Pseudosasa gracilis(Poaceae:Bambusoideae)is a temperate woody bamboo species endemic to Southcentral China with a narrow distribution.Previous phylogenetic studies revealed an unexpected,isolated phylogenetic position...Pseudosasa gracilis(Poaceae:Bambusoideae)is a temperate woody bamboo species endemic to Southcentral China with a narrow distribution.Previous phylogenetic studies revealed an unexpected,isolated phylogenetic position of Ps.gracilis.Here we conducted phylogenomic analysis by sampling populations of Ps.gracilis and its sympatric species Ps.nanunica and Sinosasa polytricha reflecting different genomic signals,by deep genome skimming.Integrating molecular evidence from chloroplast genes and genome-wide SNPs,we deciphered the phylogenetic relationships of Ps.gracilis.Both plastid and nuclear data indicate that Ps.gracilis is more closely related to Sinosasa,which is discordant with the taxonomic treatment.To further explore this molecular-morphological conflict,we screened 411“perfect-copy”syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods.We observed extensive discordance between gene trees and the putative species tree.A significant hybridization event was detected based on 411 genes from the D subgenome,showing Ps.gracilis was a hybrid descendant between Sinosasa longiligulata and Ps.nanunica,with 63.56%and 36.44%inheritance probabilities of each parent.Moreover,introgression events were detected in the C subgenome between Ps.gracilis and S.polytricha in the same distribution region.Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps.gracilis.By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters,our study represents a step forward in understanding of reticulate evolution of bamboos.展开更多
Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bam...Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.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
In this paper, we study the large time asymptotic behavior of solutions to both the Cauchy problem and the exterior problem of the Stokes approximation equations of two dimensional compressible flows.
This is a continuation of the paper (J. Math. Phys., 52(2011), 093102). We consider the Cauchy problem to the three-dimensional viscous liquid-gas two-fluid flow model. The global existence of classical solution i...This is a continuation of the paper (J. Math. Phys., 52(2011), 093102). We consider the Cauchy problem to the three-dimensional viscous liquid-gas two-fluid flow model. The global existence of classical solution is proved, where the initial vacuum is allowed.展开更多
This paper is concerned with the Cauchy problems of one-dimensional compressible Navier-Stokes equations with density-dependent viscosity coefcients.By assumingρ0∈L1(R),we will prove the existence of weak solution...This paper is concerned with the Cauchy problems of one-dimensional compressible Navier-Stokes equations with density-dependent viscosity coefcients.By assumingρ0∈L1(R),we will prove the existence of weak solutions to the Cauchy problems forθ〉0.This will improve results in Jiu and Xin’s paper(Kinet.Relat.Models,1(2):313–330(2008))in whichθ〉12is required.In addition,We will study the large time asymptotic behavior of such weak solutions.展开更多
We prove the existence and uniqueness of global strong solutions to the Cauchy problem of the three-dimensional magnetohydrodynamic equations in R3 when initial data are helically symmetric. Moreover, the large-time b...We prove the existence and uniqueness of global strong solutions to the Cauchy problem of the three-dimensional magnetohydrodynamic equations in R3 when initial data are helically symmetric. Moreover, the large-time behavior of the strong solutions is obtained simultaneously.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)the National Natural Science Foundation of China(32200193).
文摘Pseudosasa gracilis(Poaceae:Bambusoideae)is a temperate woody bamboo species endemic to Southcentral China with a narrow distribution.Previous phylogenetic studies revealed an unexpected,isolated phylogenetic position of Ps.gracilis.Here we conducted phylogenomic analysis by sampling populations of Ps.gracilis and its sympatric species Ps.nanunica and Sinosasa polytricha reflecting different genomic signals,by deep genome skimming.Integrating molecular evidence from chloroplast genes and genome-wide SNPs,we deciphered the phylogenetic relationships of Ps.gracilis.Both plastid and nuclear data indicate that Ps.gracilis is more closely related to Sinosasa,which is discordant with the taxonomic treatment.To further explore this molecular-morphological conflict,we screened 411“perfect-copy”syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods.We observed extensive discordance between gene trees and the putative species tree.A significant hybridization event was detected based on 411 genes from the D subgenome,showing Ps.gracilis was a hybrid descendant between Sinosasa longiligulata and Ps.nanunica,with 63.56%and 36.44%inheritance probabilities of each parent.Moreover,introgression events were detected in the C subgenome between Ps.gracilis and S.polytricha in the same distribution region.Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps.gracilis.By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters,our study represents a step forward in understanding of reticulate evolution of bamboos.
基金supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011)
文摘Shibataea is a genus of temperate bamboos(Poaceae:Bambusoideae)endemic to China,but little is known about its phylogenetic position and interspecific relationships.To elucidate the phylogenetic relationship of the bamboo genus Shibataea,we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing(dd RAD-seq)and whole plastid genomes generated using genome skimming.Our phylogenomic analyses based on dd RAD-seq and plastome data congruently recovered Shibataea as monophyletic.The nuclear data resolved S.hispida as the earliest diverged species,followed by S.chinensis,while the rest of Shibataea can be further divided into two clades.However,the plastid and nuclear topologies conflict significantly.By comparing the results of network analysis and topologies reconstructed from different datasets,we identify S.kumasasa as the most admixed species,which may be caused by incomplete lineage sorting(ILS)or interspecific gene flow with four sympatric species.This study highlights the power of dd RAD and plastome data in resolving complex relationships in the intractable bamboo genus.
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A The research is supported in part by the National Natural Science Foundation of China (Grant No. 10401012) and The Project Sponsored by the Scientific Research Foundation for the Returned 0verseas Chinese Scholars, State Education Ministry.Acknowledgment This is a part of my Ph.D thesis at The Institute of Mathematical Sciences, The Chinese University of Hong Kong. I express my deep gratitude to my graduate advisor, Professor Zhouping Xin, for his guidance and encouragement.
文摘In this paper, we study the large time asymptotic behavior of solutions to both the Cauchy problem and the exterior problem of the Stokes approximation equations of two dimensional compressible flows.
基金supported by the National Natural Science Foundation of China#11101331,11331005,FANEDD#201315Science and Technology Program of Shaanxi Province#2013KJXX-23+2 种基金supported by Grants YZZ13074 from Northwest University of ChinaNational Natural Science Foundation of China#11201371supported by the National Natural Science Foundation of China(NNSFC) Grant No.11331005 and SRDPC 20136101110015
文摘This is a continuation of the paper (J. Math. Phys., 52(2011), 093102). We consider the Cauchy problem to the three-dimensional viscous liquid-gas two-fluid flow model. The global existence of classical solution is proved, where the initial vacuum is allowed.
基金Supported by the National Natural Science Foundation of China(No.10771170)
文摘This paper is concerned with the Cauchy problems of one-dimensional compressible Navier-Stokes equations with density-dependent viscosity coefcients.By assumingρ0∈L1(R),we will prove the existence of weak solutions to the Cauchy problems forθ〉0.This will improve results in Jiu and Xin’s paper(Kinet.Relat.Models,1(2):313–330(2008))in whichθ〉12is required.In addition,We will study the large time asymptotic behavior of such weak solutions.
基金Supported by the National Natural Science Foundation of China(No.11071195)partially supported by the National Natural Science Foundation of China(No.11071195)a research grant at the Northwest University
文摘We prove the existence and uniqueness of global strong solutions to the Cauchy problem of the three-dimensional magnetohydrodynamic equations in R3 when initial data are helically symmetric. Moreover, the large-time behavior of the strong solutions is obtained simultaneously.