Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bi...Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.展开更多
Using Green＇s function method, we investigate the spin transport properties of armchair graphene nanoribbons （AG- NRs） under magnetic field and uniaxial strain. Our results show that it is very difficult to transfo...Using Green＇s function method, we investigate the spin transport properties of armchair graphene nanoribbons （AG- NRs） under magnetic field and uniaxial strain. Our results show that it is very difficult to transform narrow AGNRs directly from semiconductor to spin gapless semiconductors （SGS） by applying magnetic fields. However, as a uniaxial strain is exerted on the nanoribbons, the AGNRs can transform to SGS by a small magnetic field. The combination mode be- tween magnetic field and uniaxial strain displays a nonmonotonic arch-pattern relationship. In addition, we find that the combination mode is associated with the widths of nanoribbons, which exhibits group behaviors.展开更多
We study the effect of electron-phonon （e-ph） interaction on the elastic and inelastic electronic transport of a nanowire connected to two simple rigid leads within the tight-binding and harmonic approximations. The...We study the effect of electron-phonon （e-ph） interaction on the elastic and inelastic electronic transport of a nanowire connected to two simple rigid leads within the tight-binding and harmonic approximations. The model is constructed using Green＇s function and multi-channel techniques, taking into account the local and nonlocal e-ph interactions. Then, we examine the model for the gapless （simple chain） and gapped （PA-like nanowire） systems. The results show that the tunneling conductance is improved by the e-ph interaction in both local and nonlocal regimes, while for the resonance conductance, the coherent part mainly decreases and the incoherent part increases. At the corresponding energies which depend on the phonon frequency, two dips in the elastic and two peaks in the inelastic conductance spectra appear. The reason is the absorption of the phonon by the electron in transition into inelastic channels.展开更多
Layered van der Waals(vdW) topological materials, especially the recently discovered MnBi_(2)Te_(4)-family magnetic topological insulators(TIs), have aroused great attention. However, there has been a serious debate a...Layered van der Waals(vdW) topological materials, especially the recently discovered MnBi_(2)Te_(4)-family magnetic topological insulators(TIs), have aroused great attention. However, there has been a serious debate about whether the surface states are gapped or gapless for antiferromagnetic(AFM) TI MnBi_(2)Te_(4), which is crucial to the prospect of various magnetic topological phenomena. Here, a minimal three-Dirac-fermion approach is developed to generally describe topological surface states of nonmagnetic/magnetic vdW TIs under the modulation of the interlayer vdW gap. In particular, this approach is applied to address the controversial issues concerning the surface states of vdW AFM TIs. Remarkably, topologically protected gapless Dirac-cone surface states are found to arise due to a small expansion of the interlayer vdW gap on the surface, when the Chern number equals zero for the surface ferromagnetic layer;while the surface states remain gapped in all other cases. These results are further confirmed by our first-principles calculations on AFM TI MnBi_(2)Te_(4). The theorectically discovered gapless Dirac-cone states provide a unique mechanism for understanding the puzzle of the experimentally observed gapless surface states in MnBi_(2)Te_(4).This work also provides a promising way for experiments to realize the intrinsic magnetic quantum anomalous Hall efect in MnBi_(2)Te_(4) films with a large energy gap.展开更多
We study the acoustomagnetoelectric (AME) effect in two-dimensional graphene with an energy bandgap using the semiclassical Boltzmann transport equation within the hypersound regime, (where represents the acoustic wav...We study the acoustomagnetoelectric (AME) effect in two-dimensional graphene with an energy bandgap using the semiclassical Boltzmann transport equation within the hypersound regime, (where represents the acoustic wavenumber and is the mean free path of the electron). The Boltzmann transport equation and other relevant equations were solved analytically to obtain an expression for the AME current density, consisting of longitudinal and Hall components. Our numerical results indicate that both components of the AME current densities display oscillatory behaviour. Furthermore, geometric resonances and Weiss oscillations were each defined using the relationship between the current density and Surface Acoustic Wave (SAW) frequency and the inverse of the applied magnetic field, respectively. Our results show that the AME current density of bandgap graphene, which can be controlled to suit a particular electronic device application, is smaller than that of (gapless) graphene and is therefore, more suited for nanophotonic device applications.展开更多
The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb fi...The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.展开更多
Subject Code:A04Frustrated quantum magnets have developed into one of the hottest topics in condensed matter physics because of the wide range of novel physical phenomena they exhibit,which includes quantum spin-liqui...Subject Code:A04Frustrated quantum magnets have developed into one of the hottest topics in condensed matter physics because of the wide range of novel physical phenomena they exhibit,which includes quantum spin-liquid states,fractionalized spin degrees of freedom,and exotic topological properties.This trend is展开更多
Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.However, the molecular mechanism driving AsA richness in fruit remains unclear.In order to reveal the molecula...Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.However, the molecular mechanism driving AsA richness in fruit remains unclear.In order to reveal the molecular mechanism of AsA richness in A. eriantha, this study constructed a regulatory network related to AsA metabolism by combining genomics,metabolomics and transcriptomics.We assembled a high-quality genome of A. eriantha ‘Ganlv 1’ with only five remaining gaps.The assembly is comprised of 29 pseudochromosomes with a total size of 615.95 Mb, and contig N50 of 20.35 Mb.Among them,24 of the pseudochromosomes were obtained directly from telomere-to-telomere.The LTR assembly index score and consensus quality value were 21.34 and 39.90%, respectively.Subsequently, 61 metabolites and 2 092genes were found to be differentially accumulated/expressed during fruit development by metabolome and transcriptome assays, respectively.AsA metabolism and the cyclic regeneration pathway were found to have high expression levels throughout fruit growth and development,suggesting its crucial role in the regulation of AsA.Furthermore,the AsA contents are highly associated with ascorbate peroxidase genes.The genome obtained in this study provides genomic resources for the genetic and breeding research ofA. eriantha, and the constructed regulatory network can provide a public data platform for future research on kiwifruit.展开更多
基金supported by the Chinese Academy of Agricultural Sciences Innovation Project(Grant No.CAASASTIP-2013CNRRI)Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute(Grant No.CPSIBRF-CNRRI-202102)。
文摘Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.
基金supported by the National Basic Research Program of China(Grant No.2012CB921303)the National Natural Science Foundation of China(Grant Nos.51172191,11074211,11074213,51006086,and 51176161)the Joint Funds of the Natural Science Foundation of Hunan Province,China(Grant No.10JJ9001)
文摘Using Green＇s function method, we investigate the spin transport properties of armchair graphene nanoribbons （AG- NRs） under magnetic field and uniaxial strain. Our results show that it is very difficult to transform narrow AGNRs directly from semiconductor to spin gapless semiconductors （SGS） by applying magnetic fields. However, as a uniaxial strain is exerted on the nanoribbons, the AGNRs can transform to SGS by a small magnetic field. The combination mode be- tween magnetic field and uniaxial strain displays a nonmonotonic arch-pattern relationship. In addition, we find that the combination mode is associated with the widths of nanoribbons, which exhibits group behaviors.
基金Project supported by the Iranian Nanotechnology Initiativesupported by Shahrekord University through a research fund
文摘We study the effect of electron-phonon （e-ph） interaction on the elastic and inelastic electronic transport of a nanowire connected to two simple rigid leads within the tight-binding and harmonic approximations. The model is constructed using Green＇s function and multi-channel techniques, taking into account the local and nonlocal e-ph interactions. Then, we examine the model for the gapless （simple chain） and gapped （PA-like nanowire） systems. The results show that the tunneling conductance is improved by the e-ph interaction in both local and nonlocal regimes, while for the resonance conductance, the coherent part mainly decreases and the incoherent part increases. At the corresponding energies which depend on the phonon frequency, two dips in the elastic and two peaks in the inelastic conductance spectra appear. The reason is the absorption of the phonon by the electron in transition into inelastic channels.
基金supported by the National Key Projects for Research and Development of China (Grant Nos. 2021YFA1400400, 2017YFA0303203, and 2022YFA1403602)the Fundamental Research Funds for the Central Universities (Grant No. 020414380185)+3 种基金the Natural Science Foundation of Jiangsu Province (Grant No. BK20200007)the National Natural Science Foundation of China (Grant Nos. 12074181, 12104217, 11834006, and 12174182)the Fok Ying-Tong Education Foundation of China (Grant No. 161006)supported by the program A/B for Outstanding PhD candidate of Nanjing University。
文摘Layered van der Waals(vdW) topological materials, especially the recently discovered MnBi_(2)Te_(4)-family magnetic topological insulators(TIs), have aroused great attention. However, there has been a serious debate about whether the surface states are gapped or gapless for antiferromagnetic(AFM) TI MnBi_(2)Te_(4), which is crucial to the prospect of various magnetic topological phenomena. Here, a minimal three-Dirac-fermion approach is developed to generally describe topological surface states of nonmagnetic/magnetic vdW TIs under the modulation of the interlayer vdW gap. In particular, this approach is applied to address the controversial issues concerning the surface states of vdW AFM TIs. Remarkably, topologically protected gapless Dirac-cone surface states are found to arise due to a small expansion of the interlayer vdW gap on the surface, when the Chern number equals zero for the surface ferromagnetic layer;while the surface states remain gapped in all other cases. These results are further confirmed by our first-principles calculations on AFM TI MnBi_(2)Te_(4). The theorectically discovered gapless Dirac-cone states provide a unique mechanism for understanding the puzzle of the experimentally observed gapless surface states in MnBi_(2)Te_(4).This work also provides a promising way for experiments to realize the intrinsic magnetic quantum anomalous Hall efect in MnBi_(2)Te_(4) films with a large energy gap.
文摘We study the acoustomagnetoelectric (AME) effect in two-dimensional graphene with an energy bandgap using the semiclassical Boltzmann transport equation within the hypersound regime, (where represents the acoustic wavenumber and is the mean free path of the electron). The Boltzmann transport equation and other relevant equations were solved analytically to obtain an expression for the AME current density, consisting of longitudinal and Hall components. Our numerical results indicate that both components of the AME current densities display oscillatory behaviour. Furthermore, geometric resonances and Weiss oscillations were each defined using the relationship between the current density and Surface Acoustic Wave (SAW) frequency and the inverse of the applied magnetic field, respectively. Our results show that the AME current density of bandgap graphene, which can be controlled to suit a particular electronic device application, is smaller than that of (gapless) graphene and is therefore, more suited for nanophotonic device applications.
基金This study was supported by the National Natural Science Foundation of China(NSFC,nos.31770331 and 31970318)Guangdong Basic and Applied Basic Research Foundation(no.2020B1515120023).
文摘The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.
文摘Subject Code:A04Frustrated quantum magnets have developed into one of the hottest topics in condensed matter physics because of the wide range of novel physical phenomena they exhibit,which includes quantum spin-liquid states,fractionalized spin degrees of freedom,and exotic topological properties.This trend is
基金supported by the National Natural Science Foundation of China (32160692 and 31760559)the Key Research and Development Plan from Jiangxi Science and Technology Department, China (20192ACB60002)。
文摘Actinidia eriantha is one of the species of kiwifruit with a particularly high ascorbic acid (AsA) content.However, the molecular mechanism driving AsA richness in fruit remains unclear.In order to reveal the molecular mechanism of AsA richness in A. eriantha, this study constructed a regulatory network related to AsA metabolism by combining genomics,metabolomics and transcriptomics.We assembled a high-quality genome of A. eriantha ‘Ganlv 1’ with only five remaining gaps.The assembly is comprised of 29 pseudochromosomes with a total size of 615.95 Mb, and contig N50 of 20.35 Mb.Among them,24 of the pseudochromosomes were obtained directly from telomere-to-telomere.The LTR assembly index score and consensus quality value were 21.34 and 39.90%, respectively.Subsequently, 61 metabolites and 2 092genes were found to be differentially accumulated/expressed during fruit development by metabolome and transcriptome assays, respectively.AsA metabolism and the cyclic regeneration pathway were found to have high expression levels throughout fruit growth and development,suggesting its crucial role in the regulation of AsA.Furthermore,the AsA contents are highly associated with ascorbate peroxidase genes.The genome obtained in this study provides genomic resources for the genetic and breeding research ofA. eriantha, and the constructed regulatory network can provide a public data platform for future research on kiwifruit.
