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Statistical analysis on adaptive evolution of SQUA genes in angiosperms

Progress in Natural science:Materials International 2005年第1期 94-97页

作者： CHEN Yongyan 1,2, ZHONG Yang 3.*, TIAN Bo 1, YANG Ji 4 and LI Dezhu 1*(1. laboratory of Plant biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of sciences, Kunming 650204,{3. 2. College of Bioengineering, Dalian university, Dalian 116622,{3. 3. ministry of education key laboratory for biodiversity and ecological engineering, school of life science, fudan university, shanghai 200433,{3. 4. College of life sciences, Peking university, Beijing 100871,{3.) laboratory of Plant biodiversity and Biogeography，Kunming Institute of Botany，Chinese Academy of sciences，Kunming 650204 China College of Bioengineering，Dalian university，Dalian 116622，china ministry of education key {3. for biodiversity and ecological engineering，school of life science，fudan university，shanghai {13.，china laboratory of Plant biodiversity and Biogeography，Kunming Institute of Botany，Chinese Academy of sciences，Kunming 650204 China College of life sciences，Peking university，Beijing 100871，{3.

SQUAMOSA (SQUA) subfamily includes important perianth identity genes of MADS-box gene family. SQUA genes of Dendrocalamus latiflorus were sequenced, and phylogenetic form on SQUA genes in angiosperms was analyzed. Relative rate and adaptive evolution after SQUA gene duplication in recent common ancestor of monocots and eudicots were analyzed using the methods of relative rate test, statistic on synonymous and non-synonymous coden substitution sites and likelihood rate test. The results show that both of relative rate and synonymous and non-synonymous coden substitution in eudicot clade are significantly higher than those in monocot clade, and the value of d N/d S uncovered possible positive selective pressure in eudicot clade.

关键词： angiosperms Dendrocalamus latiflorus SQUA gene relative rate test likelihood rate test adaptive evolution.

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Efficient indica and japonica rice identification based on the InDel molecular method:Its implication in rice breeding and evolutionary research

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Progress in Natural science:Materials International 2009年第10期19卷 1241-1252页

作者： Bao-Rong Lu,Xingxing Cai,Xin Jin ministry of education key {3. for biodiversity science and ecological engineering,Institute of biodiversity science,fudan university,shanghai {13.,china ministry of education key {3. for biodiversity science and ecological engineering Institute of Biodiversity Science Fudan University Shanghai 200433 China

An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms of insertion/deletion(InDel) DNA fragments obtained from the basic local alignment search tool(BLAST) to the entire genomic sequences of indica(93.11) and japonica rice(Nipponbare).The 45 InDel loci were validated experimentally by the polymerase chain reaction(PCR) and polyacrylamide gel electrophoresis(PAGE) in 44 typical indica and japonica rice varieties,including 93.11 and Nipponbare.A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 3. InDel loci were strongly associated with the differentiation of indica and japonica *** extensive analyses involving cultivated rice varieties from 11 Asian countries,and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica-or japonica-specific alleles on different InDel loci across the rice *** method was named as the ’’InDel molecular index" that combines molecular and statistical methods in determining the indica and japonica characteristics of rice *** with the traditional methods based essentially on morphology,the InDel molecular index provides a very accurate,rapid,simple,and efficient method for identifying indica and japonica *** addition,the InDel index can be used to determine indica or japonica characteristics of wild Oryza species,which largely extends the utility of this *** InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice *** also offers a novel model for the study of the origin,evolution,and genetic differentiation of indica and japonica rice adapted to various environmental changes.

关键词： Cultivated rice Wild Oryza InDel Molecular marker indica-japonica identification Neutrality test

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Phylogenetic relationships of host insects of Cordyceps sinensis inferred from mitochondrial Cytochrome b sequences

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Progress in Natural science:Materials International 2007年第7期17卷 789-797页

作者： Cheng Zhou~(1,2**) Geng Yang~1 Liang Honghui~1 Yang Xiaoling~1 Li Shan~1 Zhu Yunguo~1 Guo Guangpu~1 Zhou Tongshui~2 Chen Jiakuan~2 (1.school of life science and Technology,Tongji {3.,shanghai 200092,china 2.ministry of education key laboratory for biodiversity science and ecological {13.,Institute of biodiversity science,fudan {3.,shanghai 200433,china) school of life science and Technology Tongji University Shanghai 200092 China ministry of education key Lab. for {3. science and ecological engineering Institute of Biodiversity Science Fudan University Shanghai 200433 China

This study used the sequence of the mitochondrial Cytochrome b(Cytb)to estimate phylogenetic relationships among host Hepialidae insects of Cordyceps *** DNA of host insect was extracted from the dead larva head part of 18 cordyceps populations and 2 species of Hepialus,and the Cytb fragment of host insect was amplified with PCR *** nucleotide sequence alignments and their homologous sequences of 24 species host Hepialidae insects of Cordyceps sinensis were obtained from GenBank and were used to construct phylogenetic trees based on neighbor-joining *** results showed that genus Bipectilus diverged earlier than genus Hepialus and *** host insects of Cordyceps sinensis have multitudinous species with different morphological characteristics and geographical *** interspecific genetic differentiations are obvious in ***,the genus Hepialus might be considered as polyphyletic *** sequences have abundant variations among the host insects of Cordyceps sinensis on spe- cific and generic *** divergence rate of Cytb sequences among the species in Hepialus ranged from 0.23. to 9.24%,except that Hepialus pratensis and Hepialus jinshaensis have the same *** sequence can be used for species identification of host insects of Cordyceps sinensis,but further confirmation in more host insect species is *** obtain the Cytb sequence of host insect by ampli- fying DNA extracted from the head part of dead larva in cordyceps turns out to be an effective and accurate approach,which will be useful for studies on phylogeny and genetic structure of host insects of cordyceps populations,especially for analyzing relationships between C. sinensis and its host insects.

关键词： mitochondrial Cytochrome b Cordyceps sinensis Hepialus phylogeny

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Effects of Citral on Aspergillus flavus Spores by Quasi-elastic Light Scattering and Multiplex Microanalysis Techniques

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Acta Biochimica et Biophysica Sinica 2004年第4期36卷 277-283页

作者： Man LUO1,2, Li-Ke JIANG2, Yao-Xiong HUANG3. Ming XIAO4, Bo LI4, and Guo-Lin ZOU1* 1College of life sciences, Wuhan university, Wuhan 43.072,{3. 2College of life sciences, Anhui Agricultural university, Hefei 23.03.,{3. 3.Institute of Biomedical engineering, Ji’nan university, Guangzhou 51063.,{3. 4ministry of education {13. laboratory for biodiversity science and ecological engineering, the Institute of biodiversity science, fudan university, shanghai 200433,{3. College of life sciences Wuhan UniversityWuhan 430072 China College of life sciences Anhui Agricultural UniversityHefei 230036 China Institute of Biomedical engineering Ji'nan UniversityGuangzhou 510632 China ministry of education key {3. for biodiversity science and ecological engineering the Institute of Biodiversity Science Fudan UniversityShanghai 200433 China

Citral refined from Litsea cubeba oil has been found to have a strong influence on fungi, especially Aspergillus flavus. Multiplex microanalysis and quasi-elastic light scattering techniques were applied to study the effects of citral on Aspergillus flavus spores from the levels of membrane, organelle and intracellular macromolecule. It was found that citral injured the wall and the membrane of A. flavus spore, resulting in decrease of its elasticity. After entering the cell, citral not only influenced the genetic expression of mitochondrion reduplication and its morphology, but also changed the aggregation of protein-like macromolecules. As a result, cells, organelles and macromolecules lost their normal structures and functions, eventually leading to the loss of germination ability of A. flavus spores. Since Litsea cubeba oil as food additive and antifungal agent is safe and less poisonous, it is important to elucidate the inhibitory mechanisms of Litsea cubeba oil on the germination ability of A. flavus spore.

关键词： citral Aspergillus flavus spore multiplex microanalysis techniques quasi-elastic light scattering technique

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Relationships of Aegilops tauschii revealed by DNA fingerprints:The evidence for agriculture exchange between china and the West

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Progress in Natural science:Materials International 2008年第12期18卷 1525-1531页

作者： Huiting Wei~a Jun Li~a Zhengsong Peng~b Baorong Lu~c Zhijun Zhao~d Wuyun Yang~a a Crop Research Institute,Sichuan Academy of Agricultural sciences,Chengdu 610066,china b life science College,china West Normal university,Nanchong 63.002,china c The ministry of education key laboratory for biodiversity science and {13. engineering,Institute of biodiversity science,fudan university,shanghai 200433,china d Chinese Academy of Social science,Beijing 110710,china Crop Research Institute Sichuan Academy of Agricultural Sciences Chengdu 610066 China life science College China West Normal University Nanchong 637002 China The ministry of education key {3. for biodiversity science and ecological engineering Institute of Biodiversity Science Fudan University Shanghai 200433 China Chinese Academy of Social science Beijing 110710 China

Genetic diversity and relationships of wild goat grass (Aegilops tauschii Cosson) from Iran and Xinjiang,west china,as well as its weedy type from the Yellow River region of Shaanxi and Henan provinces in china were analyzed by simple sequence repeat (SSR) fingerprints.A high level of genetic diversity in Aegilops tauschii accessions from Iran was observed,and the richness of genetic diversity was followed by accessions from Shaanxi,Henan,and *** weedy type of Aegilops tauschii showed a close genetic relationship with the wild type from different regions in *** results indicated that the weedy Aegilops tauschii found in the Yellow River region was most likely introduced from Iran—the diversity center of Aegilops *** weedy Aegilops tauschii populations found in the Yellow River region may be brought into the central part of china as a weed species together with common wheat (Triticum aestivum L.) from the West during various periods of time in *** finding has provided strong evidence for the introduction of common wheat from the West into china via the Silk Road,and also demonstrated the important role of the Silk Road in the exchange of agri- culture and other relevant technologies between china and the West.

关键词： The Silk Road Aegilops tauschii Common wheat SSR fingerprints Genetic diversity Affinity Crop dispersion

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Characterization of a novel developmentally retarded mutant (drm1) associated with the autonomous flowering pathway in Arabidopsis

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Cell Research 2005年第2期15卷 133-140页

作者： Yong ZHU1,2,*, Hui Fang ZHAO1,3.*, Guo Dong REN1, Xiao Fei YU1, Shu Qing CAO1, Ben Ke KUAI1,4,**1Department of Biochemistry, ministry of education key {3. for biodiversity science and ecological engineering, school of life sciences, fudan university, 220 Handan Road, shanghai 200433, china 2school of Horticulture and Gardening, Southwest Forestry College, Kun Ming 650224, china 3.epartment of biology, school of life and Environment science, shanghai Normal university, shanghai 20023., china4fudan Centre for Genetic Diversity and designed Agriculture, fudan university, 220 Handan Road, shanghai 200433, china Department of Biochemistry Ministry of Education Key laboratory for Biodiversity Science and Ecological Engineering School of Life Sciences Fudan University Shanghai China school of Horticulture and Gardening Southwest Forestry College Kun Ming China Department of biology School of Life and Environment Science Shanghai Normal University Shanghai China fudan Centre for Genetic Diversity and designed Agriculture Fudan University Shanghai China

A developmentally retarded mutant (drm1) was identified from ethyl methanesulfonate (EMS)-mutagenized M2 seedsin Columbia (Col-0) genetic background. The drm1 flowers 109 d after sowing, with a whole life cycle of about 160 *** also shows a pleiotropic phenotype, e.g., slow germination and lower germination rate, lower growth rate, curlingleaves and abnormal floral organs. The drm1 mutation was a single recessive nuclear mutation, which was mapped tothe bottom of chromosome 5 and located within a region of 20-3. kb around MXK3.1. There have been no mutantswith similar phenotypes reported in the literature, suggesting that DRM1 is a novel flowering promoting locus. Thefindings that the drm1 flowered lately under all photoperiod conditions and its late flowering phenotype was significantlyrestored by vernalization treatment suggest that the drm1 is a typical late flowering mutant and most likely associatedwith the autonomous flowering pathway. The conclusion was further confirmed by the revelation that the transcriptlevel of FLC was constantly upregulated in the drm1 at all the developmental phases examined, except for a very earlystage. Moreover, the transcript levels of two other important repressors, EMF and TFL1, were also upregulated in thedrm1, implying that the two repressors, along with FLC, seems to act in parallel pathways in the drm1 to regulateflowering as well as other aspects of floral development in a negatively additive way. This helps to explain why the drm1exhibits a much more severe late-flowering phenotype than most late-flowering mutants reported. It also implies that theDRM1 might act upstream of these repressors.

关键词： drm1 late-flowering autonomous flowering pathway Arabidopsis thaliana.

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Can transgenic rice cause ecological risks through transgene escape?

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Progress in Natural science:Materials International 2003年第1期 19-26页

作者： LU Baorong , SONG Zhiping and CHEN Jiakuan(ministry of education key {3. for biodiversity and ecological engineering, Institute of biodiversity science, fudan university, shanghai 200433, china) ministry of education key {3. for biodiversity and ecological engineering Institute of Biodiversity Science Fudan University Shanghai 200433 China

Abstract Alien transgene escape from genetically engineered rice to non-transgenic varieties or close wild relatives (includingweedy rice) may lead to unpredictable ecological risks. However, for transgene escape to occur three conditions need to be met: (i) spa-tially, transgenic rice and its non-transgenic counterparts or wild relatives should have sympatric distributions; (ii) temporally, the flower-ing time of transgenic rice and the non-transgenic varieties or wild relatives should overlap; and (iii) biologically, transgenic rice and itswild relative species should have such a sufficiently close relationship that their interspecific hybrids can have normal generative reproduc-tion. This paper presents research data on the geographic distribution, flowering habits, interspecific hybridization, and gene flow of culti-vated rice (Oryza sativa) and its closely related wild relatives containing the AA genome. The objective is to estimate the possibility oftransgene escape to non-transgenic rice varietie

关键词： oryza species transgene escape biosafety ecological risk introgression gene flow.

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Utility of mtDNA rps14-cob spacer sequences in phylogeny of Ericales

Utility of mtDNA rps14-cob spacer sequences in phylogeny of ...

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全国系统与进化植物学研讨会暨第九届系统与进化植物学青年研讨会

作者： QIANYi-wei WANG Yu-guo ministry of education key {3. for biodiversity science and ecological engineering, Institute of biodiversity science, fudan university, shanghai 200433, P. R. china

The mitochondnal genome had been little used in plant phylogenetic studies. Only several genes such as coxI, coxII, atpA, matR, nad1, nad4 were used in the past decades. Unlike chloroplast intergenic regions separating genes, the spacer sequences between mitochondnal genes were difficult to be amplified as well as intron sequences because the order of the genes in the mtDNA molecule was usually not conserved. The mitochondnal DNA rpsl4-cob spacer is an exception. Plant mitochondrial DNA rps14 pseudogene and cob gene have remained associated throughout evolution such as the ribosomal genes. The conserved sequences of rps14 and cob make it easy to design primers for amplification and cycle sequencing. Not all eudicots has the rps14 pseudogene. It can be found in Solanaceae (e.g. Tobacoo), Brassicaceae (e.g. Arabidopsis, Brassica), Fabaceae (e.g. Soybean), Malvaceae (e.g. Cotton), etc. In this study, the sequences of mtDNA rps14-cob specer were investigated to test whether the spacer exist in Ericales sensu Angiosperm Phylogeny Group (1998, 2003. and it can be used for phylogenetic analyses.

关键词： Ericales mtDNA rps14-cob spacer phylogeny

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Characterization of a rice （Oryza sativa L.） gene encoding a temperature-dependent chloroplast ω-3.fatty acid desaturase

Characterization of a rice （Oryza sativa L.） gene encoding...

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第二届上海市植物生理学青年学术研讨会

作者： Jingwen Wang , Shijinlei,Feng Ming*Institute of Genetics, State key laboratory of Genetic engineering, Research Center of Gene Diversity and Designed Agriculture,{3. of education key laboratory for biodiversity science and ecological engineering, school of life science, fudan university,{13. 200433, china

＜正＞A cDNA, designated Osfad8, encoding a chloroplast ω-3.fatty acid desaturase responsible for trienoic fatty acid formation, was isolated from the leaves of Oryza sativa L. by RT-PCR. Southern

关键词： Fatty acid In situ hybridization Osfad8 Oryza sativa L. ω-3.fatty acid desaturase Transgenic tobacco

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THE RELATIONSHIPS BETWEEN THE BRYOPHTES AND CARLIN GOLD DEPOSIT IN LANNIGOU GOLD MINE, GUIZHOU PROVINCE

THE RELATIONSHIPS BETWEEN THE BRYOPHTES AND CARLIN GOLD DEPO...

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中国苔鲜植物学奠基人陈邦杰先生百年诞辰国际学术研讨会

作者： Wen-Hu Huang Zhao-Hui Zhang ( school of Geography and Biology science, Guizhou Normal university, Guiyang, Guizhou 550001 {3. of education key laboratory for biodiversity science and ecological engineering, Institute of biodiversity science,{13., shanghai 200433)

＜正＞This paper is the study of the bryophytes of Lannigou Carlin Gold Mine in southwestern Guizhou Province, china. Ecology, flora of the Carlin gold deposit sites and its relationship with the distribution of the b... 详细信息

关键词： Bryophytes Carlin gold mine Lanniguo Guizhou

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