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。

Plant genomic resources at National Genomics Data Center:assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among species.Through various efforts in genomic data archiving,integrative analysis and value-added curation,the National Genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database resources.This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts.Here,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application tools.We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

SoyOmics:A deeply integrated database on soybean multi-omics

Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired.

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/.

Rice Genomics: over the Past Two Decades and into the Future

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

Genomic Epidemiology of SARS-CoV-2 in Pakistan

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.