生命与健康大数据中心资源

生命与健康多组学数据是生命科学研究和生物医学技术发展的重要基础。然而,我国缺乏生物数据管理和共享平台,不但无法满足国内日益增长的生物医学及相关学科领域的研究发展需求,而且严重制约我国生物大数据整合共享与转化利用。鉴于此,中国科学院北京基因组研究所于2016年初成立生命与健康大数据中心(BIG Data Center,BIGD),围绕国家人口健康和重要战略生物资源,建立生物大数据管理平台和多组学数据资源体系。本文重点介绍BIGD的生命与健康大数据资源系统,主要包括组学原始数据归档库、基因组数据库、基因组变异数据库、基因表达数据库、甲基化数据库、生物信息工具库和生命科学维基知识库,提供生物大数据汇交、整合与共享服务,为促进我国生命科学数据管理、推动国家生物信息中心建设奠定重要基础。

Crustal velocity structure of central Gansu Province from regional seismic waveform inversion using firework algorithm

The firework algorithm（FWA） is a novel swarm intelligence-based method recently proposed for the optimization of multi-parameter, nonlinear functions. Numerical waveform inversion experiments using a synthetic model show that the FWA performs well in both solution quality and efficiency. We apply the FWA in this study to crustal velocity structure inversion using regional seismic waveform data of central Gansu on the northeastern margin of the Qinghai-Tibet plateau. Seismograms recorded from the moment magnitude（MW） 5.4 Minxian earthquake enable obtaining an average crustal velocity model for this region. We initially carried out a series of FWA robustness tests in regional waveform inversion at the same earthquake and station positions across the study region,inverting two velocity structure models, with and without a low-velocity crustal layer; the accuracy of our average inversion results and their standard deviations reveal the advantages of the FWA for the inversion of regional seismic waveforms. We applied the FWA across our study area using three component waveform data recorded by nine broadband permanent seismic stations with epicentral distances ranging between 146 and 437 km. These inversion results show that the average thickness of the crust in this region is 46.75 km, while thicknesses of the sedimentary layer, and the upper, middle, and lower crust are 3.15,15.69, 13.08, and 14.83 km, respectively. Results also show that the P-wave velocities of these layers and the upper mantle are 4.47, 6.07, 6.12, 6.87, and 8.18 km/s,respectively.

Amplitude variation characteristics of active source airgun signals at Qilian Mountain

In this study,Qilian Mountain active source airgun signals recorded at 79 stations were obtained after stacking waveforms from July 2015 to December 2016.Based on analysis of the amplitude variation characteristics of the airgun signals,the following conclusions were drawn:along the NW-SE fault distribution direction of the Qilian Mountain area,the decrease in amplitude of airgun signals was relatively slow in relation to the epicentral distance,while the decrease in amplitude in the direction perpendicular to the fault was relatively fast.This difference may be related to the energy loss of seismic waves reflecting and scattering by the regional faults mainly distributed along the NW-SE direction,which are caused by tectonic compression of the QinghaiTibet and Alxa blocks.

IC4R-2.0:Rice Genome Reannotation Using Massive RNA-seq Data

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function.Although the availability of massive RNA-seq data provides great opportunities for gene model refinement,few efforts have been made to adopt these precious data in rice genome reannotation.Here we reannotate the rice(Oryza sativa L.ssp.japonica)genome based on integration of large-scale RNA-seq data and release a new annotation system IC4 R-2.0.In general,IC4 R-2.0 significantly improves the completeness of gene structure,identifies a number of novel genes,and integrates a variety of functional annotations.Furthermore,long non-coding RNAs(lncRNAs)and circular RNAs(circRNAs)are systematically characterized in the rice genome.Performance evaluation shows that compared to previous annotation systems,IC4 R-2.0 achieves higher integrity and quality,primarily attributable to massive RNA-seq data applied in genome annotation.Consequently,we incorporate the improved annotations into the Information Commons for Rice(IC4 R),a database integrating multiple omics data of rice,and accordingly update IC4 R by providing more user-friendly web interfaces and implementing a series of practical online tools.Together,the updated IC4 R,which is equipped with the improved annotations,bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species.The IC4 R-2.0 annotation system and related resources are freely accessible at http://ic4 r.org/.

Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades

COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months,and a global fight against both has been intensifying.Here,we describe an analysis procedure where genome composition and its variables are related,through the genetic code to molecular mechanisms,based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on the replicase-transcriptase complex.Our analysis starts with primary sequence information,identity-based phylogeny based on 22,051 SARS-CoV-2 sequences,and evaluation of sequence variation patterns as mutation spectra and its 12 permutations among organized clades.All are tailored to two key mechanisms:strand-biased and function-associated mutations.Our findings are listed as follows:1)The most dominant mutation is C-to-U permutation,whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity,albeit assumed most slightly deleterious.2)The second abundance group includes three negative-strand mutations(U-to-C,A-to-G,and G-to-A)and a positive-strand mutation(G-to-U)due to DNA repair mechanisms after cellular abasic events.3)A clade-associated biased mutation trend is found attributable to elevated level of negative-sense strand synthesis.4)Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes.These findings demand a platform where emerging mutations are mapped onto mostly subtle but fast-adjusting viral proteomes and transcriptomes,to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications.Such actions are in desperate need,especially in the middle of the War against COVID-19.

Constraining the characters of the upper mantle discontinuities beneath the NE margin of the Tibetan Plateau with a dense broadband seismic array

Based on observations from a dense broadband seismic array located along the northeastern (NE) margin of the Tibetan Plateau in southeastern Gansu Province,we use receiver functions (RFs) to pick the arrival times of P-to-S converted waves and bin the traces in different grids according to the piercing points of the 410 and 660 km discontinuities in the upper mantle.The depths of the two discontinuities are estimated by the ray tracing method with the IASP91 velocity model and a 3-D tomography model.The results indicate the following:(1) The arrival times of the P410s and P660s converted phases are delayed by approximately 1 s than those predicted by the IASP91 model.The mantle transition zone (MTZ) is thicker than that in the global model.(2) The synchronous lags in the P410s and P660s arrival times are consistent with low-velocity anomalies in the upper mantle,which are believed to result mainly from the eastward migration of materials beneath the NE margin of the Tibetan Plateau.(3) Combined with previous tomography results,the depression of the'660'discontinuity and the thickened MTZ are somewhat consistent with the big mantle wedge (BMW) model.However,due to data limitations,more studies are required to explore the BMW in the future.