2019新型冠状病毒信息库

2019年12月在中国武汉开始爆发的新型肺炎已造成全球25个国家/地区的31516人感染、638人死亡(截止2020年2月7日16时),引起该肺炎的病毒被世界卫生组织命名为2019新型冠状病毒(2019-nCoV)。为促进2019-nCoV数据共享应用并及时向全球公众提供病毒的相关信息,国家生物信息中心(CNCB)/国家基因组科学数据中心(NGDC)建立了2019新型冠状病毒信息库(2019nCoVR,https://bigd.big.ac.cn/ncov)。该信息库整合了来自德国全球流感病毒数据库、美国国家生物技术信息中心、深圳(国家)基因库、国家微生物科学数据中心及CNCB/NGDC等机构公开发布的2019-nCoV核苷酸和蛋白质序列数据、元信息、学术文献、新闻动态、科普文章等信息,开展了不同冠状病毒株的基因组序列变异分析并提供可视化展示。同时,2019nCoVR无缝对接CNCB/NGDC的相关数据库,提供新测序病毒株系的基因组原始测序数据、组装后序列的在线汇交、管理与共享、国际数据库同步发布等数据服务。本文对2019nCoVR数据汇交、管理、发布及使用等进行全面阐述,以方便用户了解该信息库各项功能及数据状况,为加速开展病毒的分类溯源、变异演化、快速检测、药物研发以及新型肺炎的精准预防与治疗等研究提供重要基础。

Calcineurin B-like interacting protein kinase OsCIPK23 functions in pollination and drought stress responses in rice (Oryza sativa L.)

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.

A snapshot of the Chinese SOL Project

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.

中国水稻功能基因组学研究计划介绍

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. ……

From BIG Data Center to China National Center for Bioinformation

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].

Identification of a Ubiquitin-Binding Structure in the S-Locus F-Box Protein Controlling S-RNase-Based Self-Incompatibility

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.

Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions

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.

The Global Landscape of SARS-CoV-2 Genomes, Variants, and Haplotypes in 2019nCoVR

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/.

F-box proteins in flowering plants

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.

Organizational Innovation of Apical Actin Filaments Drives Rapid Pollen Tube Growth and Turning

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.

Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system

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.

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters

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.

On the origin of SARS-CoV-2——The blind watchmaker argument

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.

Expression of self-incompatibility ribonucleases of Antirrhinum in Escherichia coli

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.

The Protein Arginine Methylase 5(PRMT5/SKB1) Gene Is Required for the Maintenance of Root Stem Cells in Response to DNA Damage

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.

The Chinese garden of genetics --celebrating 40th anniversary of Genetics Society of China

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.

Will the large-scale vaccination succeed in containing the COVID-19 pandemic and how soon?

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.

Metagenomic evidence for the co-existence of SARS and H1N1 in patients from 2007-2012 flu seasons in France

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.

Rice 2020： A Call For An International Coordinated Effort In Rice Functional Genomics

We describe a call for an international coordinated effort in rice functional genomics in the form of a project named RICE2020. The mission of the project will be： to determine the function of every gene in the rice genome by the year 2020, to identify functional diversity of alleles for agriculturally useful genes from the primary gene pool of rice, and to apply the findings of functional genomics research to rice genetic improvement.

OsGRAS19 May Be a Novel Component Involved in the Brassinosteroid Signaling Pathway in Rice

Dear Editor, The brassinosteroid （BR） signaling pathway has been well elucidated in Arabidopsis. The identification of BR-signaling components in rice suggested that the primary pathway is conserved in both dicot and monocot plants. However,