ITS序列的特点及其在昆虫学研究中的应用

随着PCR技术和DNA测序技术的成熟及广泛应用,分子数据的分析和利用逐渐成为生物学研究的重要手段。基因组中含有丰富的遗传信息,运用核基因序列或将核基因与线粒体基因序列相结合作为遗传标记,研究昆虫的系统发育,已成为分子系统学领域的发展趋势。由于长度适中、易于扩增、进化速度快、变异性高等优点,核糖体基因中内转录间隔区(ITS)已在昆虫系统学研究中得到广泛的应用。本文介绍了ITS序列的结构特点,重点对ITS序列在近缘种及种型快速鉴定、属及属上高级阶元系统学研究、谱系生物地理学及与其它基因联合分析昆虫系统进化关系等研究中的应用及前景进行了综述。     

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。     

Phylogenetic relationships of sect.Nummularia (Lysimachia):evidence from ITS sequences

测定了紫脉过路黄、临时救和过路黄的nrDNA ITS序列,并分析了珍珠菜属过路黄组17个物种的遗传距离及亲缘关系.结果表明,过路黄组植物的ITS序列长度在620～628间,一致性高达90.59%,种间遗传距离为0.002～0.199.系统发育树表明:(1)紫脉过路黄、临时救和小茄亲缘关系较近;(2)大叶过路黄、落地梅和过路黄亲缘关系较近;(3)山萝过路黄、贯叶过路黄、管茎过路黄、叶头过路黄、峨眉过路黄及三角叶过路黄亲缘关系较近.ITS序列分析结果为组内植物的鉴定、分类及系统进化提供了新的参考.     

DNA序列在悬钩子属植物分子系统学研究中的应用进展

悬钩子属植物种类繁多,类群复杂,而且多为多倍体和杂种。该文就近年来国内外有关DNA序列在悬钩子属植物分子系统学研究中的应用现状和进展进行了综述,并对中国悬钩子属植物系统发育研究进行了展望。研究认为:叶绿体DNA序列多应用非编码区,且多与ITS序列联合分析;核基因组中ITS序列应用最为广泛,主要用于研究悬钩子属空心莓组与木莓组的进化关系、栽培品种间亲缘关系及部分杂种和多倍体的起源等;在该属植物中发现了ITS个体内多态性,但未进行ITS假基因检测,其系统学应用价值需重新评价;低拷贝核基因只有GBSSI和LEAFY有相关应用。同时认为,悬钩子属植物系统学研究中应用的DNA序列及研究类群均较少,缺乏对整个悬钩子属全面而系统的研究。指出应进一步选择具有代表性的样本、筛选合适的DNA片段,并结合形态学、孢粉学和细胞学等手段对中国悬钩子属植物系统关系进行深入研究。     

浙江乐清铁皮石斛rDNA ITS序列的克隆及序列比对

为判断浙江乐清铁皮石斛(Zhejiang Dendrobium officinale)与石斛属(Dendrobium)其它物种的亲缘关系,本文提取了该石斛鲜样的DNA,利用真核生物ITS序列通用引物ITS4/ITS5进行了扩增,并将扩增产物连接转化至大肠杆菌,在对阳性克隆测序。将得到的序列与GenBank上我国石斛属12个组中34个种的rDNAITS进行了比对,并在此基础上构建了系统发育树。序列比对结果表明浙江乐清铁皮石斛的rDNAITS与黄石斛(D.tosaense)一致,其次与铁皮石斛(D.officinale)最相近,序列相似性99%。系统发育树也表明浙江乐清铁皮石斛的rDNAITS序列与黄石斛(D.tosaense)的相似程度高于其与铁皮石斛(D.officinale)的相似程度。本研究将为利用ITS序列鉴别石斛物种种属关系提供参考。     

线粒体基因在鳞翅目昆虫分子系统学中的研究进展

介绍近年来已测定线粒体DNA全序列的鳞翅目昆虫和其线粒体DNA结构,综述鳞翅目昆虫的分子系统学研究进展.特别对mtDNA在鳞翅目昆虫分类和界定、系统发育关系及种群遗传变异和进化等研究中的意义和存在的问题进行探讨.     

基于ITS序列分析仲彬草属植物的亲缘关系

以旱雀麦为外类群,用PAUP 4.0b10软件并采用最大简约法和邻接法对11份仲彬草属物种的ITS区序列进行系统发育分析,两种方法得到的系统发育树基本一致。结果表明:(1)整个ITS序列长度变异范围为596~601 bp;G C含量在所有ITS中的变化范围为61.20%~62.44%;序列间的遗传分化距离为0.003~0.033,平均值为0.015;(2)疏花仲彬草和塔克拉干仲彬草2个物种聚为一支,位于系统发育树的底部,在最大简约法和邻接法分析中分别获得78%和82%的自展支持率,它们之间的亲缘关系较近;(3)形态相似、地理分布一致的物种有聚在一起的倾向,表现出较近的亲缘关系;(4)ITS区序列分析的结果与细胞学、形态学的研究结果基本一致,因此ITS区序列分析能反映仲彬草属种间关系。     

ITS 假基因对栎属系统学研究的影响及其对分子系统学研究的启示*

核糖体rDNA ITS 是被子植物系统发育研究中应用最广泛的分子标记之一。以前人们认为同一物种
中的ITS 序列因致同进化而使不同拷贝高度一致, 在分子系统学研究中常以ITS1- 518S- ITS2 序列作为构建
系统进化树的基础。近年来, 在对一些被子植物的研究中发现这段序列在同一物种中具有多态性, 有些拷
贝中的518S 区不具编码功能, 人们把含有不具编码功能518S 区的ITS1-51 8S- ITS2 序列定义为ITS 假基因序
列, 它对同源基因致同进化的假设形成了新的挑战。在诸多应用ITS 序列重建系统进化关系的研究中, 栎
属系统学研究因ITS 假基因的发现而倍受关注。本文以栎属为例回顾了ITS 假基因的发现过程, 分析了其
对该属系统学研究的影响, 为分子生物学在植物系统进化研究中的应用提供一些新的参考。     

基于ITS序列探讨珍珠菜属过路黄组的系统关系

测定了紫脉过路黄、临时救和过路黄的nrDNA ITS序列,并分析了珍珠菜属过路黄组17个物种的遗传距离及亲缘关系。结果表明,过路黄组植物的ITS序列长度在620～628间,一致性高达90.59%,种间遗传距离为0.002～0.199。系统发育树表明:(1)紫脉过路黄、临时救和小茄亲缘关系较近;(2)大叶过路黄、落地梅和过路黄亲缘关系较近;(3)山萝过路黄、贯叶过路黄、管茎过路黄、叶头过路黄、峨眉过路黄及三角叶过路黄亲缘关系较近。ITS序列分析结果为组内植物的鉴定、分类及系统进化提供了新的参考。     

分子生物学技术在双翅目实蝇科昆虫系统发育研究中的应用

分子生物学技术如同工酶电泳、RFLP、RAPD、核酸序列分析、微卫星DNA和探针杂交等,在实蝇科昆虫系统发育研究中具有重要作用。利用这些技术对实蝇种群进行系统发育研究,揭示其亲缘及进化关系,从生命本质上寻找实蝇种群间的内在联系。文章综述上述几种分子生物学技术在实蝇科昆虫核酸结构、种内和种间的亲缘及进化关系等方面的研究进展,分析在应用中存在的问题,展望这些分子生物学技术在实蝇科昆虫系统发育中的应用前景。     

Ribosomal ITS Sequences Allow Resolution of Freshwater Sponge Phylogeny with Alignments Guided by Secondary Structure Prediction

Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.     

Finding NEMO: nestedness engendered by mutualistic organization in anemonefish and their hosts

The interaction structure of mutualistic relationships, in terms of relative specialization of the partners, is important to understanding their ecology and evolution. Analyses of the mutualistic interaction between anemonefish and their host sea anemones show that the relationship is highly nested in structure, generalist species interacting with one another and specialist species interacting mainly with generalists. This supports the hypothesis that the configuration of mutualistic interactions will tend towards nestedness. In this case, the structure of the interaction is at a much larger scale than previously hypothesized, across more than 180 degrees of longitude and some 60 degrees of latitude, probably owing to the pelagic dispersal capabilities of these species in a marine environment. Additionally, we found weak support for the hypothesis that geographically widespread species should be more generalized in their interactions than species with small ranges. This study extends understanding of the structure of mutualistic relationships into previously unexplored taxonomic and physical realms, and suggests how nestedness analysis can be applied to the conservation of obligate species interactions.     

Correlated evolution in fig pollination

This is the first comparative study of correlated evolution between figs (Ficus species, Moraceae) and their pollinators (Hymenoptera: Agaoninae) based on molecular phylogenies of both lineages. Fig relationships based on the internal transcribed spacer region (ITS) of nuclear ribosomal DNA and pollinator relationships inferred from mitochondrial cytochrome oxidase I (COI) sequences enabled the study of correlated evolution based on molecular phylogenies for the largest set of interacting species ever compared. Comparative methods have been applied to tests of adaptation, but the application of these methods in tests of coadaptation, defined as reciprocal evolutionary change in interacting lineages, has received less attention. I have extended tests of correlated evolution between two traits along a phylogeny to the case of interacting lineages, where two traits may or may not share a common phylogenetic history. Independent contrasts and phylogenetic autocorrelation rejected the null hypothesis that trait correlations within lineages are stronger than trait correlations between interacting lineages. Fig style lengths and pollinator ovipositor lengths, for example, were more highly correlated than were pollinator body size and ovipositor length. Mutualistic interactions between figs and their pollinators illustrate the novel ways in which phylogenies and comparative methods can detect patterns of correlated evolution. The most outstanding evidence of correlated evolution between these obligate mutualists is that interacting trait correlations are stronger than within-lineage allometric relationships.     

普通小麦基因组最可能的4个供体的ITS1和ITS2序列及其亲缘关系

对普通小麦（ＴｒｉｔｉｃｕｍａｅｓｔｉｖｕｍＬ．）基因组（ＡＡＢＢＤＤ）最可能的供体－Ｔ．ｕｒａｔｒｔｕＴｈｕｍ．（ＡＡ）、Ｔ．ｍｏｎｏｃｃｕｍｖａｒ．ｂｏｅｏｔｉｃｕｍ（Ｂｏｉｓｓ．）ＭＫ（ＡＡ）、ＡｅｇｉｌｏｐｓｓｐｅｌｔｏｉｄｅｓＴａｕｓｃｈ．和Ａｅ．ｔａｕｓｃｈｉｉ（Ｃｏｓｓ．（ＤＤ）的核糖体ＲＮＡ基因ＩＴＳ区进行了ＰＣＲ扩增和克隆,并测定了ＩＴＳ１和ＩＴＳ２的ＤＮＡ序列,讨论和纠正了前人     

ITS1 and ITS2 Sequences of Four Possible Donors to Bread Wheat Genome and Their Phylogenetic Relationships

The 1TS1 and ITS2 of rDNA of four diploid species, newly Triticum urartu Thum. (AA), T. monococcum var. boeoticum (Boiss.) MK (AA),Aegilops speltoides Tausch. (BB) and Ae. taus&ii Coss. (DD), the most possible donors of A, B and D genomes to broad wheat ( T. aestivum), were amplified by PCR, cloned and sequenced. Some published sequences were discussed and rectified. The length of ITS1 sequences in four species was 221 to 223 bp, and that of 1TS2 was 216 to 217 bp. In pairwise sequence comparisons among four species, divergence ranged from 0.029 0 to 0.064 0 in ITS1, and from 0.009 3 to 0.058 0 in ITS2. Based on ITS1, ITS2 and 1TS1 + ITS2 data respectively, the same most parsimony tree that is congruent with the phylogenetic relationships was generated which was concordant with their morphological and cytological characteristics. In the trees, T. urartu and T. monococcum var. boeoticum constituted one monophyly, whereas two species of the genus Aegilops, Ac. speltoides and Ac. tauschii, fortmed another mono- phyly but with lower bootstrap value than the first clade. This study suggests that ITS region is a useful molecular marker in the studies on the origin and evolution of Triticum.     

Faster evolution of highly conserved DNA in tropical plants

A faster rate of nuclear DNA evolution has recently been found for plants occupying warmer low latitudes relative to those in cooler high latitudes. That earlier study by our research group compared substitution rates within the variable internal transcribed spacer (ITS) region of the ribosomal gene complex amongst 45 congeneric species pairs, each member of which differed in their latitudinal distributions. To determine whether this rate differential might also occur within highly conserved DNA, we sequenced the 18S ribosomal gene in the same 45 pairs of plants. We found that the rate of evolution in 18S was 51% faster in the tropical plant species relative to their temperate sisters and that the substitution rate in 18S correlated positively with that in the more variable ITS. This result, with a gene coding for ribosomal structure, suggests that climatic influences on evolution extend to functionally important regions of the genome.     

Molecular phylogeny of Coelogyne (Epidendroideae; Orchidaceae) based on plastid RFLPS, matK, and nuclear ribosomal ITS sequences: evidence for polyphyly

To evaluate the monophyly of Coelogyne (Epidendroideae; Orchidaceae) and reveal sectional relationships and relations to allied genera in subtribe Coelogyninae, we collected PCR (polymerase chain reaction) amplified restriction fragment length polymorphisms (RFLPs) from 11 plastid regions for 42 taxa (28 Coelogyne species and 14 representatives of other genera) and three outgroups from Bletiinae and Thuniinae. We also sequenced a large portion of the plastid trnK intron (mostly matK) and the nuclear ribosomal DNA internal transcribed spacers ITS1 and ITS2 (including the 5.8S gene). Separate phylogenetic analyses on each data set using maximum parsimony produced mainly congruent (except for the position of Panisea) but weakly supported clades. Parsimony analysis of the combined data clearly identified three main clades in Coelogyninae. Whereas Coelogyninae are monophyletic, Coelogyne is polyphyletic, with species falling into at least two well-supported clades. The utility of morphological characters used in previous classifications was explored by reconstructing character state evolution on one of the four molecular trees. Lip base and petal shape were homoplasious, whereas ovary indumentum and flower number were congruent with well-supported groups. The implications of our results for the classification of Coelogyne are discussed, and a reorganization of the genus by including Neogyna and Pholidota and removing several species is proposed.     

AFLP 引物组合数量对准确研究竹子系统关系的影响

利用AFLP技术对26个竹子种类进行了多样性分析, 以探索引物组合数量对准确研究竹子类群系统关系的影响。实验共随机选取10对AFLP引物, 并对所得10组AFLP标记数据随机组合后进行Nei氏遗传距离/UPGMA聚类分析。每对AFLP引物 扩增数据为一组, 随着用于聚类统计的AFLP标记数据随机组合数量的增加, 26个竹子种类的聚类关系趋向一致。这提示我们,在系统学研究中, 足够数量的引物组合是获得供试材料间准确聚类关系的基础, 应采用对各AFLP引物组合数据随机累加后进行聚类分析的方法, 以聚类关系为标准来确定用于分析供试品种的最少引物组合数量。     

Study of the evolutionary relationships among Limonium species (Plumbaginaceae) using nuclear and cytoplasmic molecular markers

The genus Limonium, due to the patchiness of the natural habitats of its species as well as the high frequency of hybridization and polyploidy and the possibility of reproduction by apomixis, provides an example of all the principal mechanisms of rapid speciation of plants. As an initial study of evolution in this genus, we have analyzed intra- and interspecific variability in 17 species from section Limonium, the largest in the genus, based on RFLPs of cpDNA and nuclear rDNA ITS sequences. In the cpDNA analysis, 21 restriction enzymes were used, resulting in 779 fragments, 490 of which were variable and 339 parsimony informative. L. furfuraceum exhibited two relatively divergent cpDNA haplotypes. The relationships found among the species based on cpDNA restriction fragments were coincident using different methods of phylogenetic analysis. Due to the presumed reticulate evolution in the genus Limonium, the comparison of these results with data from the nuclear DNA was necessary; ITS sequences were analyzed. The final alignment contained 488 characters, of which 198 were variable and 156 parsimony informative. Two relatively divergent ITS types were present at the intraindividual level in L. delicatulum, a triploid species. Each type was related to ITS from different groups of diploid Limonium species, one with a base haploid chromosome number n = 8 (represented by L. cossonianum) and the other with n = 9 (represented by L. minutum). The different phylogenetic inference methods used for the analysis of ITS sequences rendered very similar topologies. In general, the relationships among the species studied were coincident with those obtained with the chloroplast genome. Both nuclear and cytoplasmic markers support the polyphyly of section Limonium, with at least two species, L. narbonense and L. vulgare, clearly divergent from the rest. Moreover, the remaining subsections into which section Limonium is currently divided seem to be artificial.