植原体的最新分类研究动态

简要介绍了植原体分类研究历史与现状,综述了最新的植原体分类方法和植原体候选种的描述规则,指出了我国在植原体分类鉴定方面与当今世界先进水平的差距及今后发展方向.     

植原体检测与分类研究进展

从20世纪60年代末发现植原体以来,目前已发现的植原体已有300多种,其中有多种植原体危害经济作物。综述了国内外植原体检测方法与分类研究。     

植原体遗传多样性研究现状与展望

植原体是引起众多植物病害的一类重要的无细胞壁的原核致病菌, 其寄主种类多、危害面积广, 对经济、环境等影响严重。大量研究表明植原体存在丰富的遗传多样性。本文就植原体遗传多样性研究现状作一概要评述, 并对植原体遗传变异的研究技术、产生机制、与致病性关系等今后可能的研究方向作一展望。对已完成的5个植原体全基因组序列分析发现, 它们在大小、结构和功能等方面皆存在显著差异, 缺少很多标准代谢所需的基因。不同植原体中质粒的数量、大小和功能等也存在一定差异。植原体含有2个核糖体RNA编码基因, 其序列在不同株系中的变异奠定了现今植原体分类鉴定的基础。对植原体蛋白编码基因如核糖体蛋白编码基因(rp)、蛋白延伸因子基因(tuf、fusA)、转运蛋白基因(secY、secA)、效应子及非编码区序列如启动子、假基因等的深入研究可进一步揭示植原体更丰富的遗传变异特征。由于植原体分离培养困难, 人们对其形态特征、生理代谢等了解甚少, 因而全基因组测序、多位点序列分析等现代分子生物学技术将会成为植原体遗传变异研究的主要手段。植原体遗传多样性研究进展有助于从分子水平上系统地阐明植原体遗传变异规律、系统进化特征及其与寄主(植物和昆虫)、生态环境间的互作和适应关系, 并产生新的认识。这对于提高植原体的分类鉴定、致病机制、流行预测及病害防治等研究水平具有重要的作用和意义。     

柳树黄化病植原体的分子分类

[目的]柳树黄化病是一种重要的植原体病害,本研究旨在明确柳树黄化病植原体(Willow Yellow phytoplasma,WY)的分类地位,为进一步开展致病性和防治研究奠定基础.[方法]采用植原体特异引物通过PCR方法从患病植株DNA中扩增植原体16S rDNA基因和核糖体蛋白基因(ribosomal proteins gene,rp),对所得的序列进行分析,构建同源进化树,并用限制性片段长度多态性(RFTJP)对巢式PCR产物进行分析.[结果]首次从柳树黄化病植原体中分离出了16S rDNA基因和rp基因,大小分别为1246 bp和1212 bp.通过对植原体16S rDNA和rp基因的核苷酸同源性比较和RFLP分析,发现该分离物与16S rI组的核苷酸同源性均在99%以上,与16S rI-C亚组中的小麦蓝矮病植原体同源性高达99.8%(16Sr DNA)和99.6%(rp),且RFLP分析与16SrI-C亚组的植原体有相同的酶切条带.[结论]柳树黄化植原体应划分于16SrI-C亚组.     

假臭草从枝病植原体鉴定与多样性分析

研究假臭草丛枝病植原体的多样性,并确定其分类地位,对于利用假臭草丛枝病植原体对假臭草进行生物防治具有重要的意义.本研究采集了海南省8个地区的假臭草丛枝病样品,采用PCR以及巢式PCR方法扩增了假臭草丛枝病植原体的16S rDNA序列片段,进一步选用AfaⅠ、Alu Ⅰ、EcoR Ⅰ、HaeⅢ、HpaⅡ、HhaⅠ、HinfⅠ、Kpn Ⅰ、Sau3A Ⅰ、Taq Ⅰ和Xsp Ⅰ等11种限制性内切酶对巢式PCR产物进行酶切分析(RFLP),并对16S rDNA序列进行测序,确定假臭草丛枝病植原体多样性和生物学地位.结果发现:假臭草丛枝病的病原确为植原体;8个地区的假臭草丛枝病植原体的酶切图谱基本一致,与已知植原体的相似度为0.26～0.97;8个地区假臭草丛枝病植原体的序列同源性均在99.4％以上,应为同种植原体;假臭草丛枝病植原体与16S rRNAⅡ-A组的花生丛枝病(PnWB)的同源性最高达到99.1％,说明假臭草丛枝病植原体在分类学地位上应归属于植原体16S rRNAⅡ-A组.     

枣疯病植原体tuf和rp基因的克隆与序列分析

【目的】枣疯病是一种重要的植原体病害,本研究旨在明确北京及河北地区枣疯病植原体的分类地位,为枣疯病在亚组水平上分类提供一定的参考依据。【方法】利用植原体通用引物fTufu/rTufu和rp(v)F1A/rp(v)R1A对北京和河北地区枣疯病植原体延伸因子tuf基因和核糖体蛋白基因(rp)进行PCR扩增并进行核苷酸序列测定及相似性分析。【结果】获得北京地区JWB-XFSZ株系、JWB-XFDO株系以及河北地区JWB-TXSZ株系的tuf基因片段均为824 bp;北京地区JWB-XFSZ株系的rp基因片段为1196 bp。经序列相似性比较表明:tuf基因与16SrV组的葡萄黄叶病(Flavescence dorée)相似性最高,为92.84%,而与已经公布的其它地区(陕西杨凌)的枣疯病植原体tuf基因相似性较低,为57.29%;关于rp基因,北京地区枣疯病JWB-XFSZ株系与16SrV组的枣疯病泰山株系(JWB-Taishan)以及大麻丛枝病植原体(HFWB)相似性最高,均为99.83%,与16SrV组的成员相似性均在96%以上。【结论】北京与河北地区枣疯病植原体具有较高的相似性,而在tuf基因水平上,与陕西地区枣疯病植原体具有较大的差异;本研究中北京与河北两地区枣疯病植原体归属于16SrV组。     

仙人掌丛枝病植原体CWB1株系16SrRNA基因克隆及序列分析

对表现丛枝症状的仙人掌植株总DNA进行植原体 1 6SrRNA基因PCR扩增 ,得到一条约 1 5kb的特异片段 ,表明植株中有植原体存在 ,将此植原体株系命名为CWB1。把此特异片段与pGEM Teasy载体连接并转化到大肠杆菌JM1 0 9感受态细胞中 ,通过PCR鉴定、限制性内切酶 (EcoRI)酶切分析及核苷酸序列分析 ,均表明克隆成功。序列分析结果显示 ,此株系的 1 6SrRNA基因全长 1 489个碱基 ,与属于植原体 1 6SrⅡ C亚组的Fababeanphyllody植原体同源率最高 ,为 99 7%。通过 1 6SrRNA基因核酸序列同源性比较 ,认为该株系属于 1 6SrⅡ C亚组 ,基本确定了其分类地位。     

泡桐丛枝植原体16S rDNA和延伸因子基因序列分析

对采自陕西、山西、甘肃、河南、河北、山东各省的泡桐丛枝病材料,利用巢式扩增,均得到16S rDNA基因片段约1.2kb;扩增得到植原体延伸因子(EF-Tu)tuf基因,长度约为850bp.。通过将16S rDNA基因片段和延伸因子(EF-Tu)tuf基因序列与已知植原体16Sr各组成员进行同源性比较,确定我国大陆泡桐主栽区陕西、山西、甘肃、河南、河北、山东各省与已经报道的台湾省泡桐丛枝植原体基本一致,均为同一个种,没有株系的分化,全部归属于植原体16SrI-D组,从而确定了其分类地位。     

杏褪绿卷叶植原体新疆分离物核糖体蛋白基因的克隆与序列分析

【目的】了解杏褪绿卷叶植原体新疆分离物的系统发育关系及遗传分化,确定其分类地位。【方法】利用植原体核糖体蛋白(rp)基因的特异性引物rpF1/rpR1对新疆轮台县托克逊县杏褪绿卷叶病植株总DNA进行PCR扩增,并对部分扩增片段克隆、测序及序列分析。【结果】获得杏褪绿卷叶植原体新疆分离物rp基因片段大小为1196 bp,该片段包含部分rpS19以及rpL22和rpS3基因的全部序列。序列相似性和系统进化分析表明,杏褪绿卷叶植原体新疆分离物与16SrⅤ-rp亚组中的各代表性植原体的rp基因核苷酸序列相似性达到95.7%~99.3%,其中与rpⅤ-C亚组的甜樱桃绿化植原体和枣疯病植原体的相似性最高,核苷酸及氨基酸相似性分别达到99.2%~99.3%和98.3%~98.4%。进一步虚拟RFLP分析,发现杏褪绿卷叶植原新疆分离物rp基因的酶切图谱与rpⅤ-C亚组成员相似性最高,但在MseⅠ、SspⅠ和TaqⅠ的酶切位点上存在差异。综上初步判断其可能属于16SrⅤ组(榆树黄化组)中的一个新rp亚组。【结论】本研究首次报道了杏褪绿卷叶植原体新疆分离物的rp基因序列,确定了其分类地位,为杏褪绿卷叶病的早期诊断和检测提供了基础。     

新疆小叶白蜡丛枝病植原体的鉴定及16S rRNA基因序列分析

【目的】对新疆小叶白蜡丛枝病植原体进行检测,通过其16S rRNA基因分析确定其分类地位。【方法】利用苯胺蓝和4′,6-二脒基-2-苯基吲哚(DAPI)染色,在荧光显微镜下观察新疆小叶白蜡嫩茎横切片;采用植原体16S rRNA基因的通用引物对P1/P7和R16F2n/R16R2进行直接和巢式PCR扩增,对得到的16S rRNA基因的序列进行RFLP和构建系统进化树分析。【结果】表现丛枝病症状的新疆小叶白蜡中存在植原体,暂命名为Fraxinus sogdianaBunge witches’broom phytoplasma(Fraxinus sogdianaBunge WB);其16S rRNA基因的序列GenBank登录号为KF061042,RFLP图谱与16Sr V-B亚组的枣疯病植原体相同,系统进化地位与枣疯病菌株AB052876相同。【结论】新疆小叶白蜡丛枝病植原体为16Sr V-B亚组成员。     

关于植物群丛划分的探讨

在传统的植物群落分类系统中,群丛是植物群落分类的基本单位.从群丛分类的必要性出发,综述了传统植物群落分类系统中对群丛的定义及其划分方法,即在群丛的划分中主要依据群落中不同层片的优势种或特征种;但是在利用传统植物群落分类方法划分群丛时也存在一些不确定性因素,主要表现在确定群丛的特征种(组)时需要人为确定;同时,论述了当前植物群落数量分类的研究现状,分析了利用双向指示种分析法(TWINSPAN)、主成分分析(PCA)等数量分类方法划分群丛时存在的一些问题,主要表现在数量分类结果与传统分类单位的对应关系不能达到协调一致,无法判断是否划分到了群丛的水平.最后提出了群丛划分方法的展望:数量方法是基础,特征种(组)是及其数量特征是关键.     

优势种植被分类系统的逻辑分析与示例方案化

逻辑学原理是各种分类系统科学性及规范性的必要检验工具。本文采用逻辑学原理检验基于优势种的《中国植被》的植被分类系统, 结果发现目前常用的植被分类系统存在较多逻辑错误, 需要予以纠正。于是, 在强调植物生活型分类系统和植被分类系统一致性的基础上, 依据逻辑学原理给出建立植被分类系统的步骤和方法, 提出规范的植物生活型分类系统和植被分类系统示例方案。鉴于多建群种植被的客观存在及其存在形式多样, 在分类系统中给出相应的位置——多建群种植被纲。同时, 针对国内植被分类学界从未形成统一的植被命名规则, 且又有多种命名方式并存的现状, 提出了函数命名法。     

群落排表分类的两种数学方法

本文描述两种执行群落排表分类的数学方法:X²分类法和信息熵分类法,并以德国西北部草地数据为例进行了应用和分析。结果表明这两个方法都是有效的群落排表分类方法,它们所排的群落表可直接地反映群落类型和种类组成之间的关系,体现了Braun-Blanquet传统排表法的特点。     

Numerical approaches to lake classification with special reference to macrophyte communities

Summary Various approaches to the classification of S. Swedish lakes on the basis of their macrophyte composition are discussed. A main division is made between species or life-form, and synusia or community approaches. Three steps in the classification are discussed: primary clustering of sites to arrive at a local classification, secondary classification of clusters of sites to arrive at general community types and classification of lakes according to their community composition.The estimation of species performance is discussed and a logarithmic transformation advocated. The analysis of belt transects is suggested as a satisfactory general approach.Some problems regarding synusial independence and possible synusial interactions are mentioned. A survey of boundary types in lakes is given.Examples are given of classifications based on single life-forms and life-form combinations. Helophyte community composition of lakes is effectively shown by a combination of classification and ordination. The idea of aquatic community complexes is discussed with reference to the recent sigma-syntaxon approach in phytosociology.Nomenclature follows Lid (1974).     

Supraordinal brachiopod classification

Three controversial problems of brachiopod supraordinal classification are discussed: the position of brachiopods in the classification of Metazoa, their classification at phylum and class level, and the classification of the articulate brachiopods. The position of brachiopods in the system of Metazoa remains uncertain. There are no strong reasons for changing the traditional division of the phylum Brachiopoda into the classes Inarticulata and Articulata. The class Articulata is divided into the subclasses Orthata, Strophomenata, Spiriferata, and Terebratulata.     

A preliminary review of the modern classification systems of the flowering plants

The present paper is divided into three parts: 1. The first part is devoted to the review of the historical origin of the modern classification systems of the flowering plants. Early systems of classification since the Aristotelian time provided a basis for the modern schemes of classification. This paper has reviewed briefly the history of plant systematics, which is divided into three periods: the period of mechanical systems of classification, of natural systems of classification, and of phylogenetic systems of classification. The historical development of the plant systems and the basic idea for three periods is discussed respectively. This paper also considers that the studies of the modern classification system have been entering a new period which primarily aims at overall evolutionary respects. 2. Comparison of the modern classification systems of the flowering plants. Four main modern systems (i. e. A. Cronquist 1979, A. Takhtajan 1980, J. Hutchinson 1973 and A. Engler^,s system as revised by H. Melchior in Engler^,s Syllabus der Pflanzenfamilien 1964) which have greatly influenced the systemstics of plants are compared as to their systematical principles, basic concepts and systematic positions of higher taxa (orders and families) of the flowering plants. The paper is of the opinion that there is still much important work to be done in every field. 3. A review for the modern classification systems of the flowering plants. The paper reviews the modern classification of angiosperms from six aspects: a). The flowers plants are originated from a common ancestral stock; b). The flowers of angiosperms are homogeneous, stamen and carpel are phylletic sporangiophores, all flowers of angiosperms are comparable; c). Monocotyledons are originated from primitive dicotyledons, and represent phylogenetically monophyletic branch; d). The idea advocating the subdivision of Dicotyledoneae into Lignosae and Herbaceae should be rejected as pointed out by many authors; e). The systematical position of Hamamelidae is still a crucial subject for further research; f). The evolutional trends and evaluation of taxonomic characters must be considered in connection with the cor-relation to other characters in question.     

荔枝与龙眼种质资源研究进展

荔枝和龙眼是中国著名的南亚热带果树。本文分别就荔枝、龙眼种质资源在起源与分布、分类与鉴定等方面取得的研究进展进行了综述。荔枝和龙眼的分类研究大体经历了3个阶段:根据形态特征进行分类、应用同工酶分析和DNA分子标记进行分类。形态特征常常受到环境条件的影响,而同工酶分析可以检测到的多态性位点十分有限。应用分子标记研究荔枝、龙眼种质资源的遗传多样性克服了前述2种研究方法的不足。目前,荔枝和龙眼的品种选育仍然以实生选种和芽变选种为主。为了实现对荔枝、龙眼果实品质和农艺性状的改良,建议在分子水平上进一步深入地探讨荔枝、龙眼种质资源的遗传多样性;同时通过应用分子标记辅助选择技术提高荔枝和龙眼杂交育种的效率。     

Protein classification with imbalanced data

Generally, protein classification is a multi-class classification problem and can be reduced to a set of binary classification problems, where one classifier is designed for each class. The proteins in one class are seen as positive examples while those outside the class are seen as negative examples. However, the imbalanced problem will arise in this case because the number of proteins in one class is usually much smaller than that of the proteins outside the class. As a result, the imbalanced data cause classifiers to tend to overfit and to perform poorly in particular on the minority class. This article presents a new technique for protein classification with imbalanced data. First, we propose a new algorithm to overcome the imbalanced problem in protein classification with a new sampling technique and a committee of classifiers. Then, classifiers trained in different feature spaces are combined together to further improve the accuracy of protein classification. The numerical experiments on benchmark datasets show promising results, which confirms the effectiveness of the proposed method in terms of accuracy. The Matlab code and supplementary materials are available at http://eserver2.sat.iis.u-tokyo.ac.jp/ approximately xmzhao/proteins.html.     

On the predictive power of numerical and Braun-Blanquet classification: an example from beechwoods

Abstract. A numerical classification method and the Braun-Blanquet method, based on external criteria, were compared with the aim of clarifying the differences in predictive power. The numerical analysis leads to a changed perspective on the floristic data and produces, as a whole, an ecologically more differentiated classification. The groups produced by numerical analysis are almost identical with the Braun-Blanquet classification with respect to marginal site conditions but they may differ in cases of intermediate site conditions. Nevertheless, a classification emerges which is on the whole, both floristically and as to site, very similar to the Braun-Blanquet classification. The discriminatory importance of the external variables is, to a large extent, the same in both methods, but discriminant analysis shows that the numerical classification is somewhat more predictive.