DNA分析与基因组序列和植物系统学研究

从DNA杂交、RFLP分析、DNA的限制酶图谱分析等方面描述DNA分析技术在植物学研究中的应用,讨论了DNA分析技术与植物系统学的关系及分子数据的分析方法。并以高等植物为对象,从核DNA、叶绿体DNA和线粒体DNA三方面对植物分子系统学进行了论述。     

鞘翅目昆虫核酸分子系统学研究现状

从研究对象、研究种类、研究内容等方面对鞘翅目Coleoptera核酸分子系统学研究的近况进行了总结和分析,研究中应用的技术主要有DNA序列分析、RELP技术、RAPD技术、AFLP技术、分子杂交技术和SSCD技术。并认为这些技术的应用对补充和完善传统分类方法,深入探讨各类群的分类地位和系统发育关系具有重要作用。     

苔藓植物分子系统学研究概况

结合同工酶分析技术及随机扩增多态性DNA（RAPD）、限制性片段长度多态性（RFLP）和DNA序列测序3种分子生物学技术,对苔藓植物的分子系统学研究概况进行了介绍,并指出了在苔藓植物分子系统学研究中存在的一些问题。     

苔藓植物分子系统学研究概况

结合同工酶分析技术及随机扩增多态性DNA(RAPD)、限制性片段长度多态性(RFLP)和DNA序列测序3种分子生物学技术,对苔藓植物的分子系统学研究概况进行了介绍,并指出了在苔藓植物分子系统学研究中存在的一些问题.     

核糖体DNA序列分析在昆虫系统学研究中的应用

随着分子生物学技术的迅速发展,DNA序列分析在昆虫系统学研究中的应用不断增多。本文系统阐述了核糖体DNA的结构、分类学意义、以及在昆虫不同类群不同阶元之间系统发育关系研究中的应用,概要介绍了序列分析方法,并对其应用前景进行了展望。     

叶绿体基因组变异性的植物系统学意义(综述)

CHLOROPLASTDNAVARIATIONINTHESTUDYOFPHYLOGENETICSWangTingSuYingjuan(SchoolofLifeSciences,ZhangshanUniversity,Guangzhou510275)ZhangLi(SouthChinaInstituteofBotany,AcademiaSinica,Guangzhou510650)现代分子生物学技术的不断进步和革新极大地提高了人们分析和比较大片段DNA分子的能力。这种趋势对系统学研究所产生的影响之一,就是近年来通过比较DNA性状来探讨系统发育问题业已发展成为一门专门的学科—分子系统学。在植物分子系统学领域,目前采用的分子数据主要来自两个方面：一是叶绿体基因组,…     

关于核糖体DNA序列分析在昆虫系统学中的作用浅析

在昆虫系统学中,传统分类学作为昆虫分类的主要方法,在昆虫形态分类中发挥着重要的作用,但是对于近缘种分类上却没有明确的界限。生物学技术的发展,在昆虫系统学中应用核糖体DNA序列分析的方法,有效的解决了传统分类学的局限性,在昆虫种、属和种群水平的研究中发挥了重要作用。本文对核糖体DNA序列分析的方法进行分析,探讨其在昆虫系统学中的应用。     

线粒体DNA序列特点与昆虫系统学研究

昆虫线粒体DNA是昆虫分子系统学研究中应用最为广泛的遗传物质之一。线粒体DNA具有进化速率较核DNA快 ,遗传过程不发生基因重组、倒位、易位等突变 ,并且遵守严格的母系遗传方式等特点。本文概述了mtDNA中的rRNA、tRNA、蛋白编码基因和非编码区的一般属性 ,分析了它们在昆虫分子系统学研究中的应用价值 ,以及应用DNA序列数据来推导分类阶 (单 )元的系统发育关系时 ,基因或DNA片段选择的重要性     

线粒体DNA序列在半翅目异翅亚目昆虫分子系统学上的应用

随着PCR技术的发展以及大量DNA序列的累积,昆虫分子系统学近年来快速发展。线粒体DNA(mtDNA)序列相对于核内DNA序列进化速率较快,常被用于昆虫的系统发育研究。本文综述了国内外学者利用各种线粒体DNA序列来研究半翅目异翅亚目昆虫系统发育的研究概况。总结发现,COⅠ、COⅡ、12S rDNA、16S rDNA、Cytb、ND1、ND2和ND5等线粒体区段被用于半翅目异翅亚目系统发育的研究,其中以COI、COⅡ、16S rDNA和Cytb应用最广泛,但目前尚缺乏不同分子标记间的联合分析。进一步的研究最好在选定半翅目异翅亚目昆虫的分类阶元(如科间、亚科间、科内属间、种间或种内)后,集中测定线粒体某几个区段的DNA序列,然后进行单一分析和联合分析,并与传统形态学研究结果进行比较,可望全面分析半翅目异翅亚目昆虫的系统发育关系。     

AFLP在昆虫系统学研究中的应用

AFLP是一种有效的DNA指纹分析方法,兼有RFLP标记的稳定、可靠和RAPD技术的高效、简易等优点,已经在生物学的各个领域得到了广泛应用,如遗传图谱的构建、基因定位、种及种下阶元的分类鉴定、遗传多样性和系统发育等的研究。综述了AFLP标记技术的原理、反应流程、影响AFLP分析的因素、适用范围以及在昆虫系统学研究中的应用。     

The progress of DNA analyzing techniques and its impact on plant molecular systematics

Recent advances in manipulating nucleic acids have opened a new research field called plant molecular systematics. This short review provides an overview of molecular techniques which have been used in the analysis of DNA molecules for the study of plant systematics, with a special emphasis on PCR. The early application of DNA analysis, DNA/DNA hybridization, has not become popular with plant systematists, because of several disadvantages inherent in the method. The survey of restriction fragment length polymorphisms (RFLPs), on the contrary, has become one of the preferred methods used by plant molecular systematists, since the method is relatively easy to perform. Although unambiguous data can be obtained by both long-range restriction mapping and nucleotide sequencing, these approaches may have limited use in plant molecular systematics because of their laborious experimental procedures relying on conventional molecular cloning techniques. To date, PCR based analyses of the DNA molecule seem to be the most suitable experimental approach for plant molecular systematics. Several advantages of the method have changed both the quality and quantity of the DNA data. Further application of PCR to plant molecular systematics will open up a new era in the field. The present paper is based on the contribution which was read in a symposium entitled “Organellar DNA Variations in Higher Plants and their Taxonomic Significance”, at the 50th Annual Meeting of the Botanical Society of Japan in Shizuoka on October 2, 1990, under the auspices of the Japan Society of Plant Taxonomists.     

基于trnK基因的葱属植物分子系统研究

在形态和细胞分类研究的基础上选择产于中国的9组47种葱属植物(含外类群5种),运用PCR方法扩增叶绿体trnK基因,选择26种限制性内切酶对PCR扩增片段进行了RFLP分析.结果表明:trnK基因的PCR产物在各分类群间几乎不存在长度变异,约为2 520 bp,PCR扩增片段酶切后,共得到247个变异位点,其中信息位点201个.运用PAU P 4.0 B 10.0和M EGA 3.1软件进行分析,构建葱属系统发育的D o llo和W agner最简约(M P)树及邻接(N J)树.分析表明:(1)宽叶组类群组成比较自然的单系群,洋葱组和葱组也各自形成独立分枝,表明这3个组的划分是比较自然的.多籽组和合被组在本次分析中形成1个单系群,表明这2个组具有较密切的亲缘关系.而粗根组、根茎组和单生组的划分是不自然的,需进一步研究后作适当的调整.粗根组的类群在trnK基因的RFLP分析中,得到很好的分辨,可按其染色体基数分为3个大的类群.(2)中国葱属植物可以划分为6个亚属的新等级,在各亚属下可以再分组.(3)本文还对葱属的种间亲缘、进化关系等问题进行了讨论.     

DNA条形码在鞘翅目昆虫分子系统学研究中的应用

近年来,DNA条形码(DNA Barcoding)技术已经成为生物分类学研究中备受关注的新型技术,并在鞘翅目昆虫系统发育研究中得到广泛应用。本文总结了鞘翅目昆虫DNA条形码研究所用COⅠ基因序列,概述了DNA条形码在鞘翅目昆虫的物种分类鉴定、发现新种和隐存种、系统发育关系研究等方面的应用,并对DNA条形码研究技术新进展和标准序列筛选需要注意的问题进行了讨论。     

Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF

Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.     

THE USE OF PLASTID DNA RESTRICTION ENDONUCLEASE PATTERNS IN DELINEATING RED ALGAL SPECIES AND POPULATIONS1

Plastid DNA band patterns generated by electrophoresis of endonuclease digests demonstrate remarkable conservation of DNA sequences at the species and subspecies level in flowering plants. Generally, patterns are identical or near-identical from different populations belonging to the same species. This methodology has now been applied to red algae to ascertain its value in systematic studies. Plastid DNA from nine bangiophycean and florideophycean red algae was isolated and cut with restriction endonucleases that recognize different 6-base pair sequences. The patterns generated upon the electrophoretic separation of digestion fragments show that within a species patterns are identical, but not within higher taxa. The proper identification of one Gracilaria population of uncertain taxonomic affinity was clearly established by this method of plastid DNA analysis. Differences between species in plastid DNA sequences were confirmed by probing blots of restriction fragments with known gene sequences. A number of heterologous plastid DNA probes were found to be sufficiently homologous to be useful in studying red algal DNA. Unexpectedly, supercoiled circular plasmids ranging in size from ca. 1.5–8 kb were found in some red algal species but not in others. The position of these plasmids in agarose gels following electrophoresis is uniform within a species but differs between different species of the same genus, contributing further patterns for taxonomic analysis.     

Simultaneous analysis of multiple polymorphic loci using amplified sequence polymorphisms (ASPs)

In this paper we present a systematic approach to gene mapping and genotyping based on the simultaneous analysis of multiple amplified sequence polymorphisms (ASPs). These genetic markers measure variation in DNA sequences which have been amplified by a polymerase and/or a ligase. The amplified sequence lengths are determined by appropriate choice of oligonucleotides used in the amplification reaction. We describe three classes of ASPs: restriction site polymorphisms, sequence length polymorphisms, and DNA base pair changes not associated with restriction sites. Simultaneous analysis of multiple ASPs using a modified automated DNA sequencing apparatus should be possible because amplification with oligonucleotides provides control over the fragment lengths generated. Development of an automated ASP technology is therefore the next logical step for efficient gene mapping and genotyping of individuals. With this technology, one gel would be sufficient to indicate the most probable locations of a gene and a second gel would permit the selection of the correct location while simultaneously providing a fine structure map.     

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.     

Genetic markers, genealogies and biogeographic patterns in the cladocera

Cladoceran crustaceans are an important component of zooplankton in a wide range of freshwater habitats. Although the ecological characteristics of several cladoceran species have been well studied, biogeographical studies have been hampered by problematic taxonomic affiliations. However, recently developed molecular techniques, provide a powerful tool to subject aquatic taxa to comparative analyses. Here we highlight recent molecular approaches in aquatic ecology by presenting a simple method of DNA preparation and PCR amplification of the mitochondrial DNA (16S rDNA) in species from nine different families within the cladocera. On a broad taxonomic scale, sequence analysis of this mtDNA fragment has been used to produce the first molecular based phylogeny of the cladocera. This analysis clustered the cladoceran families in a fashion similar to that suggested by previous systematic classifications. In a more detailed analysis of the family Daphniidae, nuclear randomly amplified polymorphic DNA (RAPD), mitochondrial restriction fragment length polymorphism (RFLP) and morphological analyses were combined to identify species and interspecific hybrids within the Daphnia galeata species complex across 50 lakes in 13 European countries and one lake in Africa. The study revealed interspecific hybridization and backcrossing between some taxa (D. cucullata and D. galeata) to be widespread, and species and hybrids to frequently occur in sympatry. Genetic, as well as morphological information, suggests the occurrence of D. hyalina outside the Holarctic.