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

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Genomics, Proteomics & Bioinformatics 2020年第6期18卷 648-663页

作者： Xufei Teng Qianpeng Li Zhao Li Yuansheng Zhang Guangyi Niu jingfa xiao Jun Yu Zhang Zhang Shuhui Song China National Center for Bioinformation Beijing 100101China National Genomics Data Center&CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

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 ***,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 *** 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 *** are tailored to two key mechanisms:strand-biased and function-associated *** 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 *** 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 *** actions are in desperate need,especially in the middle of the War against COVID-19.

关键词： SARS-CoV-2 Nucleotide composition Mutation spectrum Viral replication

Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

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Science China(Life Sciences) 2014年第3期57卷 340-355页

作者： ZHOU YuanYuan GONG Wei xiao jingfa WU JiaYan PAN LinLin LI xiaoNuan WANG XuMin WANG WeiWei HU SongNian YU Jun Beijing Key Laboratory of Genome and Precision Medicine Technologies CAS Key Laboratory of Genome Sciences and InformationBeijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Division of Gastroenterology Department of MedicineUniversity of Alberta

An organ unique to mammals,the mammary gland develops 90%of its mass after birth and experiences the pregnancy-lactation-involution cycle(PL cycle)during *** understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol,we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy(day 12 of pregnancy),lactation(day 14 of lactation),and involution(day 7 of involution).The pregnancy-,lactation-and involution-related sequencing reads were assembled into 17344,10160,and 13739 protein-coding transcripts and1803,828,and 1288 non-coding RNAs(ncRNAs),*** expressed genes(DEGs)were defined in the three samples,which comprised 4843 DEGs(749 up-regulated and 4094 down-regulated)from pregnancy to lactation and4926 DEGs(4706 up-regulated and 220 down-regulated)from lactation to *** the obvious and substantive upand down-regulation of the DEGs,we observe that lysosomal enzymes were highly expressed and that their expression coincided with milk *** analysis of transcription factors such as Trps1,Gtf2i,Tcf7l2,Nupr1,Vdr,Rb1,and Aebp1,and ncRNAs such as mir-125b,Let7,mir-146a,and mir-15 has enabled us to identify key regulators in mammary gland development and the PL cycle.

关键词：转录水平哺乳期周期怀孕差异表达基因非编码RNA 组分动物乳腺

Systematic analysis of intron size and abundance parameters in diverse lineages

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Science China(Life Sciences) 2013年第10期56卷 968-974页

作者： WU JiaYan xiao jingfa WANG LingPing ZHONG Jun YIN HongYan WU ShuangXiu ZHANG Zhang YU Jun Key Lab of Genomics Science and Information Chinese Academy of Sciences Beijing Institute of Genomics Chinese Academy of Sciences University of Chinese Academy of Sciences

All eukaryotic genomes have genes with introns in variable *** far as spliceosomal introns are concerned,there are at least three basic parameters to stratify introns across diverse eukaryotic taxa:size,number,and sequence *** number parameter is highly variable in lower eukaryotes,especially among protozoan and fungal species,which ranges from less than4%to 78%of the *** greater evolutionary time scales,the number parameter undoubtedly increases as observed in higher plants and higher vertebrates,reaching greater than 12.5 exons per gene in average among mammalian *** size parameter is more complex,where multiple modes appear at *** from intronless genes,there are three other types of intron-containing genes:half-sized,minimal,and size-expandable *** half-sized introns have only been found in a limited number of genomes among protozoan and fungal lineages and the other two types are prevalent in all animal and plant *** the size-expandable introns,the sizes of plant introns are expansion-limited in that the large introns exceeding 1000 bp are fewer in numbers and transposon-free as compared to the large introns among animals,where the larger introns are filled with transposable elements and appear expansion-flexible,reaching several kilobasepairs(kbp)and even thousands of kbp in *** of the intron parameters can be studied as signatures of the specific splicing machineries of different eukaryotic lineages and are highly relevant to the regulation of gene expression and *** particular,the transcription-splicing-export coupling of eukaryotic intron dispensing leads to a working hypothesis that all intron parameters are evolved to be efficient and function-related in processing and routing the spliced transcripts.

关键词：细胞谱系内含子动物基因组生物基因真核生物系统脊椎动物高等植物

Transcriptome-wide evolutionary analysis on essential brown algae(Phaeophyceae)in China

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Acta Oceanologica Sinica 2014年第2期33卷 13-19页

作者： SUN Jing WANG Liang WU Shuangxiu WANG Xumin xiao jingfa CHI Shan LIU Cui REN Lufeng ZHAO Yuhui LIU Tao YU Jun CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Brown algae （Chromista, Ochrophyta, Phaeophyceae） are a large group of multicellular algae that play im-portant roles in the ocean＇s ecosystem and biodiversity. However, poor molecular bases for studying their phylogenetic evolutions and novel metabolic characteristics have hampered progress in the field. In this study, we sequenced the de novo transcriptome of 18 major species of brown algae in China, covering six orders and seven families, using the high-throughput sequencing platform Illumina HiSeq 2000. From the transcriptome data of these 18 species and publicly available genome data of Ectocarpus siliculosus and Phaeodactylum tricornutum, we identified 108 nuclear-generated orthologous genes and clarified the phy-logenetic relationships among these brown algae based on a multigene method. These brown algae could be separated into two clades：Clade Ishigeales-Dictyotales and Clade Ectocarpales-Laminariales-Desmares-tiale-Fucales. The former was at the base of the phylogenetic tree, indicating its early divergence, while the latter was divided into two branches, with Order Fucales diverging from Orders Ectocarpales, Laminariales, and Desmarestiale. In our analysis of taxonomy-contentious species, Sargassum fusiforme and Saccharina sculpera were found to be closely related to genera Sargassum and Saccharina, respectively, while Petalonia fascia showed possible relation to genus Scytosiphon. The study provided molecular evidence for the phylo-genetic taxonomy of brown algae.

关键词： Phaeophyceae transcriptome sequencing multigene phylogeny

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浅谈船舶腐蚀及防护

船电技术 2023年第10期43卷 57-60页

作者：肖敬发江南造船(集团)有限责任公司上海200082

文章将船舶腐蚀分为三个区域:船舶水下腐蚀区域、船舶水上腐蚀区域及海洋环境腐蚀区域,介绍了腐蚀的原因。针对船舶不同腐蚀区域采取的涂层保护及电化学保护两种保护措施,具有实用价值。

关键词：船舶腐蚀防护

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深海直升机平台强度分析

船电技术 2023年第9期43卷 14-17页

作者：肖敬发江南造船(集团)有限责任公司上海200082

以某海上直升式钻井平台为例,对直升机平台结构进行有限元分析,分别对直升机正常降落工况,受恶劣环境影响下偏向降落工况,直升机着陆冲击工况及直升机系留工况下的直升机平台结构强度,变形及重要节点的疲劳进行了分析,整个计算采用Femap... 详细信息

以某海上直升式钻井平台为例,对直升机平台结构进行有限元分析,分别对直升机正常降落工况,受恶劣环境影响下偏向降落工况,直升机着陆冲击工况及直升机系留工况下的直升机平台结构强度,变形及重要节点的疲劳进行了分析,整个计算采用Femap&***软件生成有限元模型模拟工作情况并进行有效分析,分析结果显示直升机平台和支撑结构的安全性及承受能力非常优越。

关键词：直升机平台自升式钻井平台强度有限元分析

A brief review on the evolution of GPCR: conservation and diversification

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Open Journal of Genetics 2012年第4期2卷 11-17页

作者： Zaichao Zhang Jiayan Wu Jun Yu jingfa xiao CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing China College of Life Science Graduate University of Chinese Academy of Sciences Beijing China

G-protein couple receptors (GPCR) possess diversified functions and they comprise a large protein superfamily in cellular signaling. Numerous identification methods for GPCR have been employed and versatile GPCR types are discussed. Although they share conserved transmembrane structural topology, alignment results of all GPCR show no significant sequence similarities. Each GPCR type distributes diversely in different evolutionary hierarchies of eukaryotes, but it has a distinctive boundary in the era of metazoan. The common ancestor of GPCR metabotropic glutamate receptor includes 7-transmembrane structure and venus flytrap module, which is probably evolved from a compound of bacteriorhodopsin and periplasmic binding protein. Many investigations focus on fine structure shaping and GPCR classification. Here, we briefly discuss evolutionary dynamic mechanism of GPCR from the perspective of classification, diversification and conservation.

关键词： GPCR Evolution Classification Diversification Conservation

Genome Warehouse: A Public Repository Housing Genome-scale Data

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Genomics, Proteomics & Bioinformatics 2021年第4期19卷 584-589页

作者： Meili Chen Yingke Ma Song Wu Xinchang Zheng Hongen Kang Jian Sang Xingjian Xu Lili Hao Zhaohua Li Zheng Gong jingfa xiao Zhang Zhang Wenming Zhao Yiming Bao National Genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences/China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Division of Cancer Epidemiology and Genetics National Cancer InstituteNational Institutes of Health.Bethesda.MD 20X92.USA College of Computer Science Technology Inner Mongolia Normal UniversityHohhot 010010China

The Genome Warehouse(GWH)is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission,storage,release,and *** one of the core resources in the National Genomics Data Center(NGDC),part of the China National Center for Bioinformation(CNCB;https://***),GWH accepts both full and partial(chloroplast,mitochondrion,and plasmid)genome sequences with different assembly levels,as well as an update of existing genome *** each assembly,GWH collects detailed genome-related metadata of biological project,biological sample,and genome assembly,in addition to genome sequence and *** archive high-quality genome sequences and annotations,GWH is equipped with a uniform and standardized procedure for quality *** basic browse and search functionalities,all released genome sequences and annotations can be visualized with *** May 21,2021,GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of ***,GWH serves as an important resource for genomescale data management and provides free and publicly accessible data to support research activities throughout the *** is publicly accessible at https://***/gwh.

关键词： Genome submission Genome sequence Genome annotation Genome Warehouse Quality control

VTwins:有限宏基因组样本推断疾病致病微生物特征

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Science Bulletin 2023年第22期68卷 2806-2816,M0006页

作者：孟庆仁周茜时硕肖景发马勤于军陈军康禹 CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences and China National Center for BioinformationBeijing 100101China School of Medicine Southern University of Science and TechnologyShenzhen 518055China National Clinical Research Center for Infectious Diseases The Third People’s Hospital of ShenzhenThe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen 518100China International Cancer Center Shenzhen University Medical SchoolShenzhen 518055China Department of Biomedical Informatics The Ohio State UniversityColumbus OH 43210USA University of Chinese Academy of Sciences Beijing 100190China

从高维、高变宏基因组数据中挖掘与疾病强关联的微生物特征是人体微生态研究的一大难题.受遗传学双生子研究的启发,本文开发了一种新型微生物特征挖掘算法——虚拟双胞胎(VTwins)算法.该算法通过将原始队列转化为具有相近的微生物组特... 详细信息

从高维、高变宏基因组数据中挖掘与疾病强关联的微生物特征是人体微生态研究的一大难题.受遗传学双生子研究的启发,本文开发了一种新型微生物特征挖掘算法——虚拟双胞胎(VTwins)算法.该算法通过将原始队列转化为具有相近的微生物组特征但分组不同的配对样本形成的配对队列来消除混淆因素的影响.结果显示,VTwins在识别因果特征的敏感性方面超过传统方法,并且将所需样本规模减小10倍,就可鉴定与疾病相关的微生物或代谢途径,并通过模拟和真实数据进行验证.与其他16种同类软件进行的基准测试进一步验证了VTwins在处理高维数据和挖掘宏基因组研究中的因果关系的能力和适用性.总体而言,VTwins可直接且强大地处理高变、高维数据,在宏基因组和其他组学数据的因果关系挖掘方面具有广阔的应用前景.VTwins的开源访问网址为https://***/mengqingren/VTwins.

关键词： Causality High-dimensional data Metagenome Differential abundance Paired cohort