Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus r...Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.展开更多
Pea(Pisum sativum L.)is an annual cool-season legume crop.Owing to its role in sustainable agriculture as both a rotation and a cash crop,its global market is expanding and increased production is urgently needed.For ...Pea(Pisum sativum L.)is an annual cool-season legume crop.Owing to its role in sustainable agriculture as both a rotation and a cash crop,its global market is expanding and increased production is urgently needed.For both technical and regulatory reasons,neither conventional nor transgenic breeding techniques can keep pace with the demand for increased production.In answer to this challenge,CRISPR/Cas9 genome editing technology has been gaining traction in plant biology and crop breeding in recent years.However,there are currently no reports of the successful application of the CRISPR/Cas9 genome editing technology in pea.We developed a transient transformation system of hairy roots,mediated by Agrobacterium rhizogenes strain K599,to validate the efficiency of a CRISPR/Cas9 system.Further optimization resulted in an efficient vector,PsU6.3-tRNA-PsPDS3-en35S-PsCas9.We used this optimized CRISPR/Cas9 system to edit the pea phytoene desaturase(PsPDS)gene,causing albinism,by Agrobacterium-mediated genetic transformation.This is the first report of successful generation of gene-edited pea plants by this route.展开更多
Apricots,scientifically known as Prunus armeniaca L,are drupes that resemble and are closely related to peaches or plums.As one of the top consumed fruits,apricots are widely grown worldwide except in Antarctica.A hig...Apricots,scientifically known as Prunus armeniaca L,are drupes that resemble and are closely related to peaches or plums.As one of the top consumed fruits,apricots are widely grown worldwide except in Antarctica.A high-quality reference genome for apricot is still unavailable,which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background,evolutionary diversity,and population diversity in apricot.DNA from P.armeniaca was used to generate a standard,size-selected library with an average DNA fragment size of~20 kb.The library was run on Sequel SMRT Cells,generating a total of 16.54 Gb of PacBio subreads(N50=13.55 kb).The high-quality P.armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70×coverage and 171×Illumina reads(40.46 Gb),combined with a genetic map for chromosome scaffolding.The assembled genome size was 221.9 Mb,with a contig NG50 size of 1.02 Mb.Scaffolds covering 92.88%of the assembled genome were anchored on eight chromosomes.Benchmarking Universal Single-Copy Orthologs analysis showed 98.0%complete genes.We predicted 30,436 protein-coding genes,and 38.28%of the genome was predicted to be repetitive.We found 981 contracted gene families,1324 expanded gene families and 2300 apricot-specific genes.The differentially expressed gene(DEG)analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase(NCED)gene but not lycopene beta-cyclase(LcyB)gene results in a lowβ-carotenoid content in the white cultivar“Dabaixing”.This complete and highly contiguous P.armeniaca reference genome will be of help for future studies of resistance to plum pox virus(PPV)and the identification and characterization of important agronomic genes and breeding strategies in apricot.展开更多
Wearable flexible sensors attached on the neck have been developed to measure the vibration of vocal cords during speech.However,highfrequency attenuation caused by the frequency response of the flexible sensors and a...Wearable flexible sensors attached on the neck have been developed to measure the vibration of vocal cords during speech.However,highfrequency attenuation caused by the frequency response of the flexible sensors and absorption of high-frequency sound by the skin are obstacles to the practical application of these sensors in speech capture based on bone conduction.In this paper,speech enhancement techniques for enhancing the intelligibility of sensor signals are developed and compared.Four kinds of speech enhancement algorithms based on a fully connected neural network(FCNN),a long short-term memory(LSTM),a bidirectional long short-term memory(BLSTM),and a convolutional-recurrent neural network(CRNN)are adopted to enhance the sensor signals,and their performance after deployment on four kinds of edge and cloud platforms is also investigated.Experimental results show that the BLSTM performs best in improving speech quality,but is poorest with regard to hardware deployment.It improves short-time objective intelligibility(STOI)by 0.18 to nearly 0.80,which corresponds to a good intelligibility level,but it introduces latency as well as being a large model.The CRNN,which improves STOI to about 0.75,ranks second among the four neural networks.It is also the only model that is able to achieves real-time processing with all four hardware platforms,demonstrating its great potential for deployment on mobile platforms.To the best of our knowledge,this is one of the first trials to systematically and specifically develop processing techniques for bone-conduction speed signals captured by flexible sensors.The results demonstrate the possibility of realizing a wearable lightweight speech collection system based on flexible vibration sensors and real-time speech enhancement to compensate for high-frequency attenuation.展开更多
Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HIL...Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequeneed maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity.by.descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we dem on strated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function.related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.展开更多
Arabidopsis thaliana is an important and long-established model species for plant molecular biology,genetics,epigenetics,and genomics.However,the latest version of reference genome still contains a significant number ...Arabidopsis thaliana is an important and long-established model species for plant molecular biology,genetics,epigenetics,and genomics.However,the latest version of reference genome still contains a significant number of missing segments.Here,we reported a high-quality and almost complete Col-0 genome assembly with two gaps(named Col-XJTU)by combining the Oxford Nanopore Technologies ultra-long reads,Pacific Biosciences high-fidelity long reads,and Hi-C data.The total genome assembly size is 133,725,193 bp,introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome.All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality(QV)scores>60(ranging from 62 to 68),which are higher than those of the TAIR10.1 reference(ranging from 45 to 52).We completely resolved chromosome(Chr)3 and Chr5 in a telomere-to-telomere manner.Chr4 was completely resolved except the nucleolar organizing regions,which comprise long repetitive DNA fragments.The Chrl centromere(CEN1),reportedly around 9 Mb in length,is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats.Using the cutting-edge sequencing data and novel computational approaches,we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2.We also investigated the structure and epigenetics of centromeres.Four clusters of CEN180 monomers were detected,and the centromere-specific histone H3-like protein(CENH3)exhibited a strong preference for CEN180 Cluster 3.Moreover,we observed hypomethylation patterns in CENH3-enriched regions.We believe that this high-quality genome assembly,Col-XJTU,would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms,as well as the genetic and epigenetic features in plants.展开更多
Electronic skin made of thin,soft,stretchable devices that can mimic the human skin and reconstruct the tactile sensation and perception offers great opportunities for prosthesis sensing,robotics controlling,and human...Electronic skin made of thin,soft,stretchable devices that can mimic the human skin and reconstruct the tactile sensation and perception offers great opportunities for prosthesis sensing,robotics controlling,and human-machine interfaces.Advanced materials and mechanics engineering of thin film devices has proven to be an efficient route to enable and enhance flexibility and stretchability of various electronic skins;however,the density of devices is still low owing to the limitation in existing fabrication techniques.Here,we report a high-throughput one-step process to fabricate large tactile sensing arrays with a sensor density of 25 sensors/cm^(2) for electronic skin,where the sensors are based on intrinsically stretchable piezoelectric lead zirconate titanate(PZT)elastomer.The PZT elastomer sensor arrays with great uniformity and passive-driven manner enable highresolution tactile sensing,simplify the data acquisition process,and lower the manufacturing cost.The high-throughput fabrication process provides a general platform for integrating intrinsically stretchable materials into large area,high device density soft electronics for the next-generation electronic skin.展开更多
Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronica...Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronical illnesses.However,the lack of genomic information has hindered further molecular studies on this fungus.Here,we present a genome assembly of A.cylindracea together with comparative genomics and pathway analyses of Agaricales species.The draft,generated from both next-generation sequencing(NGS)and single-molecule real-time(SMRT)sequencing platforms to overcome high genetic heterozygosity,is composed of a56.5 Mb sequence and 15,384 predicted genes.This mushroom possesses a complex reproductive system,including tetrapolar heterothallic and secondary homothallic mechanisms,and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources.Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances,including B vitamins,unsaturated fatty acids,and N-acetylglucosamine.RNA-seq data show that A.cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage,whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis.These results reflect diverse functions of the two anatomical structures of the fruiting body.Our comprehensive genomic and transcriptomic data,as well as preliminary comparative analyses,provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.展开更多
The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-...The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.展开更多
Terahertz(THz)wave generation from laser-induced air plasma generally requires a short temporal laser pulse.In contrast,it was observed that THz radiation from ionized liquid water prefers a longer pulse,wherein the m...Terahertz(THz)wave generation from laser-induced air plasma generally requires a short temporal laser pulse.In contrast,it was observed that THz radiation from ionized liquid water prefers a longer pulse,wherein the mechanism remains unclear.We attribute the preference for longer pulse duration to the process of ionization and plasma formation in water,which is supported by a numerical simulation result showing that the highest electron density is achieved with a subpicosecond pulse.The explanation is further verified by the coincidence of our experimental result and simulation when the thickness of the water is varied.Other liquids are also tested to assure the preference for such a pulse is not exclusive to water.展开更多
The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male...The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.展开更多
The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences c...The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/and https://github.com/wushyer/RGAAT;2 at no cost.展开更多
Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-...Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.展开更多
基金supported by the Biodiversity Survey,Monitoring and Assessment Project(2019–2023)of the Ministry of Ecology and EnvironmentChina(No.2019HB2096001006 to ZZ)+2 种基金the National Natural Science Foundation of China(31672319)Endangered Species Scientific Commission of China(No.2022–331)supported by the China Scholarship Council,China。
文摘Population genomic data could provide valuable information for conservation efforts;however,limited studies have been conducted to investigate the genetic status of threatened pheasants.Reeves’s Pheasant(Syrmaticus reevesii)is facing population decline,attributed to increases in habitat loss.There is a knowledge gap in understanding the genomic status and genetic basis underlying the local adaptation of this threatened bird.Here,we used population genomic data to assess population structure,genetic diversity,inbreeding patterns,and genetic divergence.Furthermore,we identified candidate genes linked with adaptation across the current distribution of Reeves’s Pheasant.The present study assembled the first de novo genome sequence of Reeves’s Pheasant and annotated 19,458 genes.We also sequenced 30 individuals from three populations(Dabie Mountain,Shennongjia,Qinling Mountain)and found that there was clear population structure among those populations.By comparing with other threatened species,we found that Reeves’s Pheasants have low genetic diversity.Runs of homozygosity suggest that the Shennongjia population has experienced serious inbreeding.The demographic history results indicated that three populations experienced several declines during the glacial period.Local adaptative analysis among the populations identified 241 candidate genes under directional selection.They are involved in a large variety of processes,including the immune response and pigmentation.Our results suggest that the three populations should be considered as three different conservation units.The current study provides genetic evidence for conserving the threatened Reeves’s Pheasant and provides genomic resources for global biodiversity management.
基金the financial support of the China Agriculture Research System of MOF and MARA-Food Legumes(CARS-08)the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences。
文摘Pea(Pisum sativum L.)is an annual cool-season legume crop.Owing to its role in sustainable agriculture as both a rotation and a cash crop,its global market is expanding and increased production is urgently needed.For both technical and regulatory reasons,neither conventional nor transgenic breeding techniques can keep pace with the demand for increased production.In answer to this challenge,CRISPR/Cas9 genome editing technology has been gaining traction in plant biology and crop breeding in recent years.However,there are currently no reports of the successful application of the CRISPR/Cas9 genome editing technology in pea.We developed a transient transformation system of hairy roots,mediated by Agrobacterium rhizogenes strain K599,to validate the efficiency of a CRISPR/Cas9 system.Further optimization resulted in an efficient vector,PsU6.3-tRNA-PsPDS3-en35S-PsCas9.We used this optimized CRISPR/Cas9 system to edit the pea phytoene desaturase(PsPDS)gene,causing albinism,by Agrobacterium-mediated genetic transformation.This is the first report of successful generation of gene-edited pea plants by this route.
基金supported by the research of the National Key R&D Program of China(2018YFD1000606-4)the Beijing Academy of Agriculture and Forestry Fund for Young Scholars(QNJJ201702,QNJJ201925)+1 种基金the National Natural Science Foundation of China(31401836)the Municipal Natural Science Foundation of Beijing(6162012).
文摘Apricots,scientifically known as Prunus armeniaca L,are drupes that resemble and are closely related to peaches or plums.As one of the top consumed fruits,apricots are widely grown worldwide except in Antarctica.A high-quality reference genome for apricot is still unavailable,which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background,evolutionary diversity,and population diversity in apricot.DNA from P.armeniaca was used to generate a standard,size-selected library with an average DNA fragment size of~20 kb.The library was run on Sequel SMRT Cells,generating a total of 16.54 Gb of PacBio subreads(N50=13.55 kb).The high-quality P.armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70×coverage and 171×Illumina reads(40.46 Gb),combined with a genetic map for chromosome scaffolding.The assembled genome size was 221.9 Mb,with a contig NG50 size of 1.02 Mb.Scaffolds covering 92.88%of the assembled genome were anchored on eight chromosomes.Benchmarking Universal Single-Copy Orthologs analysis showed 98.0%complete genes.We predicted 30,436 protein-coding genes,and 38.28%of the genome was predicted to be repetitive.We found 981 contracted gene families,1324 expanded gene families and 2300 apricot-specific genes.The differentially expressed gene(DEG)analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase(NCED)gene but not lycopene beta-cyclase(LcyB)gene results in a lowβ-carotenoid content in the white cultivar“Dabaixing”.This complete and highly contiguous P.armeniaca reference genome will be of help for future studies of resistance to plum pox virus(PPV)and the identification and characterization of important agronomic genes and breeding strategies in apricot.
基金This work was supported in part by the Key Research and Development Program of Zhejiang Province,China(Grant No.2021C05005)the National Natural Science Foundation of China(Grant No.81771880)the Tianjin Municipal Government of China(Grant No.19JCQNJC12800).
文摘Wearable flexible sensors attached on the neck have been developed to measure the vibration of vocal cords during speech.However,highfrequency attenuation caused by the frequency response of the flexible sensors and absorption of high-frequency sound by the skin are obstacles to the practical application of these sensors in speech capture based on bone conduction.In this paper,speech enhancement techniques for enhancing the intelligibility of sensor signals are developed and compared.Four kinds of speech enhancement algorithms based on a fully connected neural network(FCNN),a long short-term memory(LSTM),a bidirectional long short-term memory(BLSTM),and a convolutional-recurrent neural network(CRNN)are adopted to enhance the sensor signals,and their performance after deployment on four kinds of edge and cloud platforms is also investigated.Experimental results show that the BLSTM performs best in improving speech quality,but is poorest with regard to hardware deployment.It improves short-time objective intelligibility(STOI)by 0.18 to nearly 0.80,which corresponds to a good intelligibility level,but it introduces latency as well as being a large model.The CRNN,which improves STOI to about 0.75,ranks second among the four neural networks.It is also the only model that is able to achieves real-time processing with all four hardware platforms,demonstrating its great potential for deployment on mobile platforms.To the best of our knowledge,this is one of the first trials to systematically and specifically develop processing techniques for bone-conduction speed signals captured by flexible sensors.The results demonstrate the possibility of realizing a wearable lightweight speech collection system based on flexible vibration sensors and real-time speech enhancement to compensate for high-frequency attenuation.
文摘Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequeneed maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity.by.descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we dem on strated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function.related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.
基金supported by the National Natural Science Foundation of China(Grant Nos.62172325 and 32070663)the China Postdoctoral Science Foundation(Grant No.2020M673420)+2 种基金the Fundamental Research Funds for the Central Universities,Chinathe World-Class Universities(Disciplines)the Characteristic Development Guidance Funds for the Central Universities,China。
文摘Arabidopsis thaliana is an important and long-established model species for plant molecular biology,genetics,epigenetics,and genomics.However,the latest version of reference genome still contains a significant number of missing segments.Here,we reported a high-quality and almost complete Col-0 genome assembly with two gaps(named Col-XJTU)by combining the Oxford Nanopore Technologies ultra-long reads,Pacific Biosciences high-fidelity long reads,and Hi-C data.The total genome assembly size is 133,725,193 bp,introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome.All five chromosomes of the Col-XJTU assembly are highly accurate with consensus quality(QV)scores>60(ranging from 62 to 68),which are higher than those of the TAIR10.1 reference(ranging from 45 to 52).We completely resolved chromosome(Chr)3 and Chr5 in a telomere-to-telomere manner.Chr4 was completely resolved except the nucleolar organizing regions,which comprise long repetitive DNA fragments.The Chrl centromere(CEN1),reportedly around 9 Mb in length,is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats.Using the cutting-edge sequencing data and novel computational approaches,we assembled a 3.8-Mb-long CEN1 and a 3.5-Mb-long CEN2.We also investigated the structure and epigenetics of centromeres.Four clusters of CEN180 monomers were detected,and the centromere-specific histone H3-like protein(CENH3)exhibited a strong preference for CEN180 Cluster 3.Moreover,we observed hypomethylation patterns in CENH3-enriched regions.We believe that this high-quality genome assembly,Col-XJTU,would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms,as well as the genetic and epigenetic features in plants.
基金This work was supported by the City University of Hong Kong(Grant Nos.9610423,9667199)Research Grants Council of the Hong Kong Special Administrative Region(Grant No.21210820)+2 种基金Department of Science and Technology of Sichuan Province(Grant No.2020YFH0181)Z.X.acknowledges the support from the National Natural Science Foundation of China(Grant No.12072057)Fundamental Research Funds for the Central Universities(Grant No.DUT20RC(3)032).
文摘Electronic skin made of thin,soft,stretchable devices that can mimic the human skin and reconstruct the tactile sensation and perception offers great opportunities for prosthesis sensing,robotics controlling,and human-machine interfaces.Advanced materials and mechanics engineering of thin film devices has proven to be an efficient route to enable and enhance flexibility and stretchability of various electronic skins;however,the density of devices is still low owing to the limitation in existing fabrication techniques.Here,we report a high-throughput one-step process to fabricate large tactile sensing arrays with a sensor density of 25 sensors/cm^(2) for electronic skin,where the sensors are based on intrinsically stretchable piezoelectric lead zirconate titanate(PZT)elastomer.The PZT elastomer sensor arrays with great uniformity and passive-driven manner enable highresolution tactile sensing,simplify the data acquisition process,and lower the manufacturing cost.The high-throughput fabrication process provides a general platform for integrating intrinsically stretchable materials into large area,high device density soft electronics for the next-generation electronic skin.
基金the project of “Cooperation with Localities and Industries”,Gansu,China(2012HZ-02)。
文摘Agrocybe cylindracea,an edible mushroom,is widely cultivated for its abundance of nutrients and flavor,and many of its metabolites are reported to have beneficial roles,such as medicinal effects on tumors and chronical illnesses.However,the lack of genomic information has hindered further molecular studies on this fungus.Here,we present a genome assembly of A.cylindracea together with comparative genomics and pathway analyses of Agaricales species.The draft,generated from both next-generation sequencing(NGS)and single-molecule real-time(SMRT)sequencing platforms to overcome high genetic heterozygosity,is composed of a56.5 Mb sequence and 15,384 predicted genes.This mushroom possesses a complex reproductive system,including tetrapolar heterothallic and secondary homothallic mechanisms,and harbors several hydrolases and peptidases for gradual and effective degradation of various carbon sources.Our pathway analysis reveals complex processes involved in the biosynthesis of polysaccharides and other active substances,including B vitamins,unsaturated fatty acids,and N-acetylglucosamine.RNA-seq data show that A.cylindracea stipes tend to synthesize carbohydrate for carbon sequestration and energy storage,whereas pilei are more active in carbon utilization and unsaturated fatty acid biosynthesis.These results reflect diverse functions of the two anatomical structures of the fruiting body.Our comprehensive genomic and transcriptomic data,as well as preliminary comparative analyses,provide insights into the molecular details of the medicinal effects in terms of active compounds and nutrient components.
基金supported by the National Natural Science Foundation of China(91731301 and U1902201)the Ministry of Science and Technology of the People’s Republic of China(2020YFC0847000)the Light of West China Program of the Chinese Academy of Sciences.
文摘The pandemic due to the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the etiological agent of coronavirus disease 2019(COVID-19),has caused immense global disruption.With the rapid accumulation of SARS-CoV-2 genome sequences,however,thousands of genomic variants of SARSCoV-2 are now publicly available.To improve the tracing of the viral genomes’evolution during the development of the pandemic,we analyzed single nucleotide variants(SNVs)in 121,618 high-quality SARS-CoV-2 genomes.We divided these viral genomes into two major lineages(L and S)based on variants at sites 8782 and 28144,and further divided the L lineage into two major sublineages(L1 and L2)using SNVs at sites 3037,14408,and 23403.Subsequently,we categorized them into 130 sublineages(37 in S,35 in L1,and 58 in L2)based on marker SNVs at 201 additional genomic sites.This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages.We also provide a companion website(www.covid19evolution.net)that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification.Finally,we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2’s evolution.These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2’s genome evolution.
基金This work was supported by the U.S.National Science Foundation(No.ECCS-1916068)the Army Research Office(No.W911NF-17-1-0428)the Air Force Office of Scientific Research(No.FA9550-18-1-0357).
文摘Terahertz(THz)wave generation from laser-induced air plasma generally requires a short temporal laser pulse.In contrast,it was observed that THz radiation from ionized liquid water prefers a longer pulse,wherein the mechanism remains unclear.We attribute the preference for longer pulse duration to the process of ionization and plasma formation in water,which is supported by a numerical simulation result showing that the highest electron density is achieved with a subpicosecond pulse.The explanation is further verified by the coincidence of our experimental result and simulation when the thickness of the water is varied.Other liquids are also tested to assure the preference for such a pulse is not exclusive to water.
基金the National Key R&D Program of China(2022YFC3400300)the National Natural Science Foundation of China(32125009,62172325,32070663)+1 种基金the National Key R&D Program of China(2017YFC0906501)the Key Construction Program of the National‘985’Project,and the Fundamental Research Funds for the Central Universities.
文摘The advantages of both the length and accuracy of high-fidelity(HiFi)reads enable chromosome-scale haplotype-resolved genome assembly.In this study,we sequenced a cell line named HJ,established from a Chinese Han male individual by using HiFi and Hi-C.We assembled two high-quality haplotypes of the HJ genome(haplotype 1(H1):3.1 Gb,haplotype 2(H2):2.9 Gb).The continuity(H1:contig N50=28.2 Mb,H2:contig N50=25.9 Mb)and completeness(BUSCO:H1=94.9%,H2=93.5%)are substantially better than those of other Chinese genomes,for example,HX1,NH1.0,and YH2.0.By comparing HJ genome with GRCh38,we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2,respectively.In addition,we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2,respectively.Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA08020102)National Natural Science Foundation of China (Grant Nos. 81701071, 31501042, 31271385, and 31200957)+2 种基金Shenzhen Science and Technology Program (Grant No. JCYJ20170306171013613),ChinaKing Abdulaziz City for Science and Technology (KACSTGrant No. 1035-35),Kingdom of Saudi Arabia
文摘The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/and https://github.com/wushyer/RGAAT;2 at no cost.
基金supported by the Chengdu Giant Panda Breeding Research Foundation,China(Grant No.CPF-2012-13)the Self-supporting Project of Chengdu Giant Panda Breeding Research Base,China(Grant No.2020CPBB20)+2 种基金the Sichuan International Science and Technology Innovation Cooperation/Hong Kong,Macao,and Taiwan Science and Technology Innovation Cooperation Project,China(Grant No.2019YFH0065)the National Natural Science Foundation of China(Grant No.31801048)the Highlevel Scientific Research Foundation for the Introduction of Talents of Sichuan Agricultural University of China(Grant No.03120322).
文摘Baylisascaris schroederi,a roundworm(ascaridoid)parasite specific to the bamboofeeding giant panda(Ailuropoda melanoleuca),represents a leading cause of mortality in wild giant panda populations.Here,we present a 293-megabase chromosome-level genome assembly of B.schroederi to infer its biology,including host adaptations.Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations,suggesting their potential for transmission and rapid adaptation to new hosts.Genomic and anatomical lines of evidence,including expansion and positive selection of genes related to the cuticle and basal metabolisms,indicate that B.schroederi undergoes specific adaptations to survive in the sharp-edged bamboo-enriched gut of giant pandas by structurally increasing its cuticle thickness and efficiently utilizing host nutrients through gut parasitism.Additionally,we characterized the secretome of B.schroederi and predicted potential drug and vaccine targets for new control strategies.Overall,this genome resource provides new insights into the host adaptation of B.schroederi to the giant panda as well as the host-shift events in ascaridoid parasite lineages.Our findings on the unique biology of B.schroederi will also aid in the development of prevention and treatment measures to protect giant panda populations from roundworm parasitism.
