Rice gene nomenclature
简述miRNA和其在动、植物中的不同
简述miRNA及其在动、植物中的不同生命科学学院遗传系董贤欣072023032 摘要：mi RNA，是一段超级短的非编码RNA序列，长度约为20 －23 个核苷酸。
miRNA通过与靶mRNA的互补配对而在转录、转录后和翻译水平上对基因的表达进行负调控，致使mRNA 的降解或翻译抑制,进而对多种生物学进程起调控作用。
在植物和动物中，miRNA 执行这种调控作用的机理却不尽相同。
同时miRNA 在动植物体内的形成进程也存在很多的不同的地方。
本文综述了miRNA的大体特点及其在动植物中的不同。
关键词：微小RNA；动、植物；不同Abstract：MicroRNA, is a very small section of non-coding RNA sequence with about 22-23 nucleotides length. MiRNA function as sequence-specific negative regulators in transcriptional、post-transcriptional translational gene silencing by base pairing with target mRNAs, which leadsto mRNA cleavage or translational repression. This can regulate several biological processes. Meantime，there are also many differences in the biogenesis of miRNAs in plants and animals. This review highlights the basic character of miRNA and the differences of miRNA in plants and animals.Key words：miRNA, animal and plant ,differences作为Science 2002年十大科技冲破的第一名—miRNA 已成为生物学研究的一大核心，miRNA由内源性基因编码, 可通过诱导mRNA的切割降解, 翻译抑制或其他形式的调剂机制抑制靶基因的表达.它在生物的发育时序调控和疾病的发生中起到超级重要的作用。
植物基因名称的书写方法
植物基因名称的书写方法
随着基因组学的发展，越来越多的植物基因被发现和命名。
正确的书写方法不仅能够方便科学家之间的交流和合作，也能够避免混淆和误解。
以下是植物基因名称的一些常用书写方法和规范。
1. 基因名称的首字母一般使用小写字母，而蛋白质编码基因的名称则通常使用大写字母。
例如，AT1G01010是一个基因名称，而AT1G01010是该基因的蛋白质编码基因。
2. 基因名称的前缀通常使用物种简称或物种学名的缩写。
例如，AT表示拟南芥，Os表示水稻，Sb表示高粱，Zm表示玉米等等。
如果是多个物种共享一个基因，可以使用共有的前缀，如FLC表示花期调控基因，F-box表示调控细胞周期和信号传导的基因等。
3. 基因名称中的数字通常表示其在基因组中的位置。
例如，
AT1G01010表示拟南芥第1号染色体上的第1010个基因。
4. 基因名称中的字母通常表示其功能或特征。
例如，C表示钙离子信号转导相关基因，MYB表示转录因子家族，LEA表示耐旱基因等。
5. 基因名称中的下划线通常用于分隔不同的元素。
例如，
AT4G10980_1表示拟南芥第4号染色体上的第10980个基因的第一个转录本，AT4G10980_2表示同一基因的第二个转录本。
总之，植物基因名称的书写方法应遵循以上规范，以便于科学家之间的交流和合作，同时也能够避免混淆和误解。
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3000水稻SNP发布文章-nar-gku1039
Nucleic Acids Research,20141doi:10.1093/nar/gku1039SNP-Seek database of SNPs derived from 3000rice genomesNickolai Alexandrov 1,*,†,Shuaishuai Tai 2,†,Wensheng Wang 3,†,Locedie Mansueto 1,Kevin Palis 1,Roven Rommel Fuentes 1,Victor Jun Ulat 1,Dmytro Chebotarov 1,Gengyun Zhang 2,*,Zhikang Li 3,*,Ramil Mauleon 1,Ruaraidh Sackville Hamilton 1and Kenneth L.McNally 11T .T .Chang Genetic Resources Center,IRRI,Los Ba˜nos,Laguna 4031,Philippines,2BGI,Shenzhen 518083,China and 3CAAS,Beijing 100081,ChinaReceived September 08,2014;Revised October 10,2014;Accepted October 10,2014ABSTRACTWe have identified about 20million rice SNPs by aligning reads from the 3000rice genomes project with the Nipponbare genome.The SNPs and al-lele information are organized into a SNP-Seek system (/iric-portal/),which consists of Oracle database having a total number of rows with SNP genotypes close to 60billion (20M SNPs ×3K rice lines)and web interface for con-venient querying.The database allows quick retriev-ing of SNP alleles for all varieties in a given genome region,finding different alleles from predefined vari-eties and querying basic passport and morpholog-ical phenotypic information about sequenced rice lines.SNPs can be visualized together with the gene structures in JBrowse genome browser.Evolutionary relationships between rice varieties can be explored using phylogenetic trees or multidimensional scaling plots.INTRODUCTIONThe current rate of increasing rice yield by traditional breeding is insufficient to feed the growing population in the near future (1).The observed trends in climate change and air pollution create even bigger threats to the global food supply (2).A promising solution to this problem can be the application of modern molecular breeding technolo-gies to ongoing rice breeding programs.This approach has been utilized to increase disease resistance,drought toler-ance and other agronomically important traits (3–5).Un-derstanding the differences in genome structures,combined with phenotyping observations,gene expression and otherinformation,is an important step toward establishing gene-trait associations,building predictive models and applying these models in the breeding process.The 3000rice genome project (6)produced millions of genomic reads for a di-verse set of rice varieties.SNP-Seek database is designed to provide a user-friendly access to the single nucleotide poly-morphisms,or SNPs,identified from this data.Short,83bp pair-ended Illumina reads were aligned using the BW A program (7)to the Nipponbare temperate japonica genome assembly (8),resulting in average of 14×coverage of rice genome among all the varieties.SNP calls were made using GATK pipeline (9)as described in (6).SNP DATAFor the SNP-Seek database we have considered only SNPs,ignoring indels.A union of all SNPs extracted from 3000vcf files consists of 23M SNPs.To eliminate potentially false SNPs,we have collected only SNPs that have the mi-nor allele in at least two different varieties.The number of such SNPs is 20M.All the genotype calls at these positions were combined into one file of ∼20M ×3K SNP calls,and the data were loaded into an Oracle schema using three main tables:STOCK,SNP and SNP GENOTYPE (Figure 1).Some varieties lack reads mapping to the SNP position,and for them no SNP calls were recorded.Distribution of the SNP coverage is shown in Figure 2.About 90%of all SNP calls have a number of supporting reads greater than or equal to four.Out of them,98%have a major allele fre-quency >90%and are considered to be homozygous,1.1%have two alleles with frequencies between 40and 60%and considered to be heterozygous,and the remaining 0.9%rep-resent other cases when the SNP could not be classified as neither heterozygous nor homozygous.More than 98%of SNPs have exactly two different allelic variants in 3000vari-*Towhom correspondence should be addressed.Tel:+63(2)580-5600;Fax:+63(2)580-5699;Email:n.alexandrov@.Correspondence may also be addressed to:zhanggengyun@ and lizhikang@†The authors wish it to be known that,in their opinion,the first 3authors should be regarded as joint First Authors.C The Author(s)2014.Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( /licenses /by /4.0/),which permits unrestricted reuse,distribution,and reproduction in any medium,provided the original work is properly cited.Nucleic Acids Research Advance Access published November 27, 2014 by guest on November 29, 2014/Downloaded from2Nucleic Acids Research,2014Figure 1.Basic schema of the SNP-SeekdatabaseFigure 2.Distribution of SNP coverageeties,1.7%of SNPs have three variants and 0.02%of SNPs have all four nucleotides in different genomes mapped to that SNP position.There are 2.3×more transitions than transvertions in our database (Table 1).Not all SNPs have been called in all varieties.Actually,the distribution of the called SNPs among varieties is bi-modal,with one mode at about 18M SNP calls correspond-ing to japonica varieties which are close to the reference genome,and the second peak at about 14M correspond-ing to the other varieties (Figure 3).Figure 3.SNP distribution by varieties.The major peak shows that about 14M SNPs have been called in most varieties.The bimodal plot indicates that a fraction of SNPs are missing in some varieties,likely due to lack of mapped reads in variable regions.Table 1.Types of allele variants and their frequencies in rice SNPs Allele variants Frequency,%A /G +C /T 70A /C +G /T 15A /T 9C /G6by guest on November 29, 2014/Downloaded fromNucleic Acids Research,20143Figure4.Multidimensional scaling plot of the3000rice varieties.Ind1,ind2and ind3are three groups of indica rice,indx corresponds to other indica varieties,temp is temperate japonica,trop is tropical japonica,temp/trop and trop/temp are admixed temperate and tropical japonica varieties,japx is other japonica varieties,aus is aus,inax is admixed aus and indica,aro is aromatic and admix is all other unassigned varieties.GENOME ANNOTATION DATAWe used CHADO database schema(10)to store the Nip-ponbare reference genome and gene annotation,down-loaded from the MSU rice web site(http://rice.plantbiology. /)(8).To browse and visualize genes and SNPs in the rice genome,we integrated the JBrowse genome browser (11)as a feature of our site.PASSPORT AND MORPHOLOGICAL DATAMost of the3000varieties(and eventually all)are conserved in the International Rice genebank housed at IRRI(12). Passport and basic morphological data from the source ac-cession for the purified genetic stock are accessible via SNP-Seek.INTERFACESWe deployed interfaces to facilitate the following major types of queries:(i)for two varieties find all SNPs from a gene or genomic region that differentiate them;(ii)for a gene or genome region,show all SNP calls for all va-rieties(Supplementary Figure S1);(iii)find all sequenced varieties from a certain country or a subpopulation,whichcan be viewed as a phylogenetic tree,built using TreeCon-structor class from BioJava(13)and rendered using jsPhy-loSVG JavaScript library(14)(Supplementary Figure S2)oras a multidimensional scaling plots(Figure4).The resultsof SNP search can be viewed as a table exported to text files,or visualized in JBrowse.USE CASE EXAMPLE FOR QUERYING A REGION OF INTERESTWe used Rice SNP-Seek database to quickly examine the diversity of the entire panel at a particular region of inter-est.We chose the sd-1gene as test case due to its scientific importance in rice breeding.This semi-dwarf locus,causinga semi-dwarf stature of rice,was discovered by three differ-ent research groups to be a spontaneous mutation of GA20-oxidase(formally named sd-1gene),originating fromthe Taiwanese indica variety Deo-woo-gen.Its incorpora-tion into IR8and other varieties by rice breeding programs spurred the First Green Revolution in rice production inthe late1960s(15).Sd-1is annotated in the Nipponbare genome by Michigan State University’s Rice Genome An-notation Project as LOC Os01g66100,on chromosome1by guest on November 29, 2014/Downloaded from4Nucleic Acids Research,2014Figure 5.Jbrowse view of the SNP genotypes within the sd-1gene (each variety is one row).Red blocks indicate polymorphism of the variety against Nipponbare.Shared SNP blocks are seen as vertical columns in red.The blue rectangle box in the bottom contains varieties that do not have these blocks.from position 38382382to 38385504base pairs.On the home page of SNP-Seek,the <Genotype >module was opened and the coordinates of sd-1were used to define the region to retrieve all SNPs,with <All Varieties >checked to select from all the varieties.Clicking on <Search >but-ton resulted in the identification of 80SNP positions (Sup-plementary Figure S1).An overall view of the SNP posi-tions in the polymorphic panel shows at least eight distinct SNP blocks (Figure 5).In this particular panel group of mostly temperate japonica,two distinct SNP blocks can be seen as shared (Figure 5).Variety information can be ob-tained by typing the name of the varieties you see on the genome browser into the <Variety name >field of the Vari-ety module.This use case is one of the examples detailed in the <Help >module.CONCLUSIONWe have organized the largest collection of rice SNPs into the database data structures for convenient querying and provided user-friendly interfaces to find SNPs in certaingenome regions.We have demonstrated that about 60bil-lion data points can be loaded into an Oracle database and queried with a reasonable (quick)response times.Most of the varieties in SNP-Seek database have passport and ba-sic phenotypic data inherited from their source accession enabling genome-wide or gene-specific tests of association.The database is quickly developing and will be expanding in the near future to include short indels,larger structural variations,SNPs calls using other rice reference genomes.SUPPLEMENTARY DATASupplementary Data are available at NAR Online.ACKNOWLEDGEMENTSWe would like to thank the IRRI ITS team (especially Ro-gelio Alvarez and Denis Diaz)and Rolando Santos Jr for the support in operation and administration of the database and web application servers,and Frances Borja for her help in interface design.by guest on November 29, 2014/Downloaded fromNucleic Acids Research,20145FUNDINGThe database is being supported by the Global Rice Science Partnership(GRiSP),the Bill and Melinda Gates Foundation(GD1393),International S&T Cooperation Program of China(2012DFB32280)and the Peacock Team Award to ZLI from the Shenzhen Municipal government. Conflict of interest statement.None declared. REFERENCES1.Ray,D.K.,Mueller,N.D.,West,P.C.and Foley,J.A.(2013)Yield trendsare insufficient to double global crop production by2050.PloS One, 8,e66428.2.Tai,A.P.K.,Martin,M.V.and Heald,C.L.(2014)Threat to futureglobal food security from climate change and ozone air pollution.Nat.Clim.Change,4,817–821.3.Fahad,S.,Nie,L.,Khan,F.A.,Chen,Y.,Hussain,S.,Wu,C.,Xiong,D.,Jing,W.,Saud,S.,Khan,F.A.et al.(2014)Disease resistance in riceand the role of molecular breeding in protecting rice crops againstdiseases.Biotechnol.Lett.,36,1407–1420.4.Hu,H.and Xiong,L.(2014)Genetic engineering and breeding ofdrought-resistant crops.Ann.Rev.Plant Biol.,65,715–741.5.Gao,Z.Y.,Zhao,S.C.,He,W.M.,Guo,L.B.,Peng,Y.L.,Wang,J.J.,Guo,X.S.,Zhang,X.M.,Rao,Y.C.,Zhang,C.et al.(2013)Dissecting yield-associated loci in super hybrid rice by resequencingrecombinant inbred lines and improving parental genome sequences.Proc.Natl.Acad.Sci.U.S.A.,110,14492–14497.6.3K R.G.P.(2014)The3,000rice genomes project.Gigascience,3,7.7.Li,H.and Durbin,R.(2009)Fast and accurate short read alignmentwith Burrows-Wheeler transform.Bioinformatics,25,1754–1760.8.Kawahara,Y.,de la Bastide,M.,Hamilton,J.P.,Kanamori,H.,McCombie,W.R.,Ouyang,S.,Schwartz,D.C.,Tanaka,T.,Wu,J.,Zhou,S.et al.(2013)Improvement of the Oryza sativa Nipponbarereference genome using next generation sequence and optical mapdata.Rice,6,4.9.McKenna,A.,Hanna,M.,Banks,E.,Sivachenko,A.,Cibulskis,K.,Kernytsky,A.,Garimella,K.,Altshuler,D.,Gabriel,S.,Daly,M.et al.(2010)The Genome Analysis Toolkit:a MapReduce framework foranalyzing next-generation DNA sequencing data.Genome Res.,20,1297–1303.10.Mungall,C.J.,Emmert,D.B.and FlyBase,C.(2007)A Chado casestudy:an ontology-based modular schema for representinggenome-associated biological information.Bioinformatics,23,i337–i346.11.Skinner,M.E.,Uzilov,A.V.,Stein,L.D.,Mungall,C.J.andHolmes,I.H.(2009)JBrowse:a next-generation genome browser.Genome Res.,19,1630–1638.12.Jackson,M.T.(1997)Conservation of rice genetic resources:the roleof the International Rice Genebank at IRRI.Plant Mol.Biol.,35,61–67.13.Prlic,A.,Yates,A.,Bliven,S.E.,Rose,P.W.,Jacobsen,J.,Troshin,P.V.,Chapman,M.,Gao,J.,Koh,C.H.,Foisy,S.et al.(2012)BioJava:anopen-source framework for bioinformatics in2012.Bioinformatics,28,2693–2695.14.Smits,S.A.and Ouverney,C.C.(2010)jsPhyloSVG:a javascriptlibrary for visualizing interactive and vector-based phylogenetic treeson the web.PloS One,5,e12267.15.Hedden,P.(2003)The genes of the Green Revolution.Trends Genet.,19,5–9.by guest on November 29, 2014/Downloaded from。
Rice Spikelet Development
Rice Spikelet DevelopmentRice spikelet development is a complex process that involves the coordination of various genetic, molecular, and environmental factors. This process is critical for rice production, as the spikelets contain the grains that are harvested for consumption. In this response, I will explore the different perspectives surrounding rice spikelet development, including the genetic and molecular mechanisms involved, the environmental factors that influence this process, and the significance of this process for rice production and food security.From a genetic perspective, rice spikelet development is controlled by a complex network of genes that regulate the formation and differentiation of different structures within the spikelet. These genes are expressed in a spatially and temporally specific manner, and their expression is coordinated by various transcription factors and signaling pathways. For example, the OsMADS1 gene is involved in the formation of the floral meristem, while the OsMADS14 gene is involved in the development of the lemma and palea. Mutations in these genes can lead to defects in spikelet development, which can result in reduced grain yield and quality.At the molecular level, rice spikelet development is regulated by various hormones, including auxin, cytokinin, and gibberellin. These hormones play critical roles in cell division, differentiation, and elongation, and their levels and activity are tightly controlled during spikelet development. For example, auxin promotes cell division and differentiation in the floral meristem, while cytokinin promotes cell division and elongation in the developing spikelet. The balance between these hormones is critical for proper spikelet development, and disruptions in this balance can lead to defects in spikelet morphology and grain yield.Environmental factors also play a significant role in rice spikelet development. Temperature, light, and water availability can all influence the timing and progression of this process. For example, high temperatures during the early stages of spikelet development can lead to reduced grain yield, as it can disrupt the formation of the floral meristem and the differentiation of the different structures within the spikelet. Similarly, water stressduring the later stages of spikelet development can lead to reduced grain size and weight, as it can limit the availability of nutrients and water to the developing grain.The significance of rice spikelet development for rice production and food security cannot be overstated. Rice is one of the most important staple crops in the world, and it provides a significant source of calories and nutrients for billions of people. Proper spikelet development is critical for maximizing grain yield and quality, and any disruptions in this process can have significant impacts on food security. For example, climate change is expected to increase the frequency and severity of extreme weather events, such as droughts and heatwaves, which can lead to reduced rice yields and food shortages in many regions.In conclusion, rice spikelet development is a complex and multifaceted process that involves the coordination of various genetic, molecular, and environmental factors. Proper spikelet development is critical for maximizing grain yield and quality, and disruptions in this process can have significant impacts on food security. Understanding the mechanisms that regulate spikelet development, as well as the environmental factors that influence this process, is essential for developing strategies to improve rice production and ensure global food security.。
烟草重要基因篇：8. 烟草P450基因
烟草重要基因篇：8. 烟草P450基因作者：解敏敏来源：《中国烟草科学》2015年第02期细胞色素P450单加氧酶（cytochrome P450 monooxygenases， CYP450）是一个保守的血红素硫蛋白基因超家族，广泛存在于各种动植物、真菌和细菌中，在信号传递、防御反应以及代谢产物合成等多种代谢途径中起着重要的作用。
P450酶系可能是自然界中最具催化作用的生物催化剂，它所催化的反应类型广泛而复杂。
根据其功能，大体可以分为两类：一类是参与植物次生物质的代谢，如植物激素、信号分子、萜类、防御物质等；另一类是代谢外源信号分子或环境污染物，如农药、环境毒素、有机染料等[1-3]。
1 植物P450基因家族及功能1.1 植物P450基因家族随着植物基因组大规模测序，在越来越多的植物中鉴定到P450。
基于蛋白序列的相似性和亲缘关系，将P450归类为家族和亚家族。
同一家族的成员序列相似性>40%，序列相似性>55%归类为一个亚家族[4]。
随着P450家族成员的增多，部分低于40%的蛋白序列遗传聚类分析中明显聚在一起，它们也被归为同一家族。
植物P450超家族归类为10个氏族和127个家族，是目前为止植物中最大的酶家族[5]。
1969年，Frear[6]首次在棉花（Gossypium hirsutum）中发现P450。
目前在拟南芥（Arabidopsis thaliana）[7]、水稻（Oryza sativa） [7]、苜蓿（Medicago sativa）[3]等多种植物中都鉴定到P450。
其中对拟南芥P450的研究较为广泛深入，拟南芥基因组中含有286个P450基因，其中273个基因被分类，组成45个P450家族和72个亚家族，245个全长基因有基因组注释。
芯片数据分析显示拟南芥P450基因整体上表达量要比看家基因低，但许多基因的表达还具有组织特异性。
如CYP88A3和CYP706A2在叶中的表达高于大部分看家基因，CYP81F4和CYP88A3在根中的表达高于看家基因。
水稻术语表
GLOSSARYAleurone layer 糊粉层- the peripheral layer of the endosperm胚乳, containing oil and protein.Adventitious prop roots 须根- roots formed in higher nodes above the soil surface.Axil 叶腋――叶与茎的交角处叫做叶腋。
叶片向轴一面的基部称叶腋。
大多数的侧芽是生在茎的叶腋，叶腋是生长分枝的部位。
Auricles 叶耳- a pair of small, ear-like appendages at the base of the blade, that may not be present in older leaves.Awn 芒- a thorn-like extension from the keel of the lemma. It is not present in all rice varieties.Bract苞叶small degenerated leafBrown rice (caryopsis) 颖果- the dehulled rice grain.Bud 芽苞？- a small protuberance on a node. It may give rise to a tiller. Coleoptile 胚芽鞘- the cylinder-like protective covering of the young plumule幼芽.Coleorhiza 胚根鞘- the sheath covering the radicle.Collar 叶枕- the joint between the leaf sheath and leaf blade.Culm 茎- the round, smooth-surfaced, ascending axis of the shoot consisting of hollow internodes joined by solid nodes.Embryo 胚芽- the miniature plant developed from the fertilized (diploid) egg called zygote, which upon germination gives rise to a young seedling. It is located on the ventral side of the seed next to the lemma.Endosperm 胚乳- the nutritive tissues of the ripened ovary. It consists of the aleurone layer and the starchy endosperm. It serves as food for the germinating embryo.Flag leaf 剑叶- the last leaf just below the panicle.Floret 小花- A unit of the spikelet. It includes the lemma, palea and the flower.Flower 花- It consists of two lodicules, six stamens and the pistil.Grain - the ripened ovary and its associated structures.Hull 外壳- the lemma and palea, and their associated structures. Internode 节间- the smooth, solid (when young), or hollow (when mature) part of the culm between two successive nodes.Keel 外颖的中间叶脉（龙骨瓣？）- the middle nerve of the lemma. Leaf - the vegetative part of a tiller consisting of the blade and sheath.Leaf blade - the flat and free portion of the leaf.Leaf sheath 叶鞘- the lower part of the leaf, originating from a node and wrapped around the culm above the node.Lemma 外颖- the five-nerved bract of the floret.Ligule 叶舌- a thin, upright, membranous structure attached to the base of the inside of the flower.Lodicules 浆片- the two scale-like structures near the base of the palea. Mesocotyl 中胚轴- the internode between the coleoptile node and the point of union of the culm and root in the young seedlings. It pushes the coleoptile above the soil surface.Midrib 中脉- the prominent ridge in the middle of the underside of the leaf blade.Neck (panicle base) 颈？- the nearly solid node between the uppermost internode of the culm and the panicle axis. 在茎的最上节间与花序轴之间的节。
水稻术语表——精选推荐
GLOSSARYAleurone layer 糊粉层- the peripheral layer of the endosperm胚乳, containing oil and protein.Adventitious prop roots 须根- roots formed in higher nodes above the soil surface.Axil 叶腋――叶与茎的交角处叫做叶腋。
叶片向轴一面的基部称叶腋。
大多数的侧芽是生在茎的叶腋，叶腋是生长分枝的部位。
Auricles 叶耳- a pair of small, ear-like appendages at the base of the blade, that may not be present in older leaves.Awn 芒- a thorn-like extension from the keel of the lemma. It is not present in all rice varieties.Bract苞叶small degenerated leafBrown rice (caryopsis) 颖果- the dehulled rice grain.Bud 芽苞？- a small protuberance on a node. It may give rise to a tiller. Coleoptile 胚芽鞘- the cylinder-like protective covering of the young plumule幼芽.Coleorhiza 胚根鞘- the sheath covering the radicle.Collar 叶枕- the joint between the leaf sheath and leaf blade.Culm 茎- the round, smooth-surfaced, ascending axis of the shoot consisting of hollow internodes joined by solid nodes.Embryo 胚芽- the miniature plant developed from the fertilized (diploid) egg called zygote, which upon germination gives rise to a youngseedling. It is located on the ventral side of the seed next to the lemma.Endosperm 胚乳- the nutritive tissues of the ripened ovary. It consists of the aleurone layer and the starchy endosperm. It serves as food for the germinating embryo.Flag leaf 剑叶- the last leaf just below the panicle.Floret 小花- A unit of the spikelet. It includes the lemma, palea and the flower.Flower 花- It consists of two lodicules, six stamens and the pistil.Grain - the ripened ovary and its associated structures.Hull 外壳- the lemma and palea, and their associated structures. Internode 节间- the smooth, solid (when young), or hollow (when mature) part of the culm between two successive nodes.Keel 外颖的中间叶脉（龙骨瓣？）- the middle nerve of the lemma. Leaf - the vegetative part of a tiller consisting of the blade and sheath.Leaf blade - the flat and free portion of the leaf.Leaf sheath 叶鞘- the lower part of the leaf, originating from a node and wrapped around the culm above the node.Lemma 外颖- the five-nerved bract of the floret.Ligule 叶舌- a thin, upright, membranous structure attached to the base of the inside of the flower.Lodicules 浆片- the two scale-like structures near the base of the palea. Mesocotyl 中胚轴- the internode between the coleoptile node and the point of union of the culm and root in the young seedlings. It pushes the coleoptile above the soil surface.Midrib 中脉- the prominent ridge in the middle of the underside of the leaf blade.Neck (panicle base) 颈？- the nearly solid node between the uppermost internode of the culm and the panicle axis. 在茎的最上节间与花序轴之间的节。
水稻dirigent基因家族生物信息学分析
达最为丰富 ； 同源基 因分子遗传进化分析表 明， Ｏ ｓ Ｄ Ｉ Ｒ基 因可分为 ５个亚类 ， 功能域片段与基 因的复制特 征表明 ，
Ｏ ｓ ＤＩ Ｒ基 因可能起源于共 同的祖先（ 基 因） 。
ｔ ｈ ａ ｔ ａ ｌ ｌ ｔ ｈ ｅ ｃ ｏ ｎ ｓ ｅ ｖｅ ｒ ｄ ｐ ｒ ｏ ｔ ｅ ｉ ｎ ｓ ｅ ｑ ｕ ｅ ｎ ｃ ｅ ｓ ｗｅ ｒ ｅ ｌ ｏ ｃ ａ ｔ ｅ ｄ ｉ ｎ ｈｅ ｔ ｃ ｏ ｎ ｓ ｅ ｒ ｖ ｅ ｄ ｄ ｏ ｍａ ｉ ｎ ，ａ ｎ ｄ ｍｏ ｓ ｔ ｏ ｆ ｈｅ ｔ ｐ ｒ ｏ ｔ ｅ ｉ ｎ ｓ ａ ｒ ｅ ｓ ａｂ ｔ ｉ ｌ ｉ ｚ ｅ ｄ ｈ ｙ ｄ ｒ ｏ ｐ ｈ ｏ ｂ ｉ ｃ ｐ ｒ ｏ ｔ ｅ ｉ ｎ ｓ ， ｗｈ ｉ ｃ ｈ ｅ ｘ ｐ ｒ ｅ ｓ ｓ ｅ ｄ ｉ ｎ ｍｏ ｓ ｔ ｏ ｆ ｈｅ ｔ ｏ ｒ ｇ ａ ｎ ｅ ｌ ｌ ｅ ｓ ｗｉ ｈ ｔ ｈｅ ｔ ｍｏ ｓ ｔ ｏ ｆ ｗｈ ｉ ｃ ｈ ａ ｂ ｕ ｎ ｄ ａ ｎ ｔ ｌ ｙ ｅ ｘ ｐ ｒ ｅ ｓ ｓ ｅ ｄ ｉ ｎ ｈｅ ｔ ｃ ｅ ｌ ｌ ｗａ ｌ ｌ ， ａ ｃ ｃ ｏ ｒ ｄ ｉ ｎ ｇ ｔ ｏ Ｏｓ ＤＩ Ｒ ｐ ｒ ｏ ｔ ｅ ｉ ｎ ｓ ｅ ｑ ｕ ｅ ｎ ｃ ｅ ｓ ｆ ｕ ｎ ｃ ｔ ｉ ｏ ｎ ａ ｌ ｐ ｒ ｅ ｄ ｉ ｃ ｔ ｉ ｏ ｎ ． Ｔ ｈ ｅ Ｏｓ ＤＩ Ｒ ｇ ｅ ｎ ｅ ｓ ｗｅ ｒ ｅ ｃ ｌ ａ ｓ ｓ ｉ ｉｅ ｆ ｄ ｉ ｔｏ ｎ ｉ ｆ ｖ ｅ ｓ ｕ ｂ ｇ ｒ ｏ ｕ ｐ ｓ ａ ｃ ｃ ｏ ｒ ｄ ｉ ｎ ｇ ｔ ｏ ｐ ｈ ｙ ｌ ｏ ｇ ｅ ｎ ｅ ｔ ｉ ｃ ａ ｎ ａ ｌ ｙ ｓ ｅ ｓ ｂ ａ ｓ ｅ ｄ ｏ ｎ ｃ ｏ ｎ ｓ ｅ ｖｅ ｒ ｄ ｐ ｒ ｏ ｔ ｅ ｉ ｎ ｄ ｏ ｍａ ｉ ｎ ｓ ｅ ｑ ｕ ｅ ｎ ｃ ｅ ｓ ．Ａｄ ｄ ｉ ｔ ｉ ｏ ｎ ａ ｌ ｌ ｙ ，ｔ ｈｅ ｒ ｅ ｐ ｌ ｉ ｃ ａ ｔ ｉ ｏ ｎ
生物学常见名词
生物学常见名词Abundance (mRNA 丰度)：指每个细胞中mRNA 分子的数目。
Abundant mRNA(高丰度mRNA)：由少量不同种类mRNA组成，每一种在细胞中出现大量拷贝。
Acceptor splicing site (受体剪切位点)：内含子右末端和相邻外显子左末端的边界。
Acentric fragment(无著丝粒片段)：(由打断产生的)染色体无著丝粒片段缺少中心粒，从而在细胞分化中被丢失。
Active site(活性位点)：蛋白质上一个底物结合的有限区域。
Allele(等位基因)：在染色体上占据给定位点基因的不同形式。
Allelic exclusion(等位基因排斥)：形容在特殊淋巴细胞中只有一个等位基因来表达编码的免疫球蛋白质。
Allosteric control(別构调控)：指蛋白质一个位点上的反应能够影响另一个位点活性的能力。
Alu-equivalent family(Alu 相当序列基因)：哺乳动物基因组上一组序列，它们与人类Alu 家族相关。
Alu family (Alu家族)：人类基因组中一系列分散的相关序列，每个约300bp长。
每个成员其两端有Alu 切割位点(名字的由来)。
α-Amanitin(鹅膏覃碱)：是来自毒蘑菇Amanita phalloides 二环八肽，能抑制真核RNA 聚合酶，特別是聚合酶II 轉录。
Amber codon (琥珀密码子)：核苷酸三联体UAG，引起蛋白质合成终止的三个密码子之一。
Amber mutation (琥珀突变)：指代表蛋白质中氨基酸密码子占据的位点上突变成琥珀密码子的任何DNA 改变。
Amber suppressors (琥珀抑制子)：编码tRNA的基因突变使其反密码子被改变，从而能识別UAG 密码子和之前的密码子。
Aminoacyl-tRNA (氨酰-tRNA)：是携带氨基酸的轉运RNA，共价連接位在氨基酸的NH2基团和tRNA 终止碱基的3￠或者2￠－OH 基团上。
植物基因组中微型反向重复转座元件(MITE)研究进展
植物基因组中微型反向重复转座元件(MITE)研究进展1孙海悦，张志宏*沈阳农业大学园艺学院，沈阳（110161）E-mail：zhangz@摘要：微型反向重复转座元件(miniature inverted repeat transposable element， MITE)是一类特殊的转座元件，其在结构上与有缺失的DNA转座子相似，但具有反转录转座子高拷贝数的特点。
MITE时常与基因相伴，对基因调控可能起重要作用，因此，MITE正逐渐成为基因和基因组进化及生物多样性研究的一种重要工具。
本文综述了植物基因组中MITE的研究进展，并对其应用前景进行了展望。
关键词：微型反向重复转座元件，基因，进化转座元件（transposable elements）是指在生物细胞中能从同一条染色体的一个位点转移到另一个位点或者从一条染色体转移到另一条染色体上的DNA序列。
转座元件是真核生物基因组的主要成分，根据转座媒介的不同而分为两类，即类型I和类型II (Casacuberta and Santiago， 2003)。
类型I转座元件以RNA为媒介进行转座，即作为DNA的转座元件首先被转录为RNA，再借助反转录酶/RNase H反转录为DNA，插入到新的染色体位点，因此，类型I转座元件也被称为反转录转座子(retrotransposon)。
类型II转座元件直接以DNA为媒介进行转座，因此，类型II转座元件也被称为DNA转座子（DNA transposon）。
反转录转座子的“复制和粘贴”转座机制使其可以快速地增加拷贝数，所以在真核生物基因组中占很高的比例；而DNA转座子的“剪切和粘贴”转座机制不增加拷贝数，所以其在基因组中仅有少量重复(Bennetzen， 2000)。
微型反向重复转座元件(miniature inverted repeat transposable element， MITE)是20世纪90年代发现的一类特殊的DNA 转座子(Bureau and Wessler， 1992；Bureau and Wessler， 1994)，其在结构上与非自主DNA转座子相似，但具有反转录转座子的高拷贝数特点 (Feschotte， et al.， 2002a)。
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RGAP：基因命名法
在访问水稻基因组注解计划的FTP地址或网页上的模拟分子数据时，会见到其内部使用的术语，如TU和基因模块。
这篇文章旨在解释此计划的命名法，并且将其与生物学家普遍使用的命名法联系起来。
转录单位：
一个转录单位相当于一个基因或模拟分子上的一个基因座。
转录单元以一种精确的命名规则储存在数据库中，合适名字如：x.tyyyyy 。
其中，x指的是BAC或模拟分子的收录编号，yyyyy是转录单位的特异标识符。
位点标识符：
对于最终的用户，上面命名规则介绍的复杂在于转录单位的合适名字可在版本之间转换。
为了避免这个问题，基因的位点标识符已经在模拟分子的这个版本中被实施了。
和拟南芥基因组命名使用的约定一样，对更大的水稻基因组也只有较小的改变。
每个细胞核基因被标记为LOC_OsXXg#####，其中LOC_Os代表水稻的座点，XX表示染色体编号01-12，g代表基因，5个#####表示基因在染色体上的顺序。
LOC_Osp#g#####是用于质体基因，对于线粒体基因是使用LOC_Osm#g#####。
基因（基因座）的编号是沿着染色体或细胞器的基因组，按顺序每隔10个编号的，这是考虑到了将来新基因座的插入。
在编号系统中提供了足够的空间用于物理间隔，在序列上允许已经在物理间隔上填满的新基因的插入。
为了促进基因的新位点标识符在以前两种表示方式中的整合，我们已经开发了一个版本转换器，允许使用者容易地找到以前的基因和模块所对应的新位点标识符，这些以前的基因和模块是根据合适名字被标志的
基因模块:
一个基因模块是代表一个转录单位的mRNA转录物，因此它包含着转录本的特征信息，如内含子和外显子的边界、剪切位点和非翻译序列等。
由于mRNA转录物的可变剪切，一个转录单位可以产生不止一个基因模块。
基因模块在数据库中有唯一的合适名字，并且它们和相应的转录单位也被连接起来。
合适名字采取x.myyyyy的形式，其中x代表BAC或者模拟分子收录ID，yyyyy是指基因模块独特的标识符。
其中Pseudomolecule：模拟分子；feat_name：合适名字。
感觉还是不对，但是找不到合适的词来表
示了！
RAP-DB：水稻基因命名法
自从国际水稻基因组测序计划完成了水稻日本晴的基因组测序，其希望以此解密基因组的所有基因区。
系统的基因座标识符被指定到IRGSP基因组汇编的RAP中。
一个ID(OsXXg#######)包括物种名（Os代表水稻），一个表示染色体的两位数，标识符的类型（g表示基因）和一个表示在染色体上相应顺序的七位数。
这种命名是由基因标记命
名与联合委员会在第一、二届水稻注解计划大会上提出的。
通过集中讨论基础上的改良，最终被IRGSP/RAP认定。
水稻标识符的RAP注解以AP008207-AP009218 的登录号被递交至DDBJ/EMBL/Genbank，并且在RefSeq中使用。
水稻的代码也在UniProtKB/Swiss-Prot 中作为位点标识符使用。