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Genome of Plant maca （Lepidium meyenil） Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes

molecular Plant 2016年第7期9卷 1066-1077页

作者： Jing Zhang Yang Tian Liang Yan GuanghuiZhang Xiao wang Yan Zeng Jiajin Zhang Xiao ma Yuntao Tan Ni Long Yangzi wang Yujin ma Yuqi He Yu Xue Shumei Hao Shengchao Yang wen wang Liangsheng Zhang Yang Dong wei Chen Jun Sheng College of Life Science Huazhong University of Science and Technology Wuhan 430074 China College of Life Sciences Jilin University Changchun 130012 China Key Laboratory of Pu-erh Tea Science Ministry of Education Yunnan Agricultural University Kunming 650201 China Pu'er Institute of Pu-erh Tea Pu'er 665000 China Yunnan Research center on Good Agricultural Practice for Dominant Chinese medicinal materials Yunnan Agricultural University Kunrning 650201 China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China University of Chinese Academy of Sciences Beijing 100049 China School of Science and Information Engineering Yunnan Agricultural University Kunming 650201 China College of Life Science Kunming University of Science and Technology Kunming 650504 China Public Technical Service center Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 China Yunnan University Kunming 650091 China center for genomics and Biotechnology Haixia Institute of Science and Technology Fujian Agriculture and Forestry University Fuzhou 350002 China yunnan Research Institute for Local Plateau Agriculture and Industry Kunming 650201 China These authors contributed equally to this article.

maca （Lepidium meyenii walp, 2n = 8x = 64）, belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru （4000-4500 m）. Considering that the rapid uplift of the central Andes occurred 5-10 million years ago （ma）, an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications （wGDs; ~6.7 ma） were identified. comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via wGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes （i.e., small leaf shape and self-fertility） in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation （i.e., LEAF CURLING RESPONSIVENESS） and abiotic stress response （i.e., GL YClNE-RICH RNA-BINDING PROTEINS and DNA-DAmAGE-REPAIR/TOLERATION2） under positive selection. Collectively, the maca genome provides use- ful information to understand the important roles of wGDs in the high-altitude adaptation of plants in the Andes.

关键词： genome sequencing whole-genome duplication high-altitude adaptation Brassicaceae Lepidium,leaf morphogenesis self-incompatibility

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Breast Cancer Risk Genes-Association Analysis in more than 113,000 w.m.n

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四川生理科学杂志 2021年第1期43卷 7-7页

作者： Leila Dorling The authors' affiliations are as follows: the Centre for Cancer Genetic Epidemiology Departments of Public Health and Primary Care (L.D. S. Carvalho J.A. K.A.P. Q.W. M.K.B. J.D. B.D. N. Mavaddat K. Michailidou A.C.A. P.D.P.P. D.F.E.) and Oncology (C.L. P.A.H. C. Baynes D.M.C. L.F. V.R. M. Shah P.D.P.P. A.M.D. D.F.E.) University of Cambridge Cambridge the Centre for Genomic and Experimental Medicine MRC Institute of Genetics and Molecular Medicine (A. Campbell D.J.P.) and the Centre for Cognitive Ageing and Cognitive Epidemiology Department of Psychology (D.J.P.) University of Edinburgh the Cancer Research UK Edinburgh Centre (D.A.C. J.F.) and the Usher Institute of Population Health Sciences and Informatics University of Edinburgh Medical School (A. Campbell J.F.) Edinburgh the Divisions of Informatics Imaging and Data Sciences (E.F.H.) Cancer Sciences (A. Howell) Population Health Health Services Research and Primary Care (A. Lophatananon K. Muir) and Evolution and Genomic Sciences School of Biological Sciences (W.G.N. E.M.V. D.G.E.) University of Manchester the NIHR Manchester Biomedical Research Unit (E.F.H.) and the Nightingale Breast Screening Centre Wythenshawe Hospital (E.F.H. H.I.) Academic Health Science Centre and North West Genomics Laboratory Hub and the Manchester Centre for Genomic Medicine St. Mary's Hospital Manchester University NHS Foundation Trust (W.G.N. E.M.V. D.G.E.) Manchester the School of Cancer and Pharmaceutical Sciences Comprehensive Cancer Centre Guy's Campus King's College London London (E.J.S.) the Institute of Cancer and Genomic Sciences University of Birmingham Birmingham (I.T.) and the Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre University of Oxford Oxford (I.T.) - all in the United Kingdom the Human Genotyping-CEGEN Unit Human Cancer Genetic Program (A.G.-N. M.R.A. N.Á. B.H. R.N.-T.) and the Human Genetics Group (V.F. A.O. J.B.) Spanish National Cancer Research

Background:Genetic testing for breast cancer susceptibility is widely used,but for many genes,evidence of an association with breast cancer is weak,underlying risk estimates are imprecise,and reliable subtype-specific risk estimates are ***:we used a panel of 34 putative susceptibility genes to perform sequencing on samples from 60,466 w.m.n with breast cancer and 53,461 *** separate analyses for protein-truncating variants and rare missense variants in these genes,we estimated odds ratios for breast cancer overall and tumor *** evaluated missense-variant associations according to domain and classification of pathogenicity.

关键词： cancer Breast Cancer

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ECLIPSE研究：氯维地平与硝酸甘油、硝普钠、尼卡地平治疗心外手术患者急性高血压的对比研究

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麻醉与镇痛 2009年第5期5卷 34-46页

作者： Solomon Aronson Cornelius m. Dyke Kevin A. Stierer Jerrold H. Levy Albert T. Cheung Philip D. Lumb Dean J. Kereiakes mark F. Newman 谢珺田(译) 宋文阁(校) Department of Anesthesiology Duke University Medical Center Durham North Carolina Gaston memorial Hospital Gastonia North Carolina The Heart Institute at St. Joseph medical center Towson Maryland Department of Anesthesiology Emory University School of Medicine Atlanta Georgia Department of Anesthesiology and Critical Care University of Pennsylvania Philadelphia Pennsylvania Department of Anesthesiology Keck School of Medicine University of Southern California Los Angeles California The Christ Hospital Heart and Vascular center/The Lindner Research center Cincinnati Ohio 不详

背景心外手术过程中的高血压常难以控制，并进而影响手术疗效。氯维地平是一种新型的2-氢吡啶L型钙通道阻滞剂，可有效降低动脉压，起效迅速，且半衰期极短。氯维地平治疗围手术期高血压的安全性事件评估研究（evaluation of clevidipin... 详细信息

背景心外手术过程中的高血压常难以控制，并进而影响手术疗效。氯维地平是一种新型的2-氢吡啶L型钙通道阻滞剂，可有效降低动脉压，起效迅速，且半衰期极短。氯维地平治疗围手术期高血压的安全性事件评估研究（evaluation of clevidipine in the perioperative treatment of hypertension assessing safety events trial, ECLIPSE）旨在比较氯维地平（CLV）与硝酸甘油（NTG）、硝普钠（SNP）、尼卡地平（NIC）治疗心外手术患者急性高血压的疗效与安全性。方法我们分析了3项前瞻性、随机、开放性平行对照研究的资料，这些研究由61家医疗中心参与完成，比较了氯维地平与硝酸甘油、硝普钠、尼卡地平在心外手术患者的围手术期应用情况。共选择1964例患者，1512例按临床标准需紧急治疗高血压，符合随机化纳入标准。这些患者按1：1比例随机编入3个平行的对比治疗组。主要结局为30天内的死亡事件、心肌梗死、中风和肾功能不全，次要结局为血压控制的充分性与精确度的评估报告。结果氯维地平组与其他治疗组相比，心肌梗死、中风和肾功能不全的发生率均无显著差异。硝普钠治疗组与氯维地平组相比，死亡例数显著增加（P=0．04）。与硝酸甘油（P=0．0006）和硝普钠（P=0．003）相比，氯维地平能更有效地把血压控制在预定范围内。在控制血压于一个预定范围方面氯维地平与尼卡地平等效，但当预定血压控制范围较窄时，氯维地平较尼卡地平超出范围的幅度更小。结论氯维地平用于治疗心外手术患者的急性高血压安全有效。

关键词：急性高血压尼卡地平紧急治疗硝酸甘油心外手术硝普钠 hypertension 血压控制范围

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Bioinformatic analysis of human nuclear receptor nr5a2(hb1f) genomic sequence

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Chinese Science Bulletin 2002年第7期47卷 568-572,617页

作者： Zhang Chengkang Lin wei Cai Yanning Dong Hui Li mei Fu Gang Xie Youhua Huang m.Guyang wang Yuan Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological SciencesChinese Academy of Sciences200031ShanghaiChina Chinese Human Genome center at Shanghai 201203ShanghaiChina

we have cloned the cDNA of human nuclear receptor nr5a2(hb1f) gene and obtained its whole genomic sequence previously. In this work we carried out in-depth bioinformatic analysis on the genomic sequence of nr5a2(hb1f) gene. Sequence comparison and prediction algorithms implicated that there might be additional coding regions in the 210 kb genomic sequence besides known exons, especially in the two largest introns. Comparison of the structures of nr5a loci in different species revealed distinguishable conservation and apparent gene duplication during evolution. The remarkable conservation among promoters of zebrafish, mouse and human nr5a2 genes suggested that they would be regulated by the same transcription factors.

关键词： nuclear receptor nr5a2(hb1f) gene structure bioinfor-matics comparative genomics.

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comparative analysis of the TCP gene family in celery,coriander and carrot(family Apiaceae)

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Vegetable Research 2021年第1期1卷 36-47页

作者： Qiaoying Pei Nan Li Yun Bai Tong wu Qihang Yang Tong Yu Zhiyuan wang Zhuo Liu Qiang Li Hao Lin Xiaoming Song College of Life Sciences/center for genomics and Bio-computing North China University of Science and TechnologyTangshan 063210China School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 610054China Food Science and Technology Department University of Nebraska-LincolnLincolnNE 68588USA Faculty of Life Science Tangshan Normal UniversityTangshan 063000China

Apiaceae is one of the most important families in Apiales and includes many economically important vegetables and medicinal *** TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1/2(TCP)gene family plays an important role in regulating plant growth and development,but it has not been widely studied in *** the present study,we identified 215 TCP family genes in six species of plant,of which 122 genes were present in three Apiaceae including 29 in celery(Apium graveolens),43 in coriander(Coriandrum sativum),and 50 in carrot(Daucus carota).whole-genome duplication likely contributed to TCP gene family expansion in *** were more paralogs in carrot than in coriander and celery,which was attributable to the greater number of tandem and proximal duplicated genes on chromosome *** microRNAs were found to regulate 20 TCP genes in the three Apiaceae species,with miR-319 having the most target *** TCP genes showed high expression in the root,petiole and leaf of celery and *** results provide a basis for comparative and functional genomic analyses of TCP genes in Apiaceae and other plants.

关键词： TCP IDEA whole

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Integrative and comparative Genomic Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas

Integrative and Comparative Genomic Analysis of HPV-Positive...

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中国生物工程学会第六次全国会员代表大会暨第九届学术年会

作者： Tanguy Y.Seiwert Zhixiang Zuo michaela K.keck Arun Khattri Chandra S.Pedamallu Thomas Stricker Christopher Brown Trevor J.Pugh Petar Stojanov Juok Cho michael S.Lawrence Gad Getz Johannes Br?gelmann Rebecca DeBoer Ralph R.weichselbaum Alexander Langerman Louis Portugal Elizabeth Blair Kerstin Stenson mark w.Lingen Ezra E.w.Cohen Everett E.Vokes Kevin P.white Peter S.Hammerman Section of Hematology/Oncology Department of MedicineThe University of Chicago The University of Chicago Comprehensive Cancer center Institute for genomics and Systems Biology University of Chicago Broad Institute of Harvard and mIT Department of medical Oncology Dana Farber Cancer Institute Department of Pathology Microbiologyand ImmunologyVanderbilt University Department of Genetics University of Pennsylvania Department of Radiation Oncology The University of Chicago Department of Otolaryngology/Head and Neck Surgery The University of Chicago Department of Pathology University of Chicago

Purpose:The genetic differences between human papilloma virus(HPV)–positive and –negative head and neck squamous cell carcinomas(HNSCC) remain largely *** identify differential biology and novel therapeutic targets for both entities,we determined mutations and copy-number aberrations in a large cohort of locoregionally advanced *** Design:we performed massively parallel sequencing of 617 cancer-associated genes in 120 matched tumor/normal samples(42.5% HPV-positive).mutations and copy-number aberrations were determined and results validated with a secondary ***:The overall mutational burden in HPV-negative and HPV-positive HNSCC was similar with an average of 15.2 versus14.4 somatic exonic mutations in the targeted cancer-associated ***-negative tumors showed a mutational spectrum concordant with published lung squamous cell carcinoma analyses with enrichment for mutations in TP53,CDKN2 A,mLL2,CUL3,NSD1,PIK3 CA,and NOTCH ***-positive tumors showed unique mutations in DDX3 X,FGFR2/3 and aberrations in PIK3 CA,KRAS,mLL2/3,and NOTCH1 were enriched in HPVpositive *** targetable genomic alterations were identified in FGFR1,DDR2,EGFR,FGFR2/3,EPHA2,and PIK3 ***,CCND1,and FGFR1 amplifications occurred in HPV-negative tumors,whereas 17.6% of HPV-positive tumors harbored mutations in fibroblast growth factor receptor genes(FGFR2/3),including six recurrent FGFR3 S249 C ***-positive tumors showed a 5.8% incidence of KRAS mutations,and DNArepair gene aberrations,including 7.8% BRCA1/2 mutations,were ***:The mutational makeup of HPV-positive and HPV-negative HNSCC differs significantly,including targetable *** harbors multiple therapeutically important genetic aberrations,including frequent aberrations in the FGFR and PI3K pathway genes.

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2019nCoVR—A comprehensive genomic resource for SARS-CoV-2 variant surveillance

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The Innovation 2021年第4期2卷 1-2页

作者： Guoqing Lu Etsuko N.moriyama Department of Biology University of Nebraska at OmahaOmahaNE 68182USA School of Biological Sciences and center for Plant Science Innovation University of Nebraska-LincolnLincolnNE 68588USA

The coronavirus disease 2019(COVID-19)is a once-in-a-century pandemic,and the virus,the severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2,has infected more than 180 million people and claimed almost 4 million lives worldwide(as of July 5,2021)since the first case was reported in wuhan,China,on December 31,*** China National center for Bioinformation(CNCB)responded promptly and launched the 2019 Novel Coronavirus Resource(2019nCoVR;https://***/ncov/)in January 2020 for rapid release and public sharing of SARS-CoV-2 genomic data and analysis tools(Figure 1A).

关键词： Figure prompt VR

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Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long-and Short-read multi-metagenomic Sequencing Studies

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genomics, Proteomics & Bioinformatics 2022年第2期20卷 405-417页

作者： Jacqueline Rehner Georges Pierre Schmartz Laura Groeger Jan Dastbaz Nicole Ludwig matthias Hannig Stefan Rupf Berthold Seitz Elias Flockerzi Tim Berger matthias Christian Reichert marcin Krawczyk Eckart meese Christian Herr Robert Bals Soren L.Becker Andreas Keller Rolf muller The ImAGINE Consortium Institute of medical microbiology and Hygiene Saarland UniversityD-66421 HomburgGermany Clinical Bioinformatics Saarland UniversityD-66123 SaarbruckenGermany Department of Human Genetics Saarland UniversityD-66421 HomburgGermany Helmholtz Institute for Pharmaceutical Research Saarland D-66123 SaarbruckenGermany Clinic of Operative Dentistry Periodontology and Preventive DentistrySaarland UniversityD-66421 HomburgGermany Department of Ophthalmology Saarland University Medical CenterD-66421 HomburgGermany Department of medicine Ⅱ Saarland University Medical CenterD-66421 HomburgGermany Department of Internal medicine V–Pulmonology AllergologyIntensive Care MedicineSaarland UniversityD-66421 HomburgGermany

High-quality DNA extraction is a crucial step in metagenomic *** by different isolation kits impairs the comparison across datasets.A trending topic is,however,the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with *** thus collected bile,stool,saliva,plaque,sputum,and conjunctival swab samples and performed DNA extraction with three commercial *** each combination of the specimen type and DNA extraction kit,20-gigabase(Gb)metagenomic data were generated using short-read *** profiles of the specimen types showed close proximity to each other,we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction *** kit outperformed all selected kits on every *** reached consistently good results using the Qiagen QiAamp DNA microbiome *** on the specimen,our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution,but DNA-based identification is superior to identification by mass ***,longread nanopore sequencing confirmed the results(correlation coefficient>0.98).Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

关键词： whole-genome analysis comparative genomics Short-read sequencing Long-read sequencing DNA extraction metagenomics

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Complete genome sequence of high-yield strain S. lincolnensis B48 and identification of crucial mutations contributing to lincomycin overproduction

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Synthetic and Systems Biotechnology 2020年第2期5卷 37-48页

作者： Ruida wang Fanjing Kong Haizhen wu Bingbing Hou Yajing Kang Yuan Cao Shiwei Duan Jiang Ye Huizhan Zhang State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghai200237China Department of Applied Biology East China University of Science and TechnologyShanghai200237China medical Genetics center School of MedicineNingbo UniversityNingbo315211China

The lincosamide family antibiotic lincomycin is a widely used antibacterial pharmaceutical generated by Streptomyces lincolnensis,and the high-yield strain B48 produces 2.5 g/L lincomycin,approximately 30-fold as the wild-type strain NRRL ***,the genome of *** B48 was completely sequenced,revealing a^10.0 mb single chromosome with 71.03%G+C *** on the genomic information,lincomycinrelated primary metabolism network was constructed and the secondary metabolic potential was *** order to dissect the overproduction mechanism,a comparative genomic analysis with NRRL 2936 was *** large deletions(LDI-III),one large inverted duplication(LID),one long inversion and 80 small variations(including 50 single nucleotide variations,13 insertions and 17 deletions)were found in B48 *** several crucial mutants contributing to higher production phenotype were *** of a marRtype regulator-encoding gene slinc377 from LDI,and the whole 24.7 kb LDII in NRRL 2936 enhanced lincomycin titer by 244%and 284%,***,lincomycin production of NRRL 2936 was increased to 7.7-fold when a 71 kb supercluster BGC33 from LDIII was *** for the duplication region,overexpression of the cluster situated genes lmbB2 and lmbU,as well as two novel transcriptional regulator-encoding genes(slinc191 and slinc348)elevated lincomycin titer by 77%,75%,114%and 702%,***,three negative correlation genes(slinc6156,slinc4481 and slinc6011)on lincomycin biosynthesis,participating in regulation were found *** surprisingly,inactivation of RNase J-encoding gene slinc6156 and TPR(tetratricopeptide repeat)domain-containing protein-encoding gene slinc4481 achieved lincomycin titer equivalent to 83%and 68%of B48,respectively,to 22.4 and 18.4-fold compared to NRRL ***,the comparative genomics approach combined with confirmatory experiments identified that large fragment deletion,long sequence duplicatio

关键词： Lincomycin comparative genomics Regulation Overproduction

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comparative Genome Analysis of Scutellaria baicalensis and Scutellaria barbata Reveals the Evolution of Active Flavonoid Biosynthesis

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genomics, Proteomics & Bioinformatics 2020年第3期18卷 230-240页

作者： Zhichao Xu Ranran Gao Xiangdong Pu Rong Xu Jiyong wang Sihao Zheng Yan Zeng Jun Chen Chunnian He Jingyuan Song Key Lab of Chinese medicine Resources Conservation State Administration of Traditional Chinese Medicine of ChinaInstitute of Medicinal Plant DevelopmentChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China Engineering Research center of Chinese medicine Resource Ministry of EducationBeijing 100193China China National Traditional Chinese medicine Co. LtdBeijing 102600China

Scutellaria baicalensis(***)and Scutellaria barbata(***)are common medicinal plants of the Lamiaceae *** produce specific flavonoid compounds,including baicalein,scutellarein,norwogonin,and wogonin,as well as their glycosides,which exhibit antioxidant and antitumor ***,we report chromosome-level genome assemblies of *** and *** with quantitative chromosomal variation(2 n=18 and 2 n=26,respectively).The divergence of *** and *** occurred far earlier than previously reported,and a whole-genome duplication(wGD)event was *** insertion of long terminal repeat elements after speciation might be responsible for the observed chromosomal expansion and *** genome analysis of the congeneric species revealed the species-specific evolution of chrysin and apigenin biosynthetic genes,such as the ***-specific tandem duplication of genes encoding phenylalanine ammonia lyase and chalcone synthase,and the ***-specific duplication of genes encoding 4-Co A *** addition,the paralogous duplication,colinearity,and expression diversity of CYP82 D subfamily members revealed the functional divergence of genes encoding flavone hydroxylase between *** and *** these Scutellaria genomes reveals the common and species-specific evolution of flavone biosynthetic ***,these findings would facilitate the development of molecular breeding and studies of biosynthesis and regulation of bioactive compounds.

关键词： Scutellaria whole-genome duplication Flavonoid biosynthesis Tandem duplication Species-specific evolution

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