Phylogeny of the Neotropical Alibertia group (Rubiaceae), with emphasis on the genus Alibertia, inferred from ITS and 5S ribosomal DNA sequences

Phylogenetic relationships of 38 species of the Alibertia group (Rubiaceae) and two outgroup species were investigated using the nuclear ribosomal 5S nontranscribed spacer (5S-NTS) and the internal transcribed spacers (ITS). Analysis of the data sets separately and in combination resulted in several well-supported and congruent groupings. However, the three analyses yielded different results as to the branching order of the basal clades. With the exception of Alibertia hispida, the species in the genus Alibertia appear in one weakly to moderately supported clade. This clade is in turn composed of two strongly supported subclades. One comprises several Alibertia species, including the type (A. edulis), three Borojoa species, and Randia tessmannii. The other subclade consists of Alibertia species only. This division is also generally supported morphologically by fruit size, corolla size, number of corolla lobes, and pollen aperture (porate vs. colporate). The sister group to the Alibertia clade comprises Duroia with Amaioua species internested. The close relationship of Ibetralia and Kutchubaea is corroborated. In addition, Alibertia hispida is a member of this strongly supported clade. Likewise, the two "Genipa" species are supported as a monophyletic group in 100% of the bootstrap replicates. It is concluded that the 5S spacer is superior to the commonly used ITS region in terms of resolution and robustness among closely related taxa.     

Molecular analyses of the IGS & ITS regions of rDNA of the psychrophilic yeasts in the genus Mrakia

Species of the genus Mrakia are currently classified as synonyms based on molecular sequence analyses of the large sub-unit ribosomal DNA (LrDNA). Physiological and protein electrophoretic studies, however, reveal possible species differences. To clarify this discrepancy, we undertook molecular sequence analyses of the internal transcribed spacer (ITS) and intergenic spacer (IGS) regions of rDNA from the four psychrophilic Mrakia species and the psychrophilic yeast, Cryptococcus curiosus. Identical ITS sequences were found between C. curiosus, M. nivalis and M. frigida. Although, M. stokesii and M. gelida displayed identical ITS and IGS sequences, their sequences differed from the other three species by 2.3% and 38%, respectively. The results suggest that M. stokesii is a synonym of M. gelida, whereas M. nivalis is a synonym of M. frigida. Sequence differences (1.9%) observed in the IGS region indicates that C. curiosus is a distinct strain of M. frigida.     

大白口蘑分离菌株的DNA鉴定

以松口蘑Tricholoma matsutake子实体为外类群,对大白口蘑T. giganteum 野生子实体及其组织分离菌丝进行ITS序列测序,通过DNAStar软件进行比较分析。结果表明大白口蘑ITS序列长度为589bp,松口蘑ITS序列长度为601bp,ITS1和ITS2呈现不同程度的种间多态性;ITS序列测定证实了大白口蘑野生子实体及其组织分离菌丝的同质性,并且ITS区序列在大白口蘑种内不同菌株间的变异程度很小,表明使用通用引物ITS4和ITS5,通过PCR扩增测序即可用于大白口蘑的种质鉴定。     

Chemical and Genetic Studies on Hybrid of Ligularia subspicata and Ligularia cyathiceps Collected in Yunnan Province of China

Two morphologically ambiguous Ligularia samples (samples A and B), and samples with morphology of Ligularia subspicata (sample C), Ligularia lamarum (sample D), or Ligularia cyathiceps (sample E), were collected at Tianchi Pond, Shangrila County, Yunnan Province, China. Analysis of the nucleotide sequence of the internal transcribed spacers (ITSs) in the nuclear ribosomal RNA gene cluster indicated that not only sample B but also sample D was a hybrid of L. cyathiceps and L. lamarum/L. subspicata. Although the morphology of sample A suggested that it was also a hybrid, the ITS sequence of sample A was that of L. cyathiceps. Twenty compounds were isolated from the five samples, and the structures of two new compounds 7 and 14 were determined. Furanoeremophilanes typical of L. lamarum/L. subspicata were detected not only in samples C and D, but also in samples A and B. These results indicate that the ability to produce root chemicals can spread through introgression.     

大白口蘑分离菌株的DNA鉴定

以松口蘑Tricholoma matsutake子实体为外类群,对大白口蘑T.giganteum野生子实体及其组织分离菌丝进行ITS序列测序,通过DNAStar软件进行比较分析。结果表明大白口蘑ITS序列长度为589bp,松口蘑ITS序列长度为601bp,ITS1和ITS2呈现不同程度的种间多态性;ITS序列测定证实了大白口蘑野生子实体及其组织分离菌丝的同质性,并且ITS区序列在大白口蘑种内不同菌株间的变异程度很小,表明使用通用引物ITS4和ITS5,通过PCR扩增测序即可用于大白口蘑的种质鉴定。     

Genotyping of Pneumocystis carinii f. sp. hominis isolates in Japan based on nucleotide sequence variations in internal transcribed spacer regions of rRNA genes

Genotyping of Pneumocystis carinii (Pc) isolated from 24 bronchoalveolar lavage (BAL) fluid specimens in Japan was examined based on nucleotide sequence variations in internal transcribed spacer regions 1 and 2 (ITS1 and ITS2, respectively) of rRNA genes. We found 11 ITS1 genotypes including 2 novel ones and 11 ITS2 genotypes including 3 new ones. Combining the ITS1 and ITS2 genotypes resulted in 30 ITS genotypes, of which 10 are newly described in this report. Two or more genotypes in ITS regions in a specimen were observed in 16 of 24 patients. Our results will be of help for the epidemiological investigation of Pc infection.     

利用松茸ITS特异性引物对松茸分离物进行鉴定

利用一对ITS通用引物(YIS4-ITS5)和一对松茸物ITS特异性引物(TMF-TMR)对来源于云南省不同地区的6个松茸(Tricholoma matsutake)子实体及其6株分离物,3个假松茸(Tricholoma bakamatsutake)子实体及其3株分离物、侧耳(Pleurotus astreatus)、金针菇(Flammulina velutipes)和双孢蘑菇(Agaricus bisporus)的子实体进行了PCR扩增,琼脂糖凝胶电泳分析,结果表明ITS4-ITS5能将所有的样品扩增,并得到600bp左右的DNA扩增条带,TMFTMR扩增时,只有松茸子实体及其对应分离物有扩增条带,DNA片段大小在500bp左右。进一步对松茸子实体(TG25)及其分离物(TM25112．2)进行WS序列测定表明两者的DNA同源性为100％,从而证明所分离到的6个菌株确为松茸的纯培养物。     

Phylogenetic analysis of the genus Hexachlamys (Myrtaceae) based on plastid and nuclear DNA sequences and their taxonomic implications

Myrtaceae are one of the most species‐rich families of flowering plants in the Neotropics. They include several complex genera and species; Hexachlamys is one of the complex genera. It has not been recognized as a distinct genus and has been included in Eugenia, based on morphological grounds. Therefore, molecular systematic studies may be useful to understand and to help to solve these relationships. Here, we performed a molecular phylogenetic analysis using plastid and nuclear data in order to check the inclusion of Hexachlamys in Eugenia. Plastid (accD, rpoB, rpoC1, trnH‐psbA) and nuclear (ITS2) sequence data were analysed using Bayesian and maximum parsimony methods. The trees constructed using ITS2 and trnH‐psbA were the best able to resolve the relationships between species and genera, revealing the non‐monophyly of Hexachlamys. The molecular phylogenetic analyses were in agreement with previous morphological revisions that have included Hexachlamys in Eugenia. These results reinforce the importance of uniting knowledge and strategies to understand better issues of delimitation of genera and species in groups of plants with taxonomic problems. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 532–543.     

中国香菇自然种质的rDNA遗传多样性分析

测定了全国范围内的59个野生香菇菌株rDNA的ITS区域的序列。所得序列的总长度在723-727个碱基之间,G+C含量也基本稳定在57.5%左右。用Phylip3.6软件包对59个ITS序列进行DNA数据分析。结果表明59个菌株被划分到3个不同的谱系中,其中谱系Ⅰ包括11个菌株,分布较为均衡,涉及东北、西北、西南和东部沿海等地区的8个省份;谱系Ⅱ包括14菌株,以西北、西南的4个省份为主;谱系Ⅲ包括34个菌株,覆盖范围最广,除东北和西北高原地区外,其它均有涉及。地缘关系分析表明以陕、甘为主的西北高原地区的菌株涉及Ⅰ、Ⅱ两个谱系;以闽、浙、赣和台湾为主的东部沿海地区的菌株涉及Ⅰ、Ⅲ两个谱系;而以云、贵、川为主的西南地区的菌株则覆盖到了所有的3个谱系。这三个地区的香菇遗传多样性最丰富,西南地区尤为突出,是香菇种质资源保护与利用的重点区域。     

LOW GENETIC VARIABILITY OF SARGASSUM MUTICUM (PHAEOPHYCEAE) REVEALED BY A GLOBAL ANALYSIS OF NATIVE AND INTRODUCED POPULATIONS1

Sargassum muticum (Yendo) Fensholt is one of the most well‐known invasive species in the world. There have, however, been few genetic investigations on both its introduced and native populations. There are also some questions about the taxonomic status of this species. This study is the first to assess the genetic diversity of S. muticum on a global scale, by utilizing one marker each from the extranuclear genomes, namely, plastidial RUBISCO and mitochondrial TrnW_I spacers, as well as the nuclear internal transcribed spacer 2 (ITS2). Based on the markers investigated, both the invasive as well as the native populations of this species appeared very homogenous, when compared with other invasive and brown macroalgae. No variation in ITS2 and RUBISCO spacer was revealed in S. muticum populations, including those from its native ranges in Asia and the introduced ranges in Europe and North America. Two TrnW_I spacer haplotypes with a fixed two‐nucleotide difference were found between the populations of eastern Japan and the other 15 populations examined. This study confirms that there is no cryptic diversity in the introduced range of this species. All the materials collected globally are indeed S. muticum. Results depicting the distribution range of the two TrnW_I spacer haplotypes also support the earlier suggestion that the source of the introduced S. muticum populations is most likely western and central Japan (Seto Inland Sea), where the germlings of S. muticum were likely to have been transported with the Pacific oysters previously introduced for farming in Canada, UK, and France in earlier years.     

洪湖沉积物中真菌群落结构的垂直分布

湖泊沉积物中真菌的类群及其作用所知甚少。以长江中上游代表性湖泊洪湖为研究对象,从湖心截取了一个72cm长的沉积柱,通过rDNA内转录间隔区（ITS）的变性梯度凝胶电泳（DGGE）,对洪湖沉积物中真菌群落结构的垂直变化进行了分析。结果显示,DGGE条带以14－18cm层次为过渡,在2－14cm和14－72cm之间存在一定差异。Shannon-Weaver index（H′）在上下层之间有波动。聚类分析上层2－18cm和中下层18－72cm分别以不同的小类聚在一起。表明14－18cm以上和以下的类群存在差异,     

Ribosomal DNA ITS-1 Intergenic Spacer Polymorphism in Triatomines (Triatominae, Heteroptera)

The length polymorphism of ribosomal DNA ITS-1 intergenic spacer was analyzed in eight species of triatomines belonging to Triatoma, Rhodnius, and Panstrongylus genera. The analyzed species were Rhodnius domesticus, R. neivai, R. robustus, Triatoma brasiliensis, T. infestans, T. vitticeps, Panstrongylus megistus, and P. herreri. These insects are vectors of Chagas' disease, one of the most prominent public health problems among South American countries. This work allowed the differentiation between species of the Triatomini and Rhodniini tribes through the analysis of ITS-1 length polymorphism by PCR and RFLP techniques. The species of the Triatoma and Panstrongylus genera presented an amplified ITS-1 fragment between 600 and 1000 bp, whereas Rhodnius presented a less variable ITS-1 length fragment, around 300 bp, which could reflect the monophyletic origin of the Rhodniini tribe. Species belonging to this genus were further differentiated by RFLP with HaeIII and AluI endonucleases. Our results corroborate the hypothesis of polyphyletic origin in this group of insects and contribute to knowledge about evolutionary relationships in triatomines.     

蓼属头状蓼组rDNA-ITS的序列扩增及分析

以贵州境内蓼属头状蓼组6种(含1变种)植物为材料,对其rDNA的内转录间隔区(ITS)序列进行PCR扩增,得到6种植物的ITS序列,分别为:赤胫散2个居群(Polygonum runcinatum var.sinense,GenBank登录号FJ606887、FJ648802),平卧蓼(P.strindbergii,GenBank登录号FJ648803 ),尼泊尔蓼(P.nepalense,GenBank登录号FJ648804),羽叶蓼(P.runcinatum,GenBank登录号FJ648805),火炭母(P.chinense,GenBank登录号FJ648806)和头花蓼(P.capitatum,GenBank登录号FJ648807).其中赤胫散与平卧蓼的ITS序列为首次报道.序列分析结果表明,蓼属头状蓼组6种植物ITS序列总长度为661～666 bp,ITS1区序列长度为243～246 bp,5.8 S rDNA区序列长度165 bp,ITS2区序列长度253～258 bp,6种植物的差异主要集中在ITS1和ITS2区.聚类分析显示,6种头状蓼组植物具有共同起源,结果支持赤胫散从羽叶蓼变种上升为独立物种.     

Removal of Viable Airborne Fungi from Indoor Environments by Benzalkonium Chloride-Based Aerosol Disinfectants

Fungi are ubiquitous in indoor environments, and some taxa can cause clinical symptoms in humans. Thus, from the viewpoint of public health, methods to reduce indoor airborne fungi are needed. The goal of this study was to examine the efficacies of benzalkonium chloride (BAC)–based aerosol disinfectants to remove airborne viable fungi from indoor environments. The laboratory- and field-based experiments were conducted to compare airborne culturable fungal concentrations before and after the disinfectant aerosol applications. The laboratory-based experiments showed the greater efficacies by the BAC-based disinfectant aerosol than by pure-water control aerosol (p <.05, t-test). In the field study using the BAC-based disinfectant aerosols, on average a 58% reduction of total airborne culturable fungal concentrations were observed. Additionally, the significant reduction was found for a group of airborne yeasts or yeast-like organisms (p <.05, Wilcoxon signed rank test). The BAC-based aerosol disinfectants are effective when used to reduce the numbers of airborne culturable fungi, in particular yeasts or yeast-like organisms, from indoor environments.     

Co(II), Zn(II) and Cu(II) compounds with 1,4; 1,3 or 1,2-bis-(benzimidazole-1-yl-methylene)-benzene as a flexible spacer ligand: Synthesis, characterization and X-ray structures of some polynuclear species

New dinuclear and polynuclear Co(II), Zn(II) and Cu(II) compounds with the ligands 1,4-bis-(benzimidazole-1-yl-methylene)-benzene (bbpx), 1,3-bis-(benzimidazole-1-yl-methylene)-benzene (bbmx) and 1,2-bis-(benzimidazole-1-yl-methylene)-benzene (bbox) are reported. With Co(II) and Zn(II) and the ligands bbpx, bbmx and bbox six new dinuclear and polynuclear compounds are described, i.e. [CoCl₂(bbpx)]_n(DMF)_2n (1), [CoCl₂(bbmx)]₂(DMF)₂ (2), [ZnCl₂(bbmx)]₂(DMF)₂ (3), [CoCl₂(bbmx)]_n(DMF)_n/2(CH₃OH)_n/4 (4), [CoCl₂(bbox)]_n(DMF)_3n/2 (5) and [ZnCl₂(bbox)]_n(DMF)_3n/2 (6). Also one polynuclear Cu(II) compound is reported, i.e. [Cu(bbpx)₂(C₂N₃)_1.5(OH)_0.5]₂(DMF)_4.15(CH₃OH)_1.75(H₂O)_3.5. The X-ray structures, physical and electronic properties are discussed.     

11个灵芝菌株的分子ID构建

[目的]收集11株灵芝菌种为材料,在分子水平上对其进行分类鉴定,并构建分子ID.[方法]采用ITS和SSR分子标记技术,对11株灵芝进行分子鉴定分析.[结果]通过内转录间隔区(ITS)序列测定分析表明,与GenBank上登录的灵芝(Ganoderma lucidum)菌株ITS序列相似度达到99％,在种的水平上证明实验所采用的供试菌株均属灵芝种(Ganoderma lucidum).利用SSR分子标记技术对菌株进行引物扩增,综合多态性条带,用NTSYS软件进行聚类分析,相似度在0.62水平上,1 1个灵芝菌种被分成4个类群,其中GL-2与GL-4各自聚为一类.用ID Analysis 1.0软件进行数据分析表明,用5对SSR引物可将11株灵芝供试菌种完全区分开,并构建其分子身份证.[结论]基于SSR分子标记构建灵芝菌属的分子ID是可行的.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了15种杜鹃属(Rhododendron)植物、1种杜香属(Ledum)植物和Cassiope fastigiata的内转录间隔区(ITS) (包括5.8S)序列.加上从GenBank下载的13种杜鹃属植物和Bajiaria racemosa的ITS序列,以C. fastigiata和B. racemosa为外类群,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析.结果表明: 1)杜鹃属是一个单系类群,叶状苞亚属为杜鹃属的基部类群; 2)杜香属确应归并到杜鹃属中,且与有鳞杜鹃亚属有较近的亲缘关系; 3)有鳞杜鹃亚属和杜香构成一个单系分支,该分支是其余无鳞杜鹃花的姐妹群; 4)由无鳞杜鹃花组成的一个分支的内部支持率较低,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群,而羊踯躅亚属和马银花亚属均为多系类群; 5)在马银花亚属中,长蕊杜鹃组和马银花组均分别得到强烈支持,马银花组与异蕊杜鹃亚属可能构成姐妹群关系,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系.     

基于ITS序列探讨杜鹃属的亚属和组间系统关系

首次报道了 15种杜鹃属 (Rhododendron)植物、1种杜香属 (Ledum)植物和Cassiopefastigiata的内转录间隔区(ITS) (包括 5 .8S)序列。加上从GenBank下载的 13种杜鹃属植物和Bajiariaracemosa的ITS序列 ,以C .fastigiata和B .racemosa为外类群 ,用最大简约法对杜鹃属的亚属和组间的系统关系进行了分析。结果表明 :1)杜鹃属是一个单系类群 ,叶状苞亚属为杜鹃属的基部类群 ;2 )杜香属确应归并到杜鹃属中 ,且与有鳞杜鹃亚属有较近的亲缘关系 ;3)有鳞杜鹃亚属和杜香构成一个单系分支 ,该分支是其余无鳞杜鹃花的姐妹群 ;4 )由无鳞杜鹃花组成的一个分支的内部支持率较低 ,其中常绿杜鹃亚属和映山红亚属均为内部支持率很高的单系类群 ,而羊踯躅亚属和马银花亚属均为多系类群 ;5 )在马银花亚属中 ,长蕊杜鹃组和马银花组均分别得到强烈支持 ,马银花组与异蕊杜鹃亚属可能构成姐妹群关系 ,异蕊杜鹃亚属和马银花组组成的一个分支可能与映山红亚属构成姐妹群关系。     

Molecular appraisal of Bunium and some related arid and subarid geophilic Apiaceae–Apioideae taxa of the Ancient Mediterranean

Bunium is unusual in Apiaceae in having a variable cotyledon number and broad infrageneric dysploidy. To test the monophyly of the genus, phylogenetic relationships among 39 Bunium species were investigated with DNA sequence data from nuclear (nrITS) and plastid (psbA‐trnH intergenic spacer) regions. Several other taxa with a similar ecology and geography were also included in the analyses. Our results suggest that Bunium is not monophyletic. Bunium spp. in the eastern part of the study area are more closely related to the Central Asian genera Elaeosticta, Galagania, Hyalolaena, Mogoltavia and Oedibasis than to those in the western part. Our study revealed that molecular, morphological (cotyledon number and width of fruit commissure) and karyological data reveal similar patterns in the taxa studied. © 2009 The Linnean Society of London, Botanical Journal of the Linnean Society, 2009, 160 , 149–170.