土生空团菌(Cenococcum geophilum Fr.)18S rDNA中的I型内含子

【目的】分析土生空团菌[Cenococcum geophilum Fr.(Cg)]18S rDNA中Ⅰ型内含子的核苷酸序列和二级结构特征,探讨影响土生空团菌遗传多样性的因素。【方法】对23个Cg菌株18S rDNA的3’端进行PCR扩增,对其中14个菌株的扩增片段测序。利用MAGE version 4.0软件构建Neighbor-Joining系统发育树,利用Mfold预测内含子的二级结构。【结果】序列分析表明,19个中国菌株中14个在18S rDNA中有Ⅰ型内含子。结合GenBank中的相关数据,可知Cg菌株18S rDNA中内含子的序列长度为488-590 nt,显示出92.3%-100%的同源性。在其5’端序列比较保守,在3’端序列差异较大。二级结构分析表明Cg菌株18S rDNA中的内含子都有10个配对区(P1-P10),在P5区域由P5,P5a,P5b,P5c,P5d组成,在P9的3’端有2个配对区(P9.1、P9.2)。【结论】来源于不同寄主及地域的Cg菌株有丰富的遗传多样性,本文没发现地理因素和寄主来源对Cg的遗传分化有影响。     

Ⅰ型内含子核酶研究进展

Ⅰ型内含子核酶作为最早被发现的RNA催化剂,在过去20年里得到了深入研究.相关研究成果使人们在RNA的生物学功能、催化特征、结构与折叠特征等方面的认识有了革命性更新.回顾了Ⅰ型内含子核酶研究的主要进展,重点对近年来在Ⅰ型内含子核酶的结构和折叠方面所取得的重要成果进行了介绍、分析和总结.     

Ⅱ型内含子及其生物技术应用研究进展

型内含子(groupⅡintrons)是一类具有自我剪接功能的核酶,能够通过“归巢”(retrohoming)机制高频插入到DNA靶位点。Ⅱ型内含子对DNA靶位点的识别和剪接具有高度专一性和高效性,这种特性使其在基因工程中具有重要的应用价值。文中首先综述了Ⅱ型内含子基因打靶原理及其在微生物遗传改造中的应用;然后,根据Ⅱ型内含子“归巢”特点及其依赖高浓度Mg2+的特性,分析了Ⅱ型内含子在多功能基因编辑及真核生物应用中的局限性;最后,以笔者课题组研究工作为基础,结合Ⅱ型内含子自身结构特点,分析了Ⅱ型内含子在新型基因编辑工具开发方面的潜能,为Ⅱ型内含子生物技术应用提供借鉴。     

分离自云南省的本森顿酵母属菌株的分子系统发育研究

从采自云南省的一份水稻茎杆样品上分离出一株产生掷孢子的酵母菌CH 2.310。化学分类学研究表明该株菌的主要泛醌类型为Q-9,其全细胞水解液中不存在木糖,故被归入 本森顿酵母属(Bensingtonia Ingold)中。在该属中与CH 2.310在形态和生理生化性状上最相 近的种为大和本森顿酵母(B. yamatoana),但因CH 2.310能在无外源维生素培养基中生长并不可同化D-葡糖醛酸而与该种的原始描述不符。基于小亚基rDNA (SSU rDNA)全序列的分子系统学分析显示,在所有已描述的本森顿酵母属的种中,CH 2.310与大和本森顿酵母的模式菌株的亲缘关系最近。进一步的DNA-DNA同源性研究证实CH 2.310属于大和本森顿酵母。CH 2.310为首次分离自日本以外的犬和本森顿酵母菌株。     

基于核rDNA的ITS序列在种子植物系统发育研究中的应用

种子植物核rDNA是高度重复的串联序列,由于同步进化的力量．大多数物种中这些重复单位间已发生纯合或接近纯合。5．8S rDNA把核rDNA的内转录间隔区分为ITS1和ITS2两部分．在被子植物中ITS1的长度为165～298bp,ITS2的长度为177～266bp,而在裸子植物中ITS片段较长。且其长度变化主要由ITS1的长度变异所致。可对这两个片段PCR产物进行直接测序或克隆测序。由于ITS序列变异较快．能够提供较丰富的变异位点和信息位点,已成为被子植物较低分类阶元的系统发育和分类研究中的重要分子标记,为探讨多倍体复合体网状进化关系,异源多倍体的起源提供了重要的系统学信息．但它一般不适合科以上水平的系统学研究。裸子植物中ITS片段较长,重复序列间的纯合程度不同,测序比较困难．因此对探讨裸子植物系统发育和分类受到了一定的限制,但近年来有所发展。     

寡毛类纤毛虫变游虫新属的建立及基尔变游虫(新属,新组合)的形态学重描述与系统地位分析(英文)

利用蛋白银染色技术对采自青岛沿海砂隙的寡毛类纤毛虫Strombidium kielum进行了形态学重描述,发现该种在寡毛类纤毛虫中具有独一无二的纤毛下器模式,因此为其建立了1新属Varistrombidium,特征为具有5条斜穿虫体的体动基列,其中体动基列1和2延伸到虫体背部,终止于虫体尾端。对Varistrombidium kielum(Maeda&Carey,1985)nov.comb.的小亚基RNA序列分析表明,该种位于Strombidiidae科内,与其形态学相近种Omegastrombidium elegans聚在一起。同时对其小亚基RNA序列可变区2的二级结构进行了预测并与其形态学相似种进行了比较。还对Apostrombidium pseudokielum Xuet al.,2009进行了补充性描述。     

赤潮棕囊藻(Phaeocystis globosa)rDNA ITS区序列变异与二级结构分析

测定了南海球形棕囊藻香港株P1、P2和湛江株ZhJ1的rDNAITS区序列(含5.8srDNA),结合Gen Bank的13条同源序列,比对长度为904bp,变异位点271个,简约信息位点221个,平均(A+T)(34.5%)<(G+C)(65.4%).藻株P1、P2和ZhJ1序列存在变异位点20个,序列间相似性为97.9%～98.5%.ITS序列在种间和种内的解析度高于18srDNA和28srDNA基因;构建的NJ树、MP树、贝叶斯推断系统树的结构是一致的,不同种类的棕囊藻单独聚类,不同地理来源的球形棕囊藻混杂分布但相同地理来源的藻株多聚类在一起.RNA二级结构显示,不同藻种间5.8srDNA区结构基本一致,表现出属的特异性;ITS1、2区结构表现较大的种间差异,表明ITS区RNA二级结构可为棕囊藻分类鉴定提供有用的分子结构信息.     

RNA二级结构在微生物系统发育分析上的应用

RNA二级结构用于微生物分类和系统发育分析在近年来逐渐受到注意并发展起来。文章就此方面的发展做了简要综述,其中对在系统发育分析上的应用部分作了较重点介绍。     

轮虫同域性物种形成:来自萼花臂尾轮虫克隆间的分子系统发育关系和生殖隔离的证据

对采自芜湖市三个不同水体中的萼花臂尾轮虫(Brachionus calyciflorus)17个克隆的线粒体COⅠ基因和rDNAITS1序列进行的分析结果表明:萼花臂尾轮虫不同克隆间COⅠ基因序列差异百分比为0-14.0%,平均为5.1%;ITS1序列差异百分比为0-7.4%,平均为2.2%。基于COⅠ基因序列构建的分子系统树(NJ树、MP树、ML树和贝叶斯树)均支持将17个克隆划分为三个姐妹种,各姐妹种间的序列差异百分比为7.2%-14.0%。基于ITS1序列构建的同样四种分子系统树也支持将17个克隆划分为三个姐妹种,但其中的克隆HE5在姐妹种中的归属与基于COⅠ基因序列构建的分子系统树所得出的结果不同,各姐妹种间的序列差异百分比为1.9%-7.4%。混交雌体和雄体间的交配实验结果表明,轮虫各姐妹种间存在着明显的生殖隔离,克隆HE5在姐妹种中的归属应与基于COⅠ基因序列构建的分子系统树所得出的结果一致;ITS1序列进化速率较低,不宜用于轮虫姐妹种的准确甄别。COⅠ基因进化钟计算结果显示,三个姐妹种间,克隆LE9所属的姐妹种早在8百万年前便分化形成出来,HE1、HE2、HE4-7所属的姐妹种于5百万年前分化产生。     

球孢白僵菌释放后在森林系统中定殖及持续控虫作用的证据

在皖南马尾松林中使用球孢白僵菌无纺布菌条接种式放菌防治松褐天牛。在放菌前进行球孢白僵菌本底调查,在放菌后半年内采集该菌感染的各种僵虫,得到87株分离物。利用28SrDNA-PCRⅠ型内含子标记技术,测定放菌后释放菌株的回收率。结果表明,在87株球孢白僵菌中有66株与释放菌株的核型相同,占75.86%。半年中平均回收率为81.7%(75%-90.9%之间),这表明释放菌株已在该生态系中定殖,对松褐天牛种群发挥持续控制作用。在放菌前后球孢白僵菌种群结构有所变化,释放菌株有取代土著菌株优势地位的趋向。     

Identification of group I introns within the SSU rDNA gene in species of Ceratocystiopsis and related taxa

During a recent phylogenetic study, group I introns were noted that interrupt the nuclear small subunit ribosomal RNA (SSU rDNA) gene in species of Ceratocystiopsis. Group I introns were found to be inserted at the following rDNA positions: S943, S989, and S1199. The introns have been characterized and phylogenetic analysis of the host gene and the corresponding intron data suggest that for S943 vertical transfer and frequent loss appear to be the most parsimonious explanation for the distribution of nuclear SSU rDNA introns among species of Ceratocystiopsis. The SSU rDNA data do suggest that a recent proposal of segregating the genus Ophiostoma sensu lato into Ophiostoma sensu stricto, Grosmannia, and Ceratocystiopsis has some merit but may need further amendments, as the SSU rDNA suggests that Ophiostoma s. str. may now represent a paraphyletic grouping.     

Divergent Histories of rDNA Group I Introns in the Lichen Family Physciaceae

The wide but sporadic distribution of group I introns in protists, plants, and fungi, as well as in eubacteria, likely resulted from extensive lateral transfer followed by differential loss. The extent of horizontal transfer of group I introns can potentially be determined by examining closely related species or genera. We used a phylogenetic approach with a large data set (including 62 novel large subunit [LSU] rRNA group I introns) to study intron movement within the monophyletic lichen family Physciaceae. Our results show five cases of horizontal transfer into homologous sites between species but do not support transposition into ectopic sites. This is in contrast to previous work with Physciaceae small subunit (SSU) rDNA group I introns where strong support was found for multiple ectopic transpositions. This difference in the apparent number of ectopic intron movements between SSU and LSU rDNA genes may in part be explained by a larger number of positions in the SSU rRNA, which can support the insertion and/or retention of group I introns. In contrast, we suggest that the LSU rRNA may have fewer acceptable positions and therefore intron spread is limited in this gene. Reviewing Editor: Dr. W. Ford Doolittle     

The D4 set: primers that target highly variable intron loops in plant chloroplast genomes

Chloroplast group II introns offer high-quality, rapidly evolving single-copy loci for comparative sequence analysis. These introns feature diagnostic secondary structures with loops that are among the least evolutionarily constrained sequence in plastomes. We exploited these structures to develop universal primers that amplify and sequence the large Domain IV (D4) loop in several angiosperm introns. With a single sequence read, we recover 300-600 nucleotides of highly variable sequence across angiosperms, with rates of change that are equal to or higher than many of the best known intergenic spacers in plant chloroplast genomes.     

Inheritance of the group I rDNA intron in Tetrahymena pigmentosa

We have previously argued from phylogenetic sequence data that the group I intron in the rRNA genes of Tetrahymena was acquired by different Tetrahymena species at different times during evolution. We have now approached the question of intron mobility experimentally by crossing intron⁺ and intron^? strains looking for a strong polarity in the inheritance of the intron (intron homing). Based on the genetic analysis we find that the intron in T. pigmentosa is inherited as a neutral character and that intron⁺ and intron^? alleles segregate in a Mendelian fashion with no sign of intron homing. In an analysis of vegetatively growing cells containing intron⁺ and intron^? rDNA, initially in the same macronucleus, we similarly find no evidence of intron homing. During the course of this work, we observed to our surprise that progeny clones from some crosses contained three types of rDNA. One possible explanation is that T. pigmentosa has two rdn loci in contrast to the single locus found in T. thermophila. Some of the progeny clones from the genetic analysis were expanded for several hundred generations, and allelic assortment of the rDNA was demonstrated by subcloning analysis. © 1992 Wiley-Liss, Inc.     

Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Phylogenetic analysis of nucleotide data from small subunit ribosomal DNA (SSU rDNA) sequences (ca. 1685 bp.) was performed on 19 taxa of the Onygenales and three related mitosporic fungi. Phylogenetic trees were constructed by the neighbor-joining method with the sequence data of related taxa obtained from DNA databases. The species in the Onygenales form two clusters and seven subclusters, and the tree topology reflects the traditional classification by Currah (1985) with some exceptions. The Myxotrichaceae is placed in the different lineage, separate from other plectomycetous taxa and among the Leotiales and the Erysiphales. Furthermore, two separate lineages in the Myxotrichaceae were found. Tree topology suggested the Onygenaceae is polyphyletic and composed of three subgroups; 1) most members of Onygenaceae, 2)Spiromastix warcupii, and 3) pathogenic dimorphic fungi classified inAjellomyces.     

Variability and phylogenetic incongruence of an SSU nrDNA group I intron in Artomyces,Auriscalpium, and Lentinellus (Auriscalpiaceae: Homobasidiomycetes)

Previous research has shown that a group I intron occurs in the SSU ribosomal DNA gene of isolates of Artomyces (Clavicorona, in part) and Lentinellus, but apparently it is absent in an Auriscalpium isolate. However, further investigation revealed that the intron is apparently absent in some species of Artomyces and Lentinellus and is present in at least one species of Auriscalpium. To examine this further, the presence or absence of the group I intron is reported for 13 species of Lentinellus, two species of Auriscalpium, and 16 species of Artomyces. The presence of the intron among the species was variable and is documented for seven species of Lentinellus, one species of Auriscalpium, and 12 species of Artomyces. Furthermore, the presence of the intron was variable among the isolates of several species, and variability of its presence was observed within single isolates, indicating inter-ribosomal repeat heterogeneity. Independent phylogenetic estimations were generated for the intron and nuclear ribosomal internal transcribed spacer regions (ITS). Tests of congruence for the two trees indicated that the data were heterogeneous. Some of the discontinuity between the two phylogenies is due to placement of the Ar. austropiperatus intron within the Lentinellus intron clade. Variability in the length of the intron was observed in populations of the pan-Northern Temperate species Ar. pyxidatus. This was due to the presence of an additional unknown insertional element found only within North American collections of Ar. pyxidatus and absent from European and Asian collections.