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DNA sequencing leads to genomics progress in China

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Science China(Life Sciences) 2011年第3期54卷 290-292页

作者： wu jiayan xiao jingfa ZHANG RuoSi yu jun CAS Key Laboratory of Genome Science and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

1 Science in the large-scale sequencing era Ten years ago,the first draft sequence assembly of the human genome was completed [1],bringing biomedical research one-step closer toward the goal of revolutionizing diagnosis,prevention,and treatment of human ***,journalists from the journal Nature surveyed more than 1000 life scientists regarding this laudable aim [2],obtaining substantially negative responses [3].However,almost all of those surveyed had been influenced,in one way or another,by the availability of the human genome sequence,and they also agreed with the notion that the 'sequence is the start.' The complexity of genome biology and almost every aspect of human biology is far greater than previously thought [4].

关键词：人类基因组序列 DNA测序生命科学家中国大规模测序生物医学人类疾病

A Brief Review of Software Tools for Pangenomics

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Genomics, Proteomics & Bioinformatics 2015年第1期13卷 73-76页

作者： jingfa xiao Zhewen Zhang jiayan wu jun yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline（PGAP） ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.

关键词： Pangenomics Pangenome Comparative analysis Genomic dynamics Core genes

Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction

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Journal of Genetics and Genomics 2011年第5期38卷 201-207页

作者： Ming Yang Yan Ge jiayan wu jingfa xiao jun yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China College of Biology China Agricultural University Beijing 100091 China

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein-protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using ＂Mirror tree＂ method on the respiratory chain （RC） proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions （Wilcoxon test, p-value = 4.4 × 10 6）. Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein-protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.

关键词： Coevolution Respiratory chain proteins "Mirror tree" method Supercomplex Protein--protein interaction

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

Ribogenomics: the Science and Knowledge of RNA

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Genomics, Proteomics & Bioinformatics 2014年第2期12卷 57-63页

作者： jiayan wu jingfa xiao Zhang Zhang Xumin Wang Songnian Hu jun yu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

Ribonucleic acid（RNA） deserves not only a dedicated field of biological research –– a discipline or branch of knowledge –– but also explicit definitions of its roles in cellular processes and molecular mechanisms. Ribogenomics is to study the biology of cellular RNAs, including their origin, biogenesis, structure and function. On the informational track, messenger RNAs（mRNAs） are the major component of ribogenomes, which encode proteins and serve as one of the four major components of the translation machinery and whose expression is regulated at multiple levels by other operational RNAs. On the operational track, there are several diverse types of RNAembryonic development, circadian and seasonal rhythms, defined life-span stages, pathological conditions and anatomy-driven tissue/organ/cell types.

关键词： RNA Ribogenomics Operational Informational Transcriptome

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

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

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

Precision Medicine:What Challenges Are We Facing?

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Genomics, Proteomics & Bioinformatics 2016年第5期14卷 253-261页

作者： yu Xue Eric-wubbo Lameijer Kai Ye Kunlin Zhang Suhua Chang xiaoyue Wang Jianmin wu Ge Gao Fangqing Zhao Jian Li Chunsheng Han Shuhua Xu jingfa xiao Xuerui Yang xiaomin Ying Xuegong Zhang Wei-Hua Chen yun Liu Zhang Zhang Kun Huang jun yu MOE Key Lahoratory of Molecular Biophysics College of Life Science and Technology and the Collaborative Innovation Center for Brain ScienceHuazhong University of Science and TechnologyWuhan 430074China School of Electronic and Information Engineering.Xi'an Jiaotong University.Xi'an 710049 China CAS Key Laboratory of Mental Health Institute of PsychologyChinese Academy of SciencesBeijing 100101China State Key Laboratory of'Medical Molecular Biology Institute of Basic Medical SciencesChinese Academy of Medical SciencesPeking Union Medical CollegeBeijing 100005China MOE Beijing Key Laboratory of Carcinogenesis and Translatiooal ResearchCenter for Cancer BioinformaticsPeking University Cancer Hospital&InstituteBeijing 100142China Center for Bioinformatics State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijing 100871China Beijing Institutes of Life Science.Chinese Academy of Sciences Beijing 100101China MOE Key Lahoratory of Developnlental Genes and Human Disease Institute of Life SciencesSoutheast UniversityNanjing 210096China State Key Laboratory of Stem Cell and Reproductive Biology Institute of Zoology Chinese Academy of SciencesBeijing 100101China Max Planck Independent Research Group on Population Genomics CAS-MPG Partner Institute for Computational Biology(PICB)Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China CAS Ker Laboratory of Genome Sciences and Information Chinese Academy of Sciences.Beijing 100101China MOE Key Laboratory of Bioinformatics School of Life Sciences Center for Synthetic and Systems BiologyTsinghua UniversityBeijing 100084China Computational Omics Lahoratory Center of Computational BiologyBeijing Institute of Basic Medical SciencesBeijing 100850China Bioinformatics Division TNLIST and MOE Key Laboratory for Bioinformatics Department of AutomationTsinghua UniversityBeijing 100084China Department of Bioinformatics and Systems Biology College of LifeScience and Technol

Following the publication of the US National Research Council （N RC） report ＂ Toward PrecMon Medicine.＂ Building a Knowledge Network for Biomedical Research and a New Taxonomy of Diseases＂ in 2011 [1], several n... 详细信息

关键词： PMI Precision Medicine data We