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A Scenario on the Stepwise Evolution of the Genetic Code

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genomics, Proteomics & Bioinformatics 2007年第3期5卷 143-151页

作者： jing-fa xiao jun yu cas key laboratory of genome sciences and information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China

It is believed that in the RNA world the operational （ribozymes） and the informational （riboscripts） RNA molecules were created with only three （adenosine, uridine, and guanosine） and two （adenosine and uridine） nucleosides, respectively, so that the genetic code started uncomplicated. Ribozymes subsequently evolved to be able to cut and paste themselves and riboscripts were acceptive to rigorous editing （adenosine to inosine）; the intensive diversification of RNA molecules shaped novel cellular machineries that are capable of polymerizing amino acids-a new type of cellular building materials for life. Initially, the genetic code, encoding seven amino acids, was created only to distinguish purine and pyrimidine; it was later expanded in a stepwise way to encode 12, 15, and 20 amino acids through the relief of guanine from its roles as operational signals and through the recruitment of cytosine. Therefore, the maturation of the genetic code also coincided with （1） the departure of aminoacyl-tRNA synthetases （AARSs） from the primordial translation machinery, （2） the replacement of informational RNA by DNA, and （3） the co-evolution of AARSs and their cognate tRNAs. This model predicts gradual replacements of RNA-made molecular mechanisms, cellular processes by proteins, and informational exploitation by DNA.

关键词： genetic code codon aminoacyl-tRNA synthase GC content

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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An online coronavirus analysis platform from the National genomics Data Center

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Zoological Research 2020年第6期41卷 705-708页

作者： Zheng Gong jun-Wei Zhu Cui-Ping Li Shuai Jiang Li-Na Ma Bi-Xia Tang Dong Zou Mei-Li Chen yu-Bin Sun Shu-Hui Song Zhang Zhang jing-fa xiao Yong-Biao Xue Yi-Ming Bao Zheng-Lin Du Wen-Ming Zhao china.National Center for Bioinformation&National genomics Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 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

DEAR EDITOR,Since the first reported severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)infection in December 2019,coronavirus disease 2019(COVID-19)has become a global pandemic,spreading to more than 200 countries and regions *** continued research progress and virus detection,SARS-CoV-2 genomes and sequencing data have been reported and accumulated at an unprecedented rate.

关键词： acute respiratory continued

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

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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

Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204

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Molecular Plant 2022年第9期15卷 1440-1456页

作者： xiaoli Shi fa Cui Xinyin Han Yilin He Long Zhao Na Zhang Hao Zhang Haidong Zhu Zhexin Liu Bin Ma Shusong Zheng Wei Zhang Jiajia Liu xiaoli fan Yaoqi Si Shuiquan Tian Jianqing Niu Huilan Wu Xuemei Liu Zhuo Chen Deyuan Meng xiaoyan Wang Liqiang Song Lijing Sun Jie Han Hui Zhao jun Ji Zhiguo Wang xiaoyu He Ruilin Li Xuebin Chi Chengzhi Liang Beifang Niu jun xiao junming Li Hong-Qing Ling State key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China key laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong College of AgricultureLudong UniversityYantai 264025China Computer Network information Center Chinese Academy of SciencesBeijing 100190China Center for Agricultural Resources Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang 050022China State key laboratory of Plant genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China College of Advanced Agricultural sciences University of Chinese Academy of SciencesBeijing 100049China School of Computer Science and Technology University of Chinese Academy of SciencesBeijing 100049China cas-JIC Centre of Excellence for Plant and Microbial Science Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Yazhou Bay Seed laboratory of Hainan Province Sanya 572019China

Studying the regulatory mechanisms that drive nitrogen-use efficiency(NUE)in crops is important for sustainable agriculture and environmental *** this study,we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and *** comparative analyses,we found that the high-affinity nitrate transporter gene family had expanded in *** studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility,providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various *** explore the genetic and molecular mechanisms of high NUE,we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204(KN9204)and the low-NUE cultivar jing 411 and quantified their nitrogen accumulation under high-and low-nitrogen *** with jing 411,KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and *** data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of jing 411,whereas this suppression of gene expression was much lower in *** addition,KN9204 maintained relatively high expression of NPF genes for a longer time than jing 411 during seed *** and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than jing 411,especially at the reproductive *** high NUE of KN9204 is an integrated effect controlled at different *** together,our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.

关键词： wheat genome sequencing spatiotemporal gene expression expansion and differentiation of gene family nitrogen use efficiency Kenong 9204

A large outbreak of acute gastroenteritis caused by the human norovirus GII.17 strain at a university in Henan Province,china

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Infectious Diseases of Poverty 2017年第1期6卷 42-50页

作者： Xue-Yong Huang Jia Su Qian-Chao Lu Shi-Zheng Li Jia-Yong Zhao Meng-Lei Li Yi Li xiao-jing Shen Bai-fan Zhang Hai-Feng Wang yu-Jiao Mu Shu-yu Wu Yan-Hua Du Li-Cheng Liu Wei-jun Chen John David Klena Bian-Li Xu Henan Center for Disease Control and Prevention ZhengzhouChina Henan key laboratory of Pathogenic Microorganisms ZhengzhouChina Nanyang City Center for Disease Control and Prevention NanyangChina Program of Global Disease Detection US Centers for Disease Control and PreventionBeijingChina State key laboratory of Pathogens and Biosecurity Institute of Microbiology and EpidemiologyAcademy of Military Medical SciencesBeijingChina key laboratory of genome sciences and information Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina Division of Global Health Protection Center for Global HealthCenters for Disease Control and PreventionAtlantaUSA

Background:Human noroviruses are a major cause of viral gastroenteritis and are the main etiological agents of acute gastroenteritis *** increasing number of outbreaks and sporadic cases of norovirus have been reported in china.in recent *** was a large acute gastroenteritis outbreak at a university in Henan Province,china.in the past five *** want to identify the source,transmission routes of the outbreak by epidemiological investigation and laboratory testing in order to provide the effective control ***:The clinical cases were investigated,and analysed by descriptive epidemiological methods according to factors such as time,department,grade and so *** were collected from clinical cases,healthy persons,the environment,water,and food at the *** samples were tested for potential bacteria and *** samples that tested positive for norovirus were selected for whole genome sequencing and the sequences were then ***:From 4 March to 3 April 2015,a total of 753 acute diarrhoea cases were reported at the university;the attack rate was 3.29%.The epidemic curve showed two peaks,with the main peak occurring between 10 and 20 March,accounting for 85.26%of reported *** rates of norovirus detection in samples from confirmed cases,people without symptoms,and environmental samples were 32.72%,17.39%,and 9.17%,*** phylogenetic analysis showed that the norovirus belonged to the genotype ***:This is the largest and most severe outbreak caused by genotype GII.17 norovirus in recent years in *** GII.17 viruses displayed high epidemic activity and have become a dominant strain in china.since the winter of 2014,having replaced the previously dominant GII.4 Sydney 2012 strain.

关键词： Human norovirus Acute gastroenteritis outbreak Epidemiological investigation Phylogenetic analysis Henan Province china

Atlas of dynamic spectra of fast radio burst FRB 20201124A

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chinese Physics B 2023年第2期32卷 1-4页

作者：王铂钧胥恒姜金辰徐江伟牛佳瑞陈平李柯伽张冰朱炜玮东苏勃张春风傅海周德江张永坤王培冯毅李晔李冬子鲁文宾杨元培 RNCaballero 蔡策陈卯蒸戴子高艾力·伊沙木丁甘恒谦韩金林郝龙飞黄玉祥姜鹏李承奎李菂李辉李新乔李志玄刘志勇罗睿门云鹏牛晨辉彭文溪钱磊宋黎明孙京海王发印汪敏王娜王维扬吴雪峰肖硕熊少林徐永华徐仁新杨俊杨轩姚蕊易祁彬岳友岭于东俊余文飞袁建平张彬彬张松波张双南赵一郑伟康朱岩邹金航 Kavli institute for Astronomy and Astrophysics Peking UniversityBeijing 100871China National Astronomical Observatories Chinese Academy of SciencesBeijing 100101China Department of Astronomy Peking UniversityBeijing 100871China University of chinese academy of sciences Chinese Academy of SciencesBeijing 100049China Department of Particle Physics and Astrophysics Weizmann Institute of ScienceRehovot 76100Israel Nevada Center for Astrophysics University of NevadaLas VegasNV 89154USA Department of Physics and Astronomy University of NevadaLas VegasNV 89154USA Department of Physics&Astronomy University of IowaIowa CityIA 52242USA Zhejiang laboratory HangzhouZhejiang 311121China Purple Mountain Observatory Chinese Academy of SciencesNanjing 210008China TAPIR Walter Burke Institute for Theoretical PhysicsMail Code 350-17CaltechPasadenaCA 91125USA Department of Astronomy University of California at BerkeleyBerkeleyCA 94720USA South-Western institute For Astronomy Research Yunnan UniversityYunnan 650504China key laboratory of Particle Astrophysics Institute of High Energy PhysicsChinese Academy of SciencesBeijing 100049China Xinjiang Astronomical Observatory Chinese Academy of SciencesUrumqi 830011China University of Science and Technology of china Anhui 230026China yunnan Observatories Chinese Academy of SciencesKunming 650216China Guizhou Normal University Guiyang 550001China CSIRO Space and Astronomy EppingNSW 1710Australia Max-Planck institut fur Radioastronomie Auf Dem HugelBonn53121Germany School of Astronomy and Space Science Nanjing UniversityNanjing 210093China State key laboratory of Nuclear Physics and Technology School of PhysicsPeking UniversityBeijing 100871China Shanghai Astronomical Observatory Chinese Academy of SciencesShanghai 200030China key laboratory of Modern Astronomy and Astrophysics(Nanjing University) Ministry of EducationNanjing 210093China College of Physics Hebei Normal UniversityShijiazhuang 050024China

fast radio bursts(FRBs) are highly dispersed millisecond-duration radio bursts,[1,2]of which the physical origin is still not fully understood. FRB 20201124A is one of the most actively repeating FRBs. In this paper, we present the collection of 1863 burst dynamic spectra of FRB 20201124A measured with the Five-hundred-meter Aperture Spherical radio Telescope(faST). The current collection, taken from the observation during the FRB active phase from April to june 2021, is the largest burst sample detected for any FRB so far. The standard PSRFITs format is adopted, including dynamic spectra of the burst, and the time information of the dynamic spectra, in addition, mask files help readers to identify the pulse positions are also provided. The dataset is available in Science Data Bank, with the link https://***/10.57760/sciencedb.j00113.00076.

关键词： fast radio burst faST

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