,compared with a diploid herbaceous species.Our results showed that gibberellin A1 was important for the rapid shoot growth of the world's largest bamboo,Dendrocalamus sinicus,and indicated that two gibberellins(GAs)-related genes,KAO and SLRL1,were key to the rapid shoot growth and culm size in woody bamboos.The expression of GAs-related genes exhibited significant subgenome asymmetry with subgenomes A and C demonstrating expression dominance in the large-sized woody bamboos while the generally submissive subgenomes B and D dominating in the small-sized species.The subgenome asymmetry was found to be correlated with the subgenome-specific gene structure,particularly UTRs and core promoters.Our study provides novel insights into the molecular mechanism and evolution of rapid shoot growth following allopolyploidization in woody bamboos,particularly via subgenome asymmetry.These findings are helpful for understanding of how polyploidization in general and subgenome asymmetry in particular contributed to the origin of innovative traits in plants.
文摘BACKGROUND Epigenetic involvement of methyltransferase-like factor 14(METTL14)in tumor development has not been clearly defined.AIM To investigate METTL14 expression and its relationship with pathological stage in patients undergoing radical surgery for colorectal cancer(CRC).METHODS This retrospective study included 80 patients with CRC who were admitted to the Third Hospital of Hefei and the Western District of the First Affiliated Hospital of Anhui Medical University between June 2021 and June 2024.These patients were selected for treatment.Lesions and adjacent tissues were collected from these patients,and METTL14 expression was assessed using immunohistochemistry.Expression levels of METTL14 were compared across different tissue samples.Additionally,we evaluated METTL14 expression in patients with varying pa-thological characteristics using statistical methods such asχ2 tests and analysis of variance to identify significant differences.RESULTS The positivity rate of METTL14 in tumor tissues was significantly lower than that in adjacent tissues(30%vs 60%,P<0.05).Conversely,the negative expression rate of METTL14 was higher in tumor tissues compared to adjacent tissues(P<0.05).The positive expression of METTL14 mRNA did not differ by age,sex,tumor tissue classification,tumor diameter,or tumor location(P>0.05).However,the positive expression rate of METTL14 was significantly lower in patients with lymph node metastasis,invasion depth T3+T4,and tumor,node,and metastasis(TNM)stage III/IV compared to those without lymph node metastasis,invasion depth T1+T2,and TNM stage I(P<0.05).Specifically,METTL14 mRNA expression was significantly lower in patients with lymph node metastasis(0.51±0.12 vs 1.23±0.25,P<0.001),invasion depth T3+T4(0.48±0.15 vs 1.18±0.21,P<0.001),and TNM stage III/IV(0.45±0.13 vs 1.20±0.22,P<0.001)compared to those with no lymph node metastasis,invasion depth T1+T2,and TNM stage I,respectively.CONCLUSION In CRC,low positive METTL14 expression is closely correlated with lymph node metastasis,invasion depth T3+T4,and TNM stage,indicating the malignant biological behavior of rectal cancer.
基金supported by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(Grant No:2017eLSFGBOWSe02)。
文摘Salvia is the largest genus of Lamiaceae,with almost 1000 species,and has been divided into 11 subgenera.Salvia subg.Glutinaria,native to East Asia,is particularly important because of its potential medicinal value.However,the interspecific relationships of this subgenus have not been resolved and the plastomes of Salvia have rarely been studied.In the current study,we compared plastid genome structure and organization of 19 species of Salvia(14 newly sequenced and 5 previously published).Our comparative analysis showed that all Salvia plastomes examined have a quadripartite structure typical of most angiosperms and contain an identical set of 114 unique genes(80 protein-coding genes,4 rRNA genes,and 30 tRNA genes).The plastome structure of all Salvia species is highly conserved like other Lamiaceae plastomes.Gene content,gene order,and GC content were highly similar in these plastomes.The inverted repeats/single copy region(IR/SC)boundaries of Salvia are highly conserved,and IR contraction only occurred in two species(Salvia mekongensis and S.rosmarinus).In Salvia,sequence divergence was higher in non-coding regions than in coding regions.We found that using large single copy(LSC)and small single copy regions(SSC)with exclusion of the rapidly evolving sites produced the highest resolution in phylogenetic analysis of Salvia,suggesting that using suitable informative sites to build trees is more conducive in phylogenetic research.This study assembled a powerful matrix data set for studying the phylogeny of Salvia,resolving the interspecific relationship of Salvia subg.Glutinaria.The newly sequenced plastid genomes will also enrich the plastome database of Salvia,providing the scientific basis for the development and utilization of germplasm resources of this large and important genus.
基金the National Key Research and Development Program of China(No.2018YFB1106800)。
文摘Binder jetting 3D printing is a rapid,cost effective,and efficient moulding/core making process,which can be applied to a large variety of materials.However,it exhibits a relatively low green-part strength.This may cause the collapse of the printed parts during de-caking and the pick-up procedure,especially in the case of small-scale structures,such as thin walls,tips,and channels.In this work,polyvinyl alcohol(PVA)was used as the additive in coated sand powder.By exploiting the binding effect between the two composites(thermoplastic phenolic resin and PVA)triggered by the binder,bonding necks firmly form among the sand particles,improving the green-part strength of the coated sand printed parts.Experiments based on the Taguchi method were used to investigate the relationship between the process parameters and the green-part tensile strength.The following set of optimal process parameters was identified:50wt.%alcoholicity of the binder,75%binder saturation,0.36 mm layer thickness and 4.5wt.%PVA content.Further,the effect of such parameters on the green-part tensile strength was determined via statistical analysis.The green part of an engine cylinder head sand pattern with complex cavity structures was printed,and the green-part tensile strength reached 2.31 MPa.Moreover,the ZL301 aluminum alloy impeller shape casting was prepared using sand molds printed with the optimal process parameters.The results confirm that the proposed binder jetting 3D printing process can guarantee the integrity of the printed green parts and of small-size structures during de-caking and the pick-up procedure.Furthermore,the casting made from the printed sand molds exhibits a relatively high quality.
文摘Objective Conflicting data have been generated from previous studies to determine which kind of relationship exists between HIV-1 specific CD8 Tcell responses and HIV-1 viral load or CD4 count over the course of infection.In this study,153 HIV-1 infected LTNPs were enrolled to investigate the role of HIV-1 specific CD8 T-cell responses in chronic HIV-1 infection among HIV-1 infected former blood donors.Methods The patients were stratified into three groups according to CD4 count：CD4≥500 cells/μL;350 cells/μL≤CD4〈500 cells/μL;CD4〈350 cells/μL.PBMCs were isolated from the patients＇ anticoagulated blood samples.IL-2 and IFN-γ secretions of CD 8 T cells against 17 HIV-1 consensus B full peptide pools were analyzed by using ICS assay.Results An overall inverse correlation were observed between CD4 count and plasma viral load.Although no significant difference was observed during the comparisons of frequency/breadth of HIV-1 specific CD8 T cell responses,CD4 count stratification analysis showed that different correlation pattern existed in three strata：as for patients whose CD4 counts were less than 350 cells/μL,no significant correlations were identified between frequency/breadth of HIV-1 specific CD8 T cell responses and CD4 count/viral load;as for patients whose CD4 counts ranged from 350 cells /μL to 500 cells/μL,significant correlation was only observed between the response breadth of IL-2＋IFN-γ＋ CD8 T cells and CD4 count;however,as for patients whose CD4 counts were more than 500 cells/μL,direct correlations were identified between IL-2＋IFN-γ＋/IL-2＋/IFN-γ＋ CD8 T cells and viral load or CD4 count.Conclusions Universal consistent inverse correlation was only indentified between CD4 count and viral load.The relationship between HIV-1 specific CD8 T cell responses and CD4 count/viral load varied in different CD4 strata,which showed that better preserved CD4 T cells were correlated with better CD8 T cell functions.
基金supported by the National Natural Science Foundation of China(32120103003 and 32470394)the Top-notch Young Talents Project of Yunnan Province(YNWR-QNBJ-2019-203)+1 种基金the Key Basic Research Program of Yunnan Province(202201AS070057 and 202101BC070003)supported by Sugon HPC clusters equipped with HYGON Z100L at Kunming Institute of Botany,CAS and Yunnan Province Science and Technology Department(202305AH340005)。
文摘Rates of protein evolution(d_(N)/d_(S))vary widely across the tree of life.In plants,both life-history traits and GC-biased gene conversion(gBGC)are thought to contribute to this variation,although disentangling their individual contributions remains a challenge.Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae(mostly woody)and Pooideae(exclusively herbaceous),we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies.Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size.Although g BGC slightly reduced protein evolutionary rates in both subfamilies,its contribution had only a limited effect on molecular divergence between the groups.Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC.Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and lifehistory traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences(XDB31000000)the Fundamental Research Project of Yunnan Province(202101AT070175)+2 种基金the National Natural Science Foundation of China(32120103003)Digitalization,Development and Application of Biotic Resources(202002AA100007)a grant for Reserve Talents for Young and Middle-aged Academic and Technological Leaders in Yunnan Province,China(202405AC350089).
文摘Dear Editor,Bamboos(Bambusoideae,Poaceae)are of significant economic and ecological importance,supporting billions of people and contributing to international trade(Wu et al.,2023).They play a crucial role in carbon fixation and support a multitude of other species including the giant panda(Clark et al.,2015).Since the release of the first draft genome of moso bamboo(Phyllostachys edulis)(Peng et al.,2013),there has been a notable increase in the sequencing,assembly,and annotation of diverse bamboo genomes(Guo et al.,2019;Zheng et al.,2022;Ma et al.,2024).An existing resource for bamboo genomics,BambooGDB(Zhao et al.,2014),provides information based on the individual draft reference genome of moso bamboo.What is needed,however,is a resource reinforcing multiple genome assemblies in Bambusoideae to enable researchers to unravel the evolutionary history of chromosomes and genes through cladespecific comparative genomic investigations.Here,we present BambooBase(https://bamboo.genobank.org/),a newly developed web-based database designed to provide a seamless user experience for bamboo omics and systematics.
基金funding from Strategic Priority Program of the Chinese Academy of Sciences(CAS)(XDB31000000 to D.-Z.L)the National Natural Science Foundation of China(grants 31430011 to D.-Z.L.and 31670227 to Z.-H.G.)+3 种基金Leading Talents Program of Yunnan Province(2017HA014 to D.-Z.L.)CAS Youth Innovation Promotion Association(2015321 to P.-F.M.)a grant from Germplasm Bank of Wild Species(Y77P4412Z1 to Z.-H.G.)CAS Pioneer Hundred Talents Program(292015312D11035 to J.-Y.H.).
文摘Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized.Bamboos comprise one diploid herbaceous and three polyploid woody lineages,and are members of the only major subfamily in grasses that diversified in forests,with the woody members having a tree-like lignified culm.In this study,we generated four draft genome assemblies of major bamboo lineages with three different ploidy levels(diploid,tetraploid,and hexaploid).We also constructed a high-density genetic linkage map for a hexaploid species of bamboo,and used a linkage-map-based strategy for genome assembly and identification of subgenomes in polyploids.Further phylogenomic analyses using a large dataset of syntenic genes with expected copies based on ploidy levels revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage,and experienced complex reticulate evolution through three independent allopolyploid events involving four extinct diploid ancestors.A shared but distinct subgenome was identified in all polyploid forms,and the progenitor of this subgenome could have been critical in ancient polyploidizations and the origin of woody bamboos.Important genetic clues to the unique flowering behavior and woody trait in bamboos were also found.Taken together,our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species,and offers a potential model scenario for broad-scale study of angiosperm origination by allopolyploidization.
基金supported by the National Natural Science Foundation of China (No. 32120103003, 31970355, 32300206)the Key R & D program of Yunnan Province, China (No. 202103AC100003)Postdoctoral Directional Training Foundation of Yunnan Province。
文摘The woody bamboos(Bambusoideae) exhibit distinctive biological traits within Poaceae, such as highly lignified culms, rapid shoot growth, monocarpic mass flowering and nutlike or fleshy caryopses. Much of the remarkable morphological diversity across the subfamily exists within a single hexaploid clade, the paleotropical woody bamboos(PWB), making it ideal to investigate the factors underlying morphological evolution in woody bamboos.However, the origin and biogeographical history of PWB remain elusive, as does the effect of environmental factors on the evolution of their morphological characters. We generated a robust and timecalibrated phylogeny of PWB using single nucleotide polymorphisms retrieved from optimized double digest restriction site associated DNA sequencing,and explored the evolutionary trends of habit,inflorescence, and caryopsis type in relation to environmental factors including climate, soil, and topography. We inferred that the PWB started to diversify across the Oligocene–Miocene boundary and formed four major clades, that is, Melocanninae,Racemobambosinae s.l.(comprising Dinochloinae,Greslanlinae, Racemobambosinae s.str. and Temburongiinae), Hickeliinae and Bambusinae s.l.(comprising Bambusinae s.str. plus Holttumochloinae).The ancestor of PWB was reconstructed as having erect habit, indeterminate inflorescence and basic caryopsis. The characters including climbing/scrambling habit, determinate inflorescence, and nucoid/bacoid caryopsis have since undergone multiple changes and reversals during the diversification of PWB. The evolution of all three traits was correlated with, and hence likely influenced by, aspects of climate, topography, and soil, with climate factors most strongly correlated with morphological traits, and soil factors least so. However, topography had more influence than climate or soil on the evolution of erect habit, whereas both factors had greater effect on the evolution of bacoid caryopsis than did soil. Our results provide novel insights into morphological diversity and adaptive evolution in bamboos for future ecological and evolutionary research.
