Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

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.

BambooBase:A comprehensive database of bamboo omics and systematics

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.

Comparative plastomic analysis and insights into the phylogeny of Salvia (Lamiaceae)

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.

HIV-Specific IL-2^+ and/or IFN-γ^+ CD8^+ T Cell Reponses during Chronic HIV-1 Infection in Former Blood Donors

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.

Binder jetting 3D printing process optimization for rapid casting of green parts with high tensile strength

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.

Genome Sequences Provide Insights into the Reticulate Origin and Unique Traits of Woody Bamboos

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.