Drought is very harmful to grain yield due to its adverse effect on reproduction, especially on pollination process in rice. However, the molecular basis of such an effect still remains largely unknown. Here, we repor...Drought is very harmful to grain yield due to its adverse effect on reproduction, especially on pollination process in rice. However, the molecular basis of such an effect still remains largely unknown. Here, we report the role of a member of CBL (Calcineurin B-Like) Interacting Protein Kinase (CIPK) family, OsCIPK23, in pollination and stress responses in rice. Molecular analyses revealed that it is mainly expressed in pistil and anther but up-regulated by pollination, as well as by treatments of various abiotic stresses and phytohormones. RNA interference-mediated suppression of OsCIPK23 expression significantly reduced seed set and conferred a hypersensitive response to drought stress, indicating its possible roles in pollination and drought stress. In consistent, overexpression of OsCIPK23 induced the expression of several drought tolerance related genes. Taken together, these results indicate that OsCIPK23 is a multistress induced gene and likely mediates a signaling pathway commonly shared by both pollination and drought stress responses in rice.展开更多
In 2003, the International Solanaceae Project (SOL) was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and t...In 2003, the International Solanaceae Project (SOL) was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The first major effort of the SOL aimed to produce a DNA sequence map for euchromatin regions of 12 chromosomes of tomato (Solanum lycopersicum) before 2010. Here we present an update on Chinese effort for sequencing the euchromatin region of chromosome 3.展开更多
To discover genes essential for agronomic performances of crops we initiated a program on rice functional genomics of important agronomic traits in rice in 1999. The program was funded by the Ministry of Science a... To discover genes essential for agronomic performances of crops we initiated a program on rice functional genomics of important agronomic traits in rice in 1999. The program was funded by the Ministry of Science and Technology of China through the National Basic Research Initiative and is expected to last for five years.
……展开更多
Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in angiosperms.The SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F...Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in angiosperms.The SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box(SLF)genes found in the Solanaceae,Plantaginaceae,Rosaceae,and Rutaceae.Recent studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box(SCF)SLF-mediated ubiquitin–proteasome system in a collaborative manner in Petunia,but how self-RNase functions largely remains mysterious.Here,we show that S-RNases form S-RNase condensates(SRCs)in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia hybrida.We further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs,which then sequester several actin-binding proteins,including the actin polymerization factor PhABRACL,the actin polymerization activity of which is reduced by S-RNase in vitro.Meanwhile,we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth inhibition.Taken together,our results demonstrate that phase separation of S-RNase promotes SI response in P.hybrida,revealing a new mode of S-RNase action.展开更多
Background Big data challenges In the late 1980s and early 1990s,three major international biological data centers were created:the DNA Database of Japan(DDBJ)[1],the European Bioinformatics Institute(EMBL-EBI)in the ...Background Big data challenges In the late 1980s and early 1990s,three major international biological data centers were created:the DNA Database of Japan(DDBJ)[1],the European Bioinformatics Institute(EMBL-EBI)in the United Kingdom(UK)[2],and the National Center for Biotechnology Information(NCBI)in the United States(US)[3].展开更多
Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;...Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.展开更多
On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS...On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.展开更多
In flowering plants, self-incompatibility (SI) serves as an important intraspecific reproductive barrier to promote outbreeding. In species from the Solanaceae, Plantaginaceae and Rosaceae, S-RNase and SLF (S-locus...In flowering plants, self-incompatibility (SI) serves as an important intraspecific reproductive barrier to promote outbreeding. In species from the Solanaceae, Plantaginaceae and Rosaceae, S-RNase and SLF (S-locus F-box) proteins have been shown to control the female and male specificity of SI, respectively. However, little is known about structure features of the SLF protein apart from its conserved F-box domain. Here we show that the SLF C-terminal region possesses a novel ubiquitin-binding domain (UBD) structure conserved among the SLF protein family. By using an ex vivo system of Nicotiana benthamiana, we found that the UBD mediates the SLF protein turnover by the ubiquitin-proteasome pathway. Furthermore, we detected that the SLF protein was directly involved in S-RNase degradation. Taken together, our results provide a novel insight into the SLF structure and highlight a potential role of SLF protein stability and degradation in S-RNase-based self-incompatibility.展开更多
A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investiga...A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.展开更多
Polarized tip growth is a fundamental cellular process in many eukaryotes. In this study, we examined the dynamic restructuring of the actin cytoskeleton and its relationship to vesicle transport during pollen tip gro...Polarized tip growth is a fundamental cellular process in many eukaryotes. In this study, we examined the dynamic restructuring of the actin cytoskeleton and its relationship to vesicle transport during pollen tip growth in Arabidopsis. We found that actin filaments originating from the apical membrane form a specialized structure consisting of longitudinally aligned actin bundles at the cortex and inner cytoplasmic fila- ments with a distinct distribution. Using actin-based pharmacological treatments and genetic mutants in combination with FRAP (fluorescence recovery after photobleaching) technology to visualize the transport of vesicles within the growth domain of pollen tubes, we demonstrated that cortical actin filaments facilitate tip-ward vesicle transport. We also discovered that the inner apical actin filaments prevent backward movement of vesicles, thus ensuring that sufficient vesicles accumulate at the pollen tube tip to support the rapid growth of the pollen tube. The combinatorial effect of cortical and internal apical actin filaments perfectly explains the generation of the inverted "V" cone-shaped vesicle distribution pattern at the pollen tube tip. When pollen tubes turn, apical actin filaments at the facing side undergo depolymerization and repolymerization to reorient the apical actin structure toward the new growth direction. This actin restructuring precedes vesicle accumulation and changes in tube morphology. Thus, our study provides new insights into the functional relationship between actin dynamics and vesicle transport during rapid and directional pollen tube growth.展开更多
About 25,000 rice T-DNA insertional mutant lines were generated using the vector pCAS04 which has both promoter-trapping and activation-tagging function. Southern blot analysis revealed that about 40% of these mutants...About 25,000 rice T-DNA insertional mutant lines were generated using the vector pCAS04 which has both promoter-trapping and activation-tagging function. Southern blot analysis revealed that about 40% of these mutants were single copy integration and the average T-DNA insertion number was 2.28. By extensive phenotyping in the field, quite a number of agronomically important mutants were obtained. Histochemical GUS assay with 4,310 primary mutants revealed that the GUS-staining frequency was higher than that of the previous reports in various tissues and especially high in flowers. The T-DNA flanking sequences of some mutants were isolated and the T-DNA insertion sites were mapped to the rice genome. The flanking sequence analysis demonstrated the different integration pattern of the right border and left border into rice genome. Compared with Arabidopsis and poplar, it is much varied in the T-DNA border junctions in rice.展开更多
In eukaryotes, the ubiquitin-mediated protein degradation pathway has been shown to control several key biological processes such as cell division, development, metabolism and immune response. F-box proteins, as a par...In eukaryotes, the ubiquitin-mediated protein degradation pathway has been shown to control several key biological processes such as cell division, development, metabolism and immune response. F-box proteins, as a part of SCF (Skp1-Cullin (or Cdc53)-F-box) complex, functioned by interacting with substrate proteins, leading to their subsequent degradation by the 26S proteasome. To date, several F-box proteins identified in Arabidopsis and Antirrhinum have been shown to play important roles in auxin signal transduction, floral organ formation, flowering and leaf senescence. Arabidopsis genome sequence analysis revealed that it encodes over 1000 predicted F-box proteins accounting for about 5% of total predicted proteins. These results indicate that the ubiquitin-mediated protein degradation involving the F-box proteins is an important mechanism controlling plant gene expression. Here, we review the known F-box proteins and their functions in flowering plants.展开更多
In the comparison with SARS-CoVof 2003,SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive.By the blind watchmaker arg...In the comparison with SARS-CoVof 2003,SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive.By the blind watchmaker argument,such an adaptive shift can only happen prior to the onset of the current pandemic and with the aid of step-by-step selection.展开更多
Background:The availability of vaccines provides a promising solution to contain the COVID-19 pandemic.However,it remains unclear whether the large-scale vaccination can succeed in containing the COVID-19 pandemic and...Background:The availability of vaccines provides a promising solution to contain the COVID-19 pandemic.However,it remains unclear whether the large-scale vaccination can succeed in containing the COVID-19 pandemic and how soon.We developed an epidemiological model named SUVQC(Suceptible-Unquarantined-Vaccined-Quarantined-Conflrmed)to quantitatively analyze and predict the epidemic dynamics of COVID-19 under vaccination.Methods:In addition to the impact of non-pharmaceutical interventions(NPIs),our model explicitly parameterizes key factors related to vaccination,including the duration of immunity,vaccine efficacy,and daily vaccination rate etc.The model was applied to the daily reported numbers of confirmed cases of Israel and the USA to explore and predict trends under vaccination based on their current epidemic statuses and intervention measures.We further provided a formula for designing a practical vaccination strategy,which simultaneously considers the effects of the basic reproductive number of COVID-19,intensity of NPIs,duration of immunological memory after vaccination,vaccine efficacy and daily vaccination rate.Results:In Israel,53.83%of the population is fully vaccinated,and under the current NPI intensity and vaccination scheme,the pandemic is predicted to end between May 14,2021,and May 16,2021,assuming immunity persists for 180 days to 365 days.If NPIs are not implemented after March 24,2021,the pandemic will end later,between July 4,2021,and August 26,2021.For the USA,if we assume the current vaccination rate(0.268%per day)and intensity of NPIs,the pandemic will end between January 20,2022,and October 19,2024,assuming immunity persists for 180 days to 365 days.However,assuming immunity persists for 180 days and no NPIs are implemented,the pandemic will not end and instead reach an equilibrium state,with a proportion of the population remaining actively infected.Conclusions:Overall,the daily vaccination rate should be decided according to vaccine efficacy and immunity duration to achieve herd immunity.In some situations,vaccination alone cannot stop the pandemic,and NPIs are necessary to supplement vaccination and accelerate the end of the pandemic.Considering that vaccine efficacy and duration of immunity may be reduced for new mutant strains,it is necessary to remain cautiously optimistic about the prospect of,ending the pandemic under vaccination.展开更多
Self-incompatibility is an intraspecific reproductive barrier to prevent self-fertilization inthe flowering plants. In many species, self-incompatibility is controlled by a single S locus with multiple alleles. So far...Self-incompatibility is an intraspecific reproductive barrier to prevent self-fertilization inthe flowering plants. In many species, self-incompatibility is controlled by a single S locus with multiple alleles. So far, the only gene known in the S locus of the Solanaceae, Scrophulariaceae and Rosaceae encodes a class of ribonucleases, called self-incompatibility ribonucleases (S RNases), which have been shown to mediate stylar expression of self-incompatible reaction. As the first step to investigate their three-dimensional structure, we successfully expressed three biologically active S RNases of Antirrihnum (S2, S4 and S5) in Escherichia coli (E. coli). Their functional expressions caused no detrimental effect on host bacteria growth and provided a basis for a large scale preparation of S RNase proteins. Possible reasons for non-lethality of S RNases on E. coliare discussed.展开更多
Plant root stem cells and their surrounding microenvironment,namely the stem cell niche,are hypersensitive to DNA damage.However,the molecular mechanisms that help maintain the genome stability of root stem cells rema...Plant root stem cells and their surrounding microenvironment,namely the stem cell niche,are hypersensitive to DNA damage.However,the molecular mechanisms that help maintain the genome stability of root stem cells remain elusive.Here we show that the root stem cells in the skbl(Shk1 kinase binding protein 1) mutant undergoes DNA damage-induced cell death,which is enhanced when combined with a lesion of the Ataxia-telangiectasia mutated(ATM) or the ATM/RAD3-related(ATR) genes,suggesting that the SKBI plays a synergistically effect with ATM and ATR in DNA damage pathway.We also provide evidence that SKBI is required for the maintenance of quiescent center(QC),a root stem cell niche,under DNA damage treatments.Furthermore,we report decreased and ectopic expression of SHORTROOT(SHR) in response to DNA damage in the skbl root tips,while the expression of SCARECROW(SCR) remains unaffected.Our results uncover a new mechanism of plant root stem cell maintenance under DNA damage conditions that requires SKB1.展开更多
COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Paki...COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.展开更多
In 2018, we will celebrate the 40th anniversary of Genetics Society of China (GSC), which was founded in Nanjing, China in October, 1978, soon after China adopted an open door policy for reform. One major mission of...In 2018, we will celebrate the 40th anniversary of Genetics Society of China (GSC), which was founded in Nanjing, China in October, 1978, soon after China adopted an open door policy for reform. One major mission of GSC during its inception was to publish a genetics journal, aiming to provide a window for Chinese geneticists to showcase their new discoveries. In fact, a genetics journal named Acta Genetica Sinica (AGS) had been published since June of 1974 (Fig. 1 ). This journal published two issues in its first year in Chinese. The first issue covered breeding and genetics of several crop plants, including wheat, tobacco, maize, octoploid triticale, peanut and upland cotton, protoplast isolation and fusion, observation of cell nuclei during mouse spermatogenesis, derivation of early season rice, etiology and pathogenesis of favism, a good collection of Chinese genetic studies then.展开更多
By re-analzying public metagenomic data from 101 patients infected with influenza A virus during the 2007–2012 H1N1 flu seasons in France,we identified 22 samples with SARS-CoV sequences.In three of them,the SARS gen...By re-analzying public metagenomic data from 101 patients infected with influenza A virus during the 2007–2012 H1N1 flu seasons in France,we identified 22 samples with SARS-CoV sequences.In three of them,the SARS genome sequences could be fully assembled out of each.These sequences are highly similar(99.99%and 99.70%)to the artificially constructed recombinant SARS-CoV(SARSr-CoV)strains generated by the J.Craig Venter Institute in the USA.Moreover,samples from different flu seasons have different SARS-CoV strains,and the divergence between these strains cannot be explained by natural evolution.Our study also shows that retrospective studies using public metagenomic data from past major epidemic outbreaks serve as a genomic strategy for the research of the origins or spread of infectious diseases.展开更多
基金the the National Basic Research Program (No. 2005CB120804) and Chinese Academy of Sciences.
文摘Drought is very harmful to grain yield due to its adverse effect on reproduction, especially on pollination process in rice. However, the molecular basis of such an effect still remains largely unknown. Here, we report the role of a member of CBL (Calcineurin B-Like) Interacting Protein Kinase (CIPK) family, OsCIPK23, in pollination and stress responses in rice. Molecular analyses revealed that it is mainly expressed in pistil and anther but up-regulated by pollination, as well as by treatments of various abiotic stresses and phytohormones. RNA interference-mediated suppression of OsCIPK23 expression significantly reduced seed set and conferred a hypersensitive response to drought stress, indicating its possible roles in pollination and drought stress. In consistent, overexpression of OsCIPK23 induced the expression of several drought tolerance related genes. Taken together, these results indicate that OsCIPK23 is a multistress induced gene and likely mediates a signaling pathway commonly shared by both pollination and drought stress responses in rice.
文摘In 2003, the International Solanaceae Project (SOL) was initiated by an international consortium of ten countries including Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States. The first major effort of the SOL aimed to produce a DNA sequence map for euchromatin regions of 12 chromosomes of tomato (Solanum lycopersicum) before 2010. Here we present an update on Chinese effort for sequencing the euchromatin region of chromosome 3.
文摘 To discover genes essential for agronomic performances of crops we initiated a program on rice functional genomics of important agronomic traits in rice in 1999. The program was funded by the Ministry of Science and Technology of China through the National Basic Research Initiative and is expected to last for five years.
……
基金supported by the National Natural Science Foundation of China(32030007)the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27010302).
文摘Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in angiosperms.The SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box(SLF)genes found in the Solanaceae,Plantaginaceae,Rosaceae,and Rutaceae.Recent studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box(SCF)SLF-mediated ubiquitin–proteasome system in a collaborative manner in Petunia,but how self-RNase functions largely remains mysterious.Here,we show that S-RNases form S-RNase condensates(SRCs)in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia hybrida.We further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs,which then sequester several actin-binding proteins,including the actin polymerization factor PhABRACL,the actin polymerization activity of which is reduced by S-RNase in vitro.Meanwhile,we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth inhibition.Taken together,our results demonstrate that phase separation of S-RNase promotes SI response in P.hybrida,revealing a new mode of S-RNase action.
基金funded by the“Strategic Priority Research Program”of CAS(Grant No.XDB38030200)the Open Biodiversity and Health Big Data Programme of International Union of Biological Sciences awarded to YB.
文摘Background Big data challenges In the late 1980s and early 1990s,three major international biological data centers were created:the DNA Database of Japan(DDBJ)[1],the European Bioinformatics Institute(EMBL-EBI)in the United Kingdom(UK)[2],and the National Center for Biotechnology Information(NCBI)in the United States(US)[3].
基金supported by the Chinese Academy of Sciences “Strategic Priority Research Program” fund (XDA08020302)grants from State Key Laboratory of Plant Genomics。
文摘Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.
基金This work was supported by grants from the Strategic PriorityResearch Program of Chinese Academy of Sciences(GrantNos.XDA19090116,XDA19050302,and XDB38030400)awarded to SS,ZZ,and MLthe National Key R&D Programof China(Grant Nos.2020YFC0848900,2020YFC0847000,2016YFE0206600,and 2017YFC0907502)+5 种基金the 13th Five-yearInformatization Plan of Chinese Academy of Sciences(GrantNo.XXH13505-05)Genomics Data Center Construction ofChinese Academy of Sciences(Grant No.XXH-13514-0202)the Open Biodiversity and Health Big Data Programme ofInternational Union of Biological Sciences,International Part-nership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008)the Professional Association of theAlliance of International Science Organizations(Grant No.ANSO-PA-2020-07)This work was also supported by KCWong Education Foundation to ZZthe YouthInnovation Promotion Association of Chinese Academy ofSciences(Grant Nos.2017141 and 2019104)awarded to SSand ML.
文摘On January 22,2020,China National Center for Bioinformation(CNCB)released the 2019 Novel Coronavirus Resource(2019nCoVR),an open-access information resource for the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates,which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline.Of particular note,2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale.It provides all identified variants and their detailed statistics for each virus isolate,and congregates the quality score,functional annotation,and population frequency for each variant.Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available.Moreover,2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019(COVID-19),including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC.Furthermore,by linking with relevant databases in CNCB,2019nCoVR offers data submission services for raw sequence reads and assembled genomes,and data sharing with NCBI.Collectively,SARS-CoV-2 is updated daily to collect the latest information on genome sequences,variants,haplotypes,and literature for a timely reflection,making 2019nCoVR a valuable resource for the global research community.2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.
基金supported by the National Basic Research Program of China(973 Program)(Nos.2007CB108703 and 2011CB915404)the National Natural Science Foundation of China(No.30921003)
文摘In flowering plants, self-incompatibility (SI) serves as an important intraspecific reproductive barrier to promote outbreeding. In species from the Solanaceae, Plantaginaceae and Rosaceae, S-RNase and SLF (S-locus F-box) proteins have been shown to control the female and male specificity of SI, respectively. However, little is known about structure features of the SLF protein apart from its conserved F-box domain. Here we show that the SLF C-terminal region possesses a novel ubiquitin-binding domain (UBD) structure conserved among the SLF protein family. By using an ex vivo system of Nicotiana benthamiana, we found that the UBD mediates the SLF protein turnover by the ubiquitin-proteasome pathway. Furthermore, we detected that the SLF protein was directly involved in S-RNase degradation. Taken together, our results provide a novel insight into the SLF structure and highlight a potential role of SLF protein stability and degradation in S-RNase-based self-incompatibility.
基金This study was supported by the National Key R&D Program of China(Grant No.2020YFC0847000)the National Natural Science Foundation of China(Grant Nos.31571370,91731302,and 31772435).
文摘A novel RNA virus,the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is responsible for the ongoing outbreak of coronavirus disease 2019(COVID-19).Population genetic analysis could be useful for investigating the origin and evolutionary dynamics of COVID-19.However,due to extensive sampling bias and existence of infection clusters during the epidemic spread,direct applications of existing approaches can lead to biased parameter estimations and data misinterpretation.In this study,we first present robust estimator for the time to the most recent common ancestor(TMRCA)and the mutation rate,and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2.The mutation rate is inferred to be 8.69×10^(−4) per site per year with a 95%confidence interval(CI)of[8.61×10^(−4),8.77×10^(−4)],and the TMRCA of the samples inferred to be Nov 28,2019 with a 95%CI of[Oct 20,2019,Dec 9,2019].The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market.We further demonstrate that genetic polymorphism patterns,including the enrichment of specific haplotypes and the temporal allele frequency trajectories generated from infection clusters,are similar to those caused by evolutionary forces such as natural selection.Our results show that population genetic methods need to be developed to efficiently detangle the effects of sampling bias and infection clusters to gain insights into the evolutionary mechanism of SARS-CoV-2.Software for implementing VirusMuT can be downloaded at https://bigd.big.ac.cn/biocode/tools/BT007081.
基金This work was supported by grants from the Ministry of Science and Technology of China (2013CB945100) and the National Natural Science Foundation of China (31671390 and 31471266). X.Q. was supported by post-doctoral fellowships from Tsinghua-Peking Joint Center for Life Sciences and the China Postdoctoral Science Foundation (grant no. 2015M571028).
文摘Polarized tip growth is a fundamental cellular process in many eukaryotes. In this study, we examined the dynamic restructuring of the actin cytoskeleton and its relationship to vesicle transport during pollen tip growth in Arabidopsis. We found that actin filaments originating from the apical membrane form a specialized structure consisting of longitudinally aligned actin bundles at the cortex and inner cytoplasmic fila- ments with a distinct distribution. Using actin-based pharmacological treatments and genetic mutants in combination with FRAP (fluorescence recovery after photobleaching) technology to visualize the transport of vesicles within the growth domain of pollen tubes, we demonstrated that cortical actin filaments facilitate tip-ward vesicle transport. We also discovered that the inner apical actin filaments prevent backward movement of vesicles, thus ensuring that sufficient vesicles accumulate at the pollen tube tip to support the rapid growth of the pollen tube. The combinatorial effect of cortical and internal apical actin filaments perfectly explains the generation of the inverted "V" cone-shaped vesicle distribution pattern at the pollen tube tip. When pollen tubes turn, apical actin filaments at the facing side undergo depolymerization and repolymerization to reorient the apical actin structure toward the new growth direction. This actin restructuring precedes vesicle accumulation and changes in tube morphology. Thus, our study provides new insights into the functional relationship between actin dynamics and vesicle transport during rapid and directional pollen tube growth.
基金supported by the National High Technology Research and Development Program of China (No.2002AAZ2001)the National Natural Sciences Foundation of China (No.30270758 and 30621001)
文摘About 25,000 rice T-DNA insertional mutant lines were generated using the vector pCAS04 which has both promoter-trapping and activation-tagging function. Southern blot analysis revealed that about 40% of these mutants were single copy integration and the average T-DNA insertion number was 2.28. By extensive phenotyping in the field, quite a number of agronomically important mutants were obtained. Histochemical GUS assay with 4,310 primary mutants revealed that the GUS-staining frequency was higher than that of the previous reports in various tissues and especially high in flowers. The T-DNA flanking sequences of some mutants were isolated and the T-DNA insertion sites were mapped to the rice genome. The flanking sequence analysis demonstrated the different integration pattern of the right border and left border into rice genome. Compared with Arabidopsis and poplar, it is much varied in the T-DNA border junctions in rice.
基金This work was supported by the National Natural Science Foundation of China (Grant No. 39825103)the Chinese Academy of Sciences.
文摘In eukaryotes, the ubiquitin-mediated protein degradation pathway has been shown to control several key biological processes such as cell division, development, metabolism and immune response. F-box proteins, as a part of SCF (Skp1-Cullin (or Cdc53)-F-box) complex, functioned by interacting with substrate proteins, leading to their subsequent degradation by the 26S proteasome. To date, several F-box proteins identified in Arabidopsis and Antirrhinum have been shown to play important roles in auxin signal transduction, floral organ formation, flowering and leaf senescence. Arabidopsis genome sequence analysis revealed that it encodes over 1000 predicted F-box proteins accounting for about 5% of total predicted proteins. These results indicate that the ubiquitin-mediated protein degradation involving the F-box proteins is an important mechanism controlling plant gene expression. Here, we review the known F-box proteins and their functions in flowering plants.
文摘In the comparison with SARS-CoVof 2003,SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive.By the blind watchmaker argument,such an adaptive shift can only happen prior to the onset of the current pandemic and with the aid of step-by-step selection.
基金This study was supported by the National Key R&D Program of China(No.2020YFC0847000)the National Natural Science Foundation of China(Nos.31571370,91731302 and 31772435).
文摘Background:The availability of vaccines provides a promising solution to contain the COVID-19 pandemic.However,it remains unclear whether the large-scale vaccination can succeed in containing the COVID-19 pandemic and how soon.We developed an epidemiological model named SUVQC(Suceptible-Unquarantined-Vaccined-Quarantined-Conflrmed)to quantitatively analyze and predict the epidemic dynamics of COVID-19 under vaccination.Methods:In addition to the impact of non-pharmaceutical interventions(NPIs),our model explicitly parameterizes key factors related to vaccination,including the duration of immunity,vaccine efficacy,and daily vaccination rate etc.The model was applied to the daily reported numbers of confirmed cases of Israel and the USA to explore and predict trends under vaccination based on their current epidemic statuses and intervention measures.We further provided a formula for designing a practical vaccination strategy,which simultaneously considers the effects of the basic reproductive number of COVID-19,intensity of NPIs,duration of immunological memory after vaccination,vaccine efficacy and daily vaccination rate.Results:In Israel,53.83%of the population is fully vaccinated,and under the current NPI intensity and vaccination scheme,the pandemic is predicted to end between May 14,2021,and May 16,2021,assuming immunity persists for 180 days to 365 days.If NPIs are not implemented after March 24,2021,the pandemic will end later,between July 4,2021,and August 26,2021.For the USA,if we assume the current vaccination rate(0.268%per day)and intensity of NPIs,the pandemic will end between January 20,2022,and October 19,2024,assuming immunity persists for 180 days to 365 days.However,assuming immunity persists for 180 days and no NPIs are implemented,the pandemic will not end and instead reach an equilibrium state,with a proportion of the population remaining actively infected.Conclusions:Overall,the daily vaccination rate should be decided according to vaccine efficacy and immunity duration to achieve herd immunity.In some situations,vaccination alone cannot stop the pandemic,and NPIs are necessary to supplement vaccination and accelerate the end of the pandemic.Considering that vaccine efficacy and duration of immunity may be reduced for new mutant strains,it is necessary to remain cautiously optimistic about the prospect of,ending the pandemic under vaccination.
文摘Self-incompatibility is an intraspecific reproductive barrier to prevent self-fertilization inthe flowering plants. In many species, self-incompatibility is controlled by a single S locus with multiple alleles. So far, the only gene known in the S locus of the Solanaceae, Scrophulariaceae and Rosaceae encodes a class of ribonucleases, called self-incompatibility ribonucleases (S RNases), which have been shown to mediate stylar expression of self-incompatible reaction. As the first step to investigate their three-dimensional structure, we successfully expressed three biologically active S RNases of Antirrihnum (S2, S4 and S5) in Escherichia coli (E. coli). Their functional expressions caused no detrimental effect on host bacteria growth and provided a basis for a large scale preparation of S RNase proteins. Possible reasons for non-lethality of S RNases on E. coliare discussed.
文摘Plant root stem cells and their surrounding microenvironment,namely the stem cell niche,are hypersensitive to DNA damage.However,the molecular mechanisms that help maintain the genome stability of root stem cells remain elusive.Here we show that the root stem cells in the skbl(Shk1 kinase binding protein 1) mutant undergoes DNA damage-induced cell death,which is enhanced when combined with a lesion of the Ataxia-telangiectasia mutated(ATM) or the ATM/RAD3-related(ATR) genes,suggesting that the SKBI plays a synergistically effect with ATM and ATR in DNA damage pathway.We also provide evidence that SKBI is required for the maintenance of quiescent center(QC),a root stem cell niche,under DNA damage treatments.Furthermore,we report decreased and ectopic expression of SHORTROOT(SHR) in response to DNA damage in the skbl root tips,while the expression of SCARECROW(SCR) remains unaffected.Our results uncover a new mechanism of plant root stem cell maintenance under DNA damage conditions that requires SKB1.
基金supported by grants from the National Key R&D Program of China(Grant Nos.2021YFC0863300,2020YFC0848900,and 2016YFE0206600)the National Natural Science Foundation of China(Grant No.82161148009)+3 种基金the Strategic Priority Research Program of Chinese Academy of Sciences,China(Grant Nos.XDA19090116 and XDB38060100)the Open Biodiversity and Health Big Data Programme of International Union of Biological Sciences,International Partnership Program of Chinese Academy of Sciences(Grant No.153F11KYSB20160008)the Professional Association of the Alliance of International Science Organizations(Grant No.ANSO-PA-2020-07)the Youth Innovation Promotion Association of Chinese Academy of Sciences(Grant No.2017141)。
文摘COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control.
文摘In 2018, we will celebrate the 40th anniversary of Genetics Society of China (GSC), which was founded in Nanjing, China in October, 1978, soon after China adopted an open door policy for reform. One major mission of GSC during its inception was to publish a genetics journal, aiming to provide a window for Chinese geneticists to showcase their new discoveries. In fact, a genetics journal named Acta Genetica Sinica (AGS) had been published since June of 1974 (Fig. 1 ). This journal published two issues in its first year in Chinese. The first issue covered breeding and genetics of several crop plants, including wheat, tobacco, maize, octoploid triticale, peanut and upland cotton, protoplast isolation and fusion, observation of cell nuclei during mouse spermatogenesis, derivation of early season rice, etiology and pathogenesis of favism, a good collection of Chinese genetic studies then.
基金supported by the National Key R&D Program of China(2021YFC0863400)the Key Program of Chinese Academy of Sciences(KJZD-SW-L14)the National Natural Science Foundation of China(Grant No.31571370 and 91731302).
文摘By re-analzying public metagenomic data from 101 patients infected with influenza A virus during the 2007–2012 H1N1 flu seasons in France,we identified 22 samples with SARS-CoV sequences.In three of them,the SARS genome sequences could be fully assembled out of each.These sequences are highly similar(99.99%and 99.70%)to the artificially constructed recombinant SARS-CoV(SARSr-CoV)strains generated by the J.Craig Venter Institute in the USA.Moreover,samples from different flu seasons have different SARS-CoV strains,and the divergence between these strains cannot be explained by natural evolution.Our study also shows that retrospective studies using public metagenomic data from past major epidemic outbreaks serve as a genomic strategy for the research of the origins or spread of infectious diseases.