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Comparative analysis of the pig BAC sequence involved in the regulation of myostatin gene

Science china(Life sciences) 2005年第2期48卷 168-180页

作者： YU Zhengquan1,LI Yan2,MENG Qingyong1,YUAN Jing1,ZHAO Zhihui1,LI Wei2,HU Xiaoxiang1,YAN Bingxue1,FAN Baoliang1,YU Shuyang1 & LI Ning1 1.State Key Laboratory for Agrobiotechnology,china Agricultural University,beijing 100094,china 2.beijing genomics institute / genomics and bioinformatics center,institute of genetics and development biology,chinese academy of sciences,beijing 100101,china 1. State Key Laboratory for Agrobiotechnology China Agricultural University 100094 Beijing China 2. beijing genomics institute / genomics and bioinformatics center Institute of Genetics and Development Biology Chinese Academy of Sciences 100101 Beijing China

Myostatin (GDF8, MSTN) is a member of the transforming growth factor beta su- perfamily that is essential for proper regulation of skeletal muscle mass. In order to study its ex- pression and regulatory mechanism deeply, we have presented a comparative analysis of about 170-kb pig BAC sequence containing the myostatin gene among pig, human and mouse. The genomic region is characterized by high interspersed repeats and low G+C content. As for the myostatin gene, a higher sequence similarity is found between human and pig than between these species and the mouse. One striking feature is that the structure of two TATA-boxes in the nearby downstream of CCAAT-box is identified in the promoter. Further analysis reveals that the TATA-box1 is responsible for the transcription in pig and human, but the TATA-box2 acts on the transcription in mouse. The other interesting feature is that two polyadenylation signal sequences (AATAAA) exist in 3′UTR of the pig myostatin gene. Moreover, a large number of potential tran- scription factor-binding sites are also identified in evolutionary conserved regions (ECRs), which may be associated with the regulation of myostatin. Many putative transcription factors play an important role in the muscle development, and the complex interaction between myostatin and these factors may be required for proper muscle development.

关键词： myostatin, comparative analysis, transcriptional factors, muscle development.

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A seed-specific AP2-domain transcription factor from soybean plays a certain role in regulation of seed ger-mination

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Science china(Life sciences) 2008年第4期51卷 336-345页

作者： WANG ChunMei, WANG HuiWen, ZHANG JinSong & CHEN ShouYi National Key Laboratory of Plant genomics, institute of genetics and developmental biology, chinese academy of sciences, Bei-jing 100101, china National Key Laboratory of Plant genomics Institute of Genetics developmental biology Chinese Academy of Sciences Beijing 100101 China

Plant seed development and germination are under strict temporal and spatial regulation, and tran-scription factors play important roles in this regulation. In the present study we identified an EST ex-pressed specifically in the developing soybean seeds. The full length of the gene was obtained through further RACE analysis and the gene was named GmSGR. Sequence analysis revealed that this gene belonged to the AP2/ERF transcription factor family. Its AP2 domain had the highest similarity with that of the A-3 member AtABI4 of DREB subgroup in the AP2/ERF family in Arabidopsis. GmSGR did not exhibit transcriptional activation activity in the yeast assay system. GmSGR was overexpressed in Arabidopsis and the germination rates of the transgenic seeds were significantly higher than that of the wild type seeds under higher concentrations of ABA and glucose respectively. However, the germina-tion rates of the transgenic seeds were lower than that of control under salt stress. The expression of AtEm6 and AtRD29B was higher in the seedlings of the transgenic plants than that in the wild-type seedlings. These results suggest that GmSGR may confer reduced ABA sensitivity and enhanced salt sensitivity to the transgenic seeds through regulating the expression of AtEm6 and AtRD29B genes.

关键词： ABA AP2/ERF transcription factor salt stress seed germination soybean

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Cloning and expression of putative ethylene receptor genes in soybean plant

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Progress in Natural Science:Materials International 2007年第10期17卷 1152-1160页

作者： Xie Zongming1,2,3, Lei Gang1,2, Wuriyanghan Hada1,2, Tian Aiguo1, Zhang Jinsong1 and Chen Shouyi1(1. National Key Laboratory of Plant genomics, institute of genetics and developmental biology, chinese academy of sciences, beijing 100101, china 2. Graduate School of chinese academy of sciences, beijing 100039, china 3. Xinjiang academy of Agricultural and Reclamation Science, Shihezi 832000, china) National Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China Graduate School of chinese academy of sciences Beijing 100039 China Xinjiang academy of Agricultural and Reclamation Science Shihezi 832000 China

Ethylene plays important roles in plant growth, development, and stress responses, and ethylene receptors have been identified and studied extensively in various plant species. Here we report the cloning of four ethylene receptor genes from soybean, i.e. GmETR1, GmERS1, GmETR2 and GmEIN4. Construction of the phylogenic tree showed that GmETR1 and GmERS1 belong to subfamily I whereas GmETR2 and GmEIN4 belong to subfamily II. The four ethylene receptor genes showed different tissue-specific expression patterns in roots, stems, leaves, cotyledons, flowers, pods and seeds of soybean. These genes were differentially regulated by various abiotic stresses and plant hormones. The possible roles of the four genes in soybean plant were also discussed.

关键词： abiotic stress expression analysis ethylene receptor plant hormone soybean.

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Expressed sequence tag analysis and cloning of trehalose-6-phosphate synthase gene from marine alga Laminaria japonica(Phaeophyta)

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Acta Oceanologica Sinica 2012年第6期31卷 139-148页

作者： XUAN Jinsong 1,4,FENG Yanbin 1,WENG Manli 1,ZHAO Ge 1,SHI Jinfeng 1,YAO Jianting 2,WANG Xiuliang 2,GUO Baotai 3,QIAO Lixian 3,DUAN Delin 2,WANG Bin 1 1 The State Key Laboratory of Plant genomics,institute of genetics and developmental biology,chinese academy of sciences,beijing 100101,china 2 The State Key Laboratory of Marine biology,institute of Oceanology,chinese academy of sciences,Qingdao 266071,china 3 College of Life sciences,Qingdao Agricultural University,Qingdao 266109,china 4 Department of Biological Science and Engineering,School of Chemical and Biological Engineering,University of Science and Technology beijing,beijing 100083,china 1. The State Key Laboratory of Plant genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing 100101 China 4. Department of Biological Science and Engineering School of Chemical and Biological Engineering University of Science and Technology Beijing Beijing 100083 China 2. The State Key Laboratory of Marine biology Institute of Oceanology Chinese Academy of Sciences Qingdao 266071 China 3. College of Life sciences Qingdao Agricultural University Qingdao 266109 China

A high quality cDNA library was constructed from the brown alga Laminaria japonica,with the titer of 1.2×10 5 pfu/*** average insert size of the cDNA library is about 1.6 *** the cDNA library,591 cDNA clones were randomly selected and *** a result,574 EST(expressed sequence tag) sequences were *** of the 574 ESTs were submitted to the dbEST database section of GenBank with the accession numbers from CX942625 to *** cDNA library was screened with a α-32 p labeled 453 bp T P S gene probe,which is a partial sequence yielded from Porphyra *** positive cDNA clones were screened and the sequencing data showed that these four cDNA clones covered majority of *** TPS cDNA *** PCR amplification,sequencing and assembling,the entire ORF(open reading frame) sequence of the T P S gene was obtained,which was named *** encodes a protein containing 908 amino acids with a calculated molecular mass of 101 674 *** LjTPS gene was successfully expressed in *** and *** LjTPS gene has potential application both in plant breeding to stress tolerance and in deciphering the T P S gene function and mechanism to stress tolerance.

关键词： cDNA library comparative study expressed sequence tag(EST) analysis Laminaria japonica trehalose-6-phosphate synthase(TPS) T P S gene

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A draft sequence of the rice (Oryza sativa ssp. indica) genome

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chinese Science Bulletin 2001年第23期46卷 1937-1942页

作者： YU Jun, HU Songnian, WANG Jun,LI Songgang WONG Ka-Shu Gane, LIU Bin,DENG Yajun, DAI Li, ZHOU Yan,ZHANG Xiuqing, CAO Mengliang, LIU Jing,SUN Jiandong , TANG Jiabin, CHEN Yanjiong,HUANG Xiaobing, LIN Wei, YE Chen, TONG Wei,CONG Lijuan, GENG Jianing, HAN Yujun, LI Lin,LI Wei, HU Guangqiang, HUANG Xiangang,LI Wenjie, LI Jian, LIU Zhanwei, LI Long,LIU Jianping, Ql Qiuhui, LIU Jinsong, LI Li,WANG Xuegang, LU Hong, WU Tingling,ZHU Miao, Nl Peixiang, HAN Hua, DONG Wei,REN Xiaoyu, FENG Xiaoli, GUI Peng,LI Xianran, WANG Hao, XU Xin, ZHAI Wenxue,XU Zhao, ZHANG Jinsong, HE Sijie,ZHANG Jianguo, XU Jichen, ZHANG Kunlin,ZHENG Xianwu, DONG Jianhai, ZENG Wanyong,TAO Lin, CHEN Xuewei, HE Jun, LIU Daofeng,TIAN Wei, TIAN Chaoguang, XIA Hongai,LI Gang, GAO Hui, LI Ping, CHEN Wei ,WANG Xudong, ZHANG Yong, HU Jianfei,WANG Jing, LIU Song, YANG Jian,ZHANG Guangyu, XIONG Yuqing, LI Zhijie,MAO Long, ZHOU Chengshu, ZHU Zhen,CHEN Runsheng, HAO Bailin,ZHENG Weimou, CHEN Shouyi, QUO Wei,LI Guojie, LIU Siqi, HUANG Guyang,TAO Ming, WANG Jian, ZHU Lihuang,YUAN Longping& YANG Huanmingbeijing genomics institute/center of genomics & bioinformatics, chinese academy of sciences, beijing 101300, china Hangzhou genomics institute/institute of bioinformatics of Zhejiang University/Key Laboratory of bioinformatics of Zhejiang Province, Hangzhou 310007, china institute of genetics, chinese academy of sciences, beijing 100101, china National Hybrid Rice R & D center, Changsha 410125, china Laboratory of bioinformatics, institute of Biophysics, chinese academy of sciences, beijing 100101, china College of Life sciences, Peking University, beijing 100871, china institute of Theoretical Physics, chinese academy of sciences, beijing 1Q0080, china Digital china Ltd., beijing 100080, china institute of Computing Technology, chinese academy of sciences, beijing 100080, china Medical College, Xi’an Jiaotong University, Xi’an 710061, chinaThese authors contributed equally to this work.Corresponding author.Corresponden beijing genomics institute/center of genomics & bioinformatics Chinese Academy of Sciences Beijing China Hangzhou genomics institute/institute of bioinformatics of Zhejiang University/Key Laboratory of bioinformatics of Zhejiang Province Hangzhou China College of Life sciences Peking University Beijing China Medical College Xi’an Jiaotong University Xi’an China institute of genetics Chinese Academy of Sciences Beijing China Laboratory of bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing China National Hybrid Rice R & D center Changsha China institute of Theoretical Physics Chinese Academy of Sciences Beijing China Digital china Ltd. Beijing China institute of Computing Technology Chinese Academy of Sciences Beijing China

The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have pro-duced a draft rice genome sequence of Oryza sativa ssp. in-dica, the major crop rice subspecies in china and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM-BLER, a custom-designed software package

关键词： rice genome draft sequences.

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Induction of chromosomal inversion by integration of T-DNA in the rice genome

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Journal of genetics and genomics 2010年第3期37卷 189-196页

作者： Chuanfeng Zhu,Jiahe Wu,Chaozu He State Key Laboratory of Plant genomics,institute of Microbiology,chinese academy of sciences,beijing 100101,china [a] State Key Laboratory of Plant genomics Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

Transfer DNA （T-DNA） of Agrobacterium tumefaciens integration in the plant genome may lead to rearrangements of host plant chromosomal fragments, including inversions. However, there is very little information concerning the inversion. The present study re- ports a transgenic rice line selected from a T-DNA tagged population, which displays a semi-dwarf phenotype. Molecular analysis of this mutant indicated an insertion of two tandem copies of T-DNA into a locus on the rice genome in a head to tail mode. This insertion of T-DNA resulted in the inversion of a 4.9 Mb chromosomal segment. Results of sequence analysis suggest that the chromosomal inversion resulted from the insertion of T-DNA with the help of sequence microhomology between insertion region of T-DNA and target sequence of the host plant.

关键词： Agrobacterium tumefaciens-mediated transformation (ATMT) T-DNA chromosomal inversion

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Being the Pioneer of Life sciences in china——Introduction to beijing genomics institute

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genomics, Proteomics & bioinformatics 2004年第1期2卷 59-63页

作者： Xin Zhang beijing genomics institute, beijing 101300, china. beijing genomics institute Beijing 101300 China

The beijing genomics institute (BGI) of chinese academy of sciences (CAS) wasofficially founded in December 2003. Its predecessor, beijing Huada genomics Research center, haspresented significant contributions to the development of life sciences in china by its excellentscientific innovations and achievements in the last five years. From the participation ofInternational Human Genome Project (HGP) to the independent completion of the whole-genome draft andfine maps of chinese super hybrid rice genome, from the porcine genome research cooperated withDenmark to the international chicken genome research, and from the silkworm genome projectaccomplished together with The Southwest Agriculture University of china to the great contributionsto the national campaign against SARS, all these facts illustrate that BGI not only has afirst-class scientific research power in the world but also is full of devotion to the flourish ofscience and nation. During these years, we have upheld the strategy of ''Advance through projects,strive for innovation, grow through cooperation'', in the aim of making BGI as one of the pioneers ofCAS climbing the peak of life sciences in the world.

关键词： chinese academy of sciences beijing genomics institute innovation life sciences

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BUD2,encoding an S-adenosylmethionine decarboxylase,is required for Arabidopsis growth and development

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Cell Research 2006年第5期16卷 446-456页

作者： Chunmin Ge~(1,2,*) Xia Cui~(1,2,*) Yonghong Wang~1 Yuxin Hu~3 Zhiming Fu~1 Dongfen Zhang~(1,2) Zhukuan Cheng~1 Jiayang Li~1 ~1State Key Laboratory of Plant genomics and National center for Plant Gene Research,institute of genetics and developmental biology,chinese academy of sciences,beijing 100101,china ~2Graduate School,chinese academy of sciences,beijing 100101,china ~3institute of Botany,chinese academy of sciences,beijing 100093,china StateKeyLaboratoryofPlantgenomicsandNationalcenterforPlantGeneResearch InstituteofGeneticsandDevelopmentalBiologyChineseAcademyofSciencesBeijing100101China GraduateSchool ChineseAcademyofSciencesBeijing100101

Polyamines are implicated in regulating various developmental processes in plants,but their exact roles and how theygovern these processes still remain *** report here an Arabidopsis bushy and dwarf mutant,bud2,which resultsfrom the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases(SAMDCs) necessary for the formation of the indispensable intermediate in the polyamine biosynthetic ***2 plant has enlarged vascular systems in inflorescences,roots,and petioles,and an altered homeostasis *** double mutant of bud2 and samdcl,a knockdown mutant of another SAMDC member,is embryo lethal,demonstrat-ing that SAMDCs are essential for plant *** results suggest that polyamines are required for the normalgrowth and development of higher plants.

关键词： BUD2 polyamines embryogenesis plant architecture Arabidopsis

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Bioinformatic analysis of expressed sequence tags from sporophyte of Porphyra yezoensis (Bagiaceae, Rhodophyta)

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Progress in Natural Science:Materials International 2006年第1期16卷 39-49页

作者： XU Minjun1, MAO Yunxiang1,ZHANG Xuecheng1, ZHOU Xiaojun1, SUI Zhenghong1, ZHOU Hailin2 and LI Jinhong 2(1.Laboratory of Marine genetics and Breeding, College of Marine Life sciences, Ocean University of china, Qingdao 266003, china 2.James D Watson institute of Genome sciences, Zhejtang University / Key Laboratory of Genomic bioinformatics of Zhejiang Province, Hangzhou genomics institute, Hangzhou 310008, china) [a]Laboratory of Marine genetics and Breeding College of Marine Life Sciences Ocean University of China Qingdao China [b]James D Watson institute of Genome sciences Zhejiang University Hangzhou China

A total of 719 expressed sequence tags （EST） clustered into 329 non-redundant EST groups are obtained from the sporophyte cDNA library of red algae, Porphyra yezoensis. Gene Ontology （GO） analysis is employed in characterizing 60 strictest annotated unique genes out of the 329 EST groups and some domains such as COX1, SodFeC, GST-N, SHMT, and RNase-PH related to the enzymes and proteins functioning in cells have been identified by HMMPFAM search. As its leafy gametophyte, the similar codon usage with strong bias is found in P. yezoensis filamentous sporophyte, regardless of some differences found in given amino acids. The average GC content of the 329 unique genes is 53. 0 % . In contrast, the third nucleotide of codon exhibits a higher GC content （ 72 % ） than that of the first （58%） and the second （42%） nucleotides. Similarity search of the present study shows a novel EST ratio of 60.2%, which is against the Porphyra ESTs database, suggesting further investigations towards elucidating the characteristics of Porphyra functional genome.

关键词： Porphyra yezoensis expressed sequence tags (EST) bionformatic analysis.

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A Strategy for Searching Antigenic Regions in the SARS-CoV Spike Protein

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genomics, Proteomics & bioinformatics 2003年第3期1卷 207-215页

作者： Yan Ren, Zhengfeng Zhou, Jinxiu Liu, Liang Lin, Shuting Li, Hao Wang, Ji Xia, Zhe Zhao, Jie Wen, Cuiqi Zhou, Jingqiang Wang, Jianning Yin, Ningzhi Xu, and Siqi Liubeijing genomics institute, chinese academy of sciences, beijing 101300, china & beijing Proteomics institute, beijing 101300, china. beijing genomics institute Chinese Academy of Sciences Beijing 101300 China.

In the face of the worldwide threat of severe acute respiratory syndrome (SARS) to human life, some of the most urgent challenges are to develop fast and accurate analytical methods for early diagnosis of this disease as well as to create a safe anti-viral vaccine for prevention. To these ends, we investigated the antigenicity of the spike protein (S protein), a major structural protein in the SARS-coronavirus (SARS-CoV). Based upon the theoretical analysis for hydrophobicity of the S protein, 18 peptides were synthesized. Using Enzyme-Linked Immunosorbent Assay (ELISA),these peptides were screened in the sera from SARS patients. According to these results, two fragments of the S gene were amplified by PCR and cloned into pET-32a. Both S fragments were expressed in the BL-21 strain and further purified with an affinity chromatography. These recombinant S fragments were confirmed to have positive cross-reactions with SARS sera, either by Western blot or by ELISA. Our results demonstrated that the potential epitope regions were located at Codons 469-882 in the S protein, and one epitope site was located at Codons 599-620. Identification of antigenic regions in the SARS-CoV S protein may be important for the functional studies of this virus or the development of clinical diagnosis.

关键词： SARS the spike protein expression antigenicity

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