Isolation of Dermatophytes and other Keratinophilic Fungi from the Vicinity of Salt Pan Soils of Mumbai,India

Soil samples from twenty salt pans and their vicinity around Mumbai and Thane were screened for the occurrence of keratinophilic fungi and related dermatophytes. Ten species classified in six genera were recovered using horse hair as bait. The isolated species were reported in the following order of dominance: Chrysosporium indicum (12.0%), Microsporum gypseum complex (7.2%), C. tropicum (5.6%), C. state of Ctenomyces serratus (4.0%), Trichophyton terrestre (3.2%), Malbranchea aurantiaca (2.4%), C. fluviale (1.6%), Uncinocarpus reesii (1.6%), Malbranchea sp. (0.8%), and T. mentagrophytes (0.8%).     

基于ITS序列探讨忍冬属的系统发育关系

以七子花(Heptacodium miconioides)为外类群,运用MEGA软件对20种忍冬属植物进行系统发育分析,采用邻接法(NJ)和最大简约法(MP)构建系统发育树,从分子系统学角度探讨忍冬属下的亲缘关系.结果表明:(1)在NJ和MP系统树中,没有形成系统树的基部分支,忍冬亚属(Subg.Chamaecerasus)和轮花亚属(Subg.Lonicera)没有形成姐妹群关系.(2)在各系统树中,囊管组内的各种没有聚为一支,故认为对囊管组的划分应进一步探讨.(3)忍冬属ITS区(ITS1+ITS2)的信息位点达到11.0%,信息位点比较丰富,证明ITS序列可以为解决忍冬属植物的系统发育问题提供较强的证据.     

山羊草属二倍体物种核rDNA ITS区序列及其系统发育关系分析

测定了山羊草属（Ａｅｇｉｌｏｐｓ）二倍物种核ｒＤＮＡ ＩＴＳ区序列,发现其碱基粉介于６０１－６０７之间,比报道的小ｒｉｕｃｅａｅ）其他属的ＩＴＳ区我略长,Ｇ＋Ｃ含量达６１．１％～６２．９％,序列间的分化距离为０．００５０～０．０４６８。用ＰＨＹＬＩＰ３．５ｅ软件包对所测得的ＤＮＡ数据进行聚类分析,结果显示：１．Ａｅ．ｓｐｅｌｔｏｉｄｅｓ与该组其他种相距很远,支持将其从Ｓｉｔｏｐｓｉｓ组中独立出来,     

基于nLSU rDNA序列分析探讨侧耳属系统发育关系

以PCR产物直接测序分析了侧耳属（Pleurotus）27个种41个茵株的nLSU rDNA序列,以Hohenbuehelia serotina和Lentinula edodes为外群,运用MEGA3．1软件中的邻接法（neighbor—joining）和最大简约法（maximums parsimony）分别构建侧耳属的系统发育树。分子系统发育树表明：Coremiopleurotus组和Pleurotus属内单、二系茵丝系统均为多系起源;P．rattenburyi,刺芹侧耳种族群（P．eryngii species—complex）与被划分在Lepiotarii组的栎侧耳P．dryinus能与侧耳属其他成员明显分开;红侧耳P．djamor、桃红侧耳P．salmoneostramineus、扇形侧耳P．flabellatus与贝盖侧耳P．calyptratus关系密切;金顶侧耳P．citrinopileatus与P．euosmus聚在一起,而与黄白侧耳P．conucopiae为不同的分类单元;肺形侧耳P．pulmonarius与P．abieticale亲缘关系较近。     

基于ITS序列探讨法落海的系统分类学地位

为研究法落海的系统分类地位,检测了法落海以及当归属和独活属共12种代表植物的核糖体DNA ITS序列,并结合GenBank中独活属4种代表植物的ITS序列,以羌活属的羌活(Notopterygium incisum)作为外类群,应用序列特征、遗传距离与系统树分析等方法对法落海的系统分类地位进行了分析。结果表明,依据不同的ITS区序列会得出不同甚至截然相反的结论:若依据ITS1序列,法落海应该归属到当归属;若依据ITS2序列,法落海应该归属到独活属。进一步分析法落海与当归属、独活属植物ITS区序列的碱基组成时发现,法落海在ITS1区拥有当归属植物的序列特征,而其ITS2区拥有独活属植物的序列特征。综上分析,支持法落海是介于当归属与独活属之间的一个分类群的系统分类观点。     

Relationships of the Insect-Pathogenic Order Entomophthorales (Zygomycota, Fungi) Based on Phylogenetic Analyses of Nuclear Small Subunit Ribosomal DNA Sequences (SSU rDNA)

We sequenced the nuclear small subunit of ribosomal DNA (SSU rDNA) from seven species within the insect-pathogenic order Entomophthorales. These sequences were aligned with other published SSU rDNA sequences and phylogenies were inferred using phenetic and cladistic methods. Based on three different phylogenetic methods the Entomophthorales (excludingBasidiobolus ranarum) is monophyletic;B. ranarumwas more closely related to chytrids from Chytridiales and Neocallimasticales than to Entomophthorales, as was proposed by Nagahamaet al.(Mycologia87:203–209, 1995). Nuclear characters (large nuclei containing conspicuous condensed chromatin and lack of a prominent nucleolus) were of predictive value for the monophyly of the family Entomophthoraceae. Conidial characters separate the Entomophthoraceae, which only includes obligate pathogens, into at least two lineages: one lineage with uninucleate conidia and another with multinucleate conidia. The two species ofConidiobolusstudied were paraphyletic in our analyses and only distantly related to each other. This information may prove to be important in the use of these fungi as biocontrol agents.     

Phylogenetic Analysis ofBambusa (Poaceae: Bambusoideae) Based on Internal Transcribed Spacer Sequences of Nuclear Ribosomal DNA

Phylogenetic analyses of Bambusa species were performed using internal transcribed spacer sequences of nuclear ribosomal DNA. The 21 species sampled included members of Bambusa (sensu stricto), Dendrocalamopsis, Dendrocalamus, Guadua, Leleba, and Lingnania. Arundinaria gigantea was used as an outgroup. Using the maximum parsimony method with PAUP*, gaps were treated as missing states or new states. Parsimonious analysis revealed that Dendrocalamus latiflorus was closely related to the members of Dendrocalamopsis. Dendrocalamus membranaceus was a sister species to Dendrocalamus strictus. Three Dendrocalamus species were closely related to and nested in a polyphyletic Bambusa. Bambusa subaequalis was a sister species to B. multiplex, B. emeiensis to B. chungii, B. contracta to B. hainanensis, and B. flexuosa was a sister species to B. sinospinosa, B. tuldoides, B. surrecta, B. intermedia, and B. valida group, which raised doubts about the monophyly of the subgenera Bambusa (sensu stricto), Dendrocalamopsis, Leleba, and Lingnania under the genus Bambusa.     

Keratinophilic fungi isolated from soils of Mumbai,India

Eighty-seven soil samples were collected from various areas of Mumbai and its vicinity to determine the prevalence of keratinophilic fungi. From the 55 positive samples (63.21%), a total of four genera with nine species were isolated viz. Chrysosporium indicum (28.73%),C. lobatum (2.29 %), C. sp.I (1.14%), C. sp. II (1.14%),C. tropicum (1.14%),C. zonatum (2.29%),Ctenomyces serratus (2.29%) Malbranchea aurantiaca (2.29%) and Microsporum gypseum complex (21.83%). This revised version was published online in June 2006 with corrections to the Cover Date.     

四药门花属及其近缘植物ITS区序列分析和系统学意义

测定和分析了四药门花等１３种金缕梅科（Ｈａｍａｍｅｌｉｄａｃｅａｅ）植物的核糖体ＤＮＡ转录间隔区（ＩＴＳ区）及５８Ｓ编码区的序列。应用最大简约法构建的分子系统树表明：被分析的金缕梅亚科（Ｈａｍａｍｅｌｉｄｏｉｄｅａｅ）植物形成一个单系类群,亚科内及其中的金缕梅族（Ｈａｍａｍｅｌｉｄｅａｅ）内部呈复系演化（ｐｏｌｙｐｈｙｌｅｔｉｃ）的特征;支持秀柱花族（Ｅｕｓｔｉｇｍａｔｅａｅ）（含秀柱花属Ｅｕｓｔｉｇｍａ、牛鼻栓属Ｆｏｒｔｕｎｅａｒｉａ和山白树属Ｓｉｎｏｗｉｌｓｏｎｉａ）成立以及将蚊母树族（Ｄｉｓｔｙｌｉｅａｅ）与弗特吉族（Ｆｏｔｈｅｒｇｉｌｅａｅ）合并的观点,此结果与Ｅｎｄｒｅｓ（１９８９）系统接近;金缕梅族中金缕梅属（Ｈａｍａｍｅｌｉｓ）与弗特吉族中的弗特吉属（Ｆｏｒｔｈｅｒｇｉｌａ）、银缕梅属（Ｓｈａｎｉｏｄｅｎｄｒｏｎ）和水丝梨属（Ｓｙｃｏｐｓｉｓ）系统发育关系密切;四药门花属（Ｔｅｔｒａｔｈｙｒｉｕｍ）与木属（Ｌｏｒｏｐｅｔａｌｕｍ）属于同一个单系类群,它们与Ｈａｍａｍｅｌｉｓ的亲缘关系较远     

Specific Ribosomal DNA Sequences from Diverse Environmental Settings Correlate with Experimental Contaminants

Phylogenetic analysis of 16S ribosomal DNA (rDNA) clones obtained by PCR from uncultured bacteria inhabiting a wide range of environments has increased our knowledge of bacterial diversity. One possible problem in the assessment of bacterial diversity based on sequence information is that PCR is exquisitely sensitive to contaminating 16S rDNA. This raises the possibility that some putative environmental rRNA sequences in fact correspond to contaminant sequences. To document potential contaminants, we cloned and sequenced PCR-amplified 16S rDNA fragments obtained at low levels in the absence of added template DNA. 16S rDNA sequences closely related to the genera Duganella (formerly Zoogloea), Acinetobacter, Stenotrophomonas, Escherichia, Leptothrix, and Herbaspirillum were identified in contaminant libraries and in clone libraries from diverse, generally low-biomass habitats. The rRNA sequences detected possibly are common contaminants in reagents used to prepare genomic DNA. Consequently, their detection in processed environmental samples may not reflect environmentally relevant organisms.     

Unveiling the Organisms behind Novel Eukaryotic Ribosomal DNA Sequences from the Ocean

Despite the fact that the smallest eukaryotes (cells less than 5 μm in diameter) play key roles in marine food webs, particularly in open oligotrophic areas, the study of their in situ diversity started just one year ago. Perhaps the most remarkable finding of the most recent studies has been the discovery of completely new phylogenetic lineages, such as novel clades belonging to the stramenopile and alveolate phyla. The two new groups account for a significant fraction of clones in genetic libraries from North Atlantic, equatorial Pacific, Antarctic, and Mediterranean Sea waters. However, the identities and ecological relevance of these organisms remain unknown. Here we investigate the phylogenetic relationships, morphology, in situ abundance, and ecological role of novel stramenopiles. They form at least eight independent clades within the stramenopile basal branches, indicating a large phylogenetic diversity within the group. Two lineages were visualized and enumerated in field samples and enrichments by fluorescent in situ hybridization using specific rRNA-targeted oligonucleotide probes. The targeted organisms were 2- to 3-μm-diameter, round-shaped, nonpigmented flagellates. Further, they were found to be bacterivorous. One lineage accounted for up to 46% (average during an annual cycle, 19%) of heterotrophic flagellates in a coastal environment, providing evidence that novel stramenopiles are important and unrecognized components of the total stock of bacterial grazers.     

Phylogenetic Analyses of Aurantioideae (Rutaceae) Based on Non-Coding Plastid DNA Sequences and Phytochemical Features

Abstract: Sequences of the plastid DNA atp B/ rbc L intergenic spacer and rps16 intron from 23 genera and 47 species of Rutaceae were used to resolve phylogenetic relationships in subfamily Aurantioideae. According to these, the subfamily is monophyletic, but its classical subdivision into tribes Clauseneae and Citreae is only justified if the genus Murraya s.s. (exclusive of the species segregated as Bergera , e.g., Murraya koenigii and M. siamensis ) and Merrillia are transferred to Citreae s.l. This conclusion is also well supported by phytochemistry, demonstrating accumulation of carbazoles in Bergera and Clausena , and of 8-prenylated coumarins and polyoxygenated flavonoids in Murraya s.s. and Merrillia. Formation of both carbazoles, as well as 8-prenylated coumarins, and polyoxygenated flavonoids in Micromelum suggests relationships between Clauseneae s.s. and Citreae s.l. The monophyly of several larger genera in both tribes is supported by relatively high bootstrap percentages and specific chemical profiles for e.g., Clausena, Micromelum, Glycosmis and Atalantia. In contrast, molecular, chemical, and other data show that none of the subtribes recognized within Aurantioideae reflect phylogenetic relationships. Only the clades with Clausena + Bergera, Murraya s.s. + Merrillia, and Citrus + Clymenia + Eremocitrus + Fortunella + Poncirus ("true Citrus fruit trees") are well supported by such data. Among the outgroup genera, Zanthoxylum (Rutoideae) and Toddalia (Toddalioideae) are much closer to each other than to Ruta (Rutoideae).     

ITS1 Sequences of Nuclear Ribosomal DNA in Wild Rices and Cultivated Rices of China and Their Phylogenetic Implications

he first internal transcribed spacer (ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3%to 72.7%. In pairwise comparison among the five taxa, sequence site divergence ranged from 1.5 % to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well-resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) of the genus Oryza.     

DNA序列在蕨类分子系统学研究中的应用

在分子系统学研究中,目的基因或者基因片段的选择是最关键的一步,由于进化速率的差异,不同的DNA序列适用于不同分类阶元的系统发育研究.本文综述了目前蕨类分子系统发育研究中常用的DNA序列分析,它们分别来自叶绿体基因组、核基因组和线粒体基因组,着重阐明叶绿体基因在蕨类分子系统学研究中的应用.本文还简要介绍了分子系统学研究中常见的问题及解决方法(如内类群和外类群的选择.适宜DNA片段的选择策略),总结了目前蕨类植物分子系统学研究所取得的进展和研究现状,展望了当今国际蕨类分子系统学的研究趋势.     

DNA序列在植物系统学研究中的应用

植物DNA序列由于进化速率上的差异而适用于不同分类阶元的系统发育研究,因此,针对某一特定的系统学问题选择相应合适的分子片段是分子系统学研究中最为关键的一步。在前人研究的基础上,主要讨论了目前分子系统发育和进化研究中一些常用的DNA序列的适用范围,包括nrDNA的18S基因及ITS等非编码区,cpDNA的编码基因（rbcI、matK、ndhF、atpB）及非编码区序列（rpL16、rpoC1、rps16、trnL-F和trnT-L）和应用较少的mtDNA。研究表明,18S、rbcI等编码基因及mtDNA一般适用于较高分类阶元甚至整个种子植物谱系间的系统发育的探讨,而ITS及cpDNA的非编码区序列等因其较快的进化速率多用于较低分类阶元的系统关系研究。     

DNA 序列在蕨类分子系统学研究中的应用

在分子系统学研究中, 目的基因或者基因片段的选择是最关键的一步, 由于进化速率的差异, 不同的DNA序列适用于不同分类阶元的系统发育研究。本文综述了目前蕨类分子系统发育研究中常用的DNA序列分析, 它们分别来自叶绿体基因组、核基因组和线粒体基因组, 着重阐明叶绿体基因在蕨类分子系统学研究中的应用。本文还简要介绍了分子系统学研究中常见的问题及解决方法(如内类群和外类群的选择, 适宜DNA片段的选择策略), 总结了目前蕨类植物分子系统学研究所取得的进展和研究现状, 展望了当今国际蕨类分子系统学的研究趋势。     

Phylogenetic Relationships of 12 Penaeoidea Shrimp Species Deduced from Mitochondrial DNA Sequences

DNA sequences of an 847 bp fragment of mitochondrial cytochrome oxidase subunit I (COI) gene and a 514 bp fragment of 16s rRNA gene were determined to examine the phylogenetic relationships of 12 Penaeoidea shrimp species (Penaeus chinensis, Penaeus japonicus, Penaeus penicillatus, Penaeus vannamei, Penaeus canaliculatus, Trachypenaeus curvirostris, Metapenaeus affinis, Metapenaeus ensis, Metapenaeopsis barbata, Parapenaeus fissuroides, Parapenaeopsis hardiwickii, Solenocera crassicomis). Both fragments of the swimming crab Portunus trituberculaus chosen as the outgroup were also sequenced. Intraspecific sequence divergence of 0.24-1.2% in the COI gene was found in 5 species, while no intraspecific variation was observed in the 16s rRNA gene. Three phylogenetic trees based on the 1361 bp combined sequences of COI and 16s rRNA were concordant in indicating the following suggestions: (1) phylogenetic relationship of the 11 Penaeidae species based on our result support the opinion of Burkenroad (Burkenroad, M.D. (1983). Crustacean Issues 3:279-290) on the basis of morphological features; (2) it seems more reasonable to class Solenocera crassicorni in the family Penaeidae; (3) the fragment of the COI gene chosen here appears to be a good marker for speciation studies and population analysis in Crustaceans, while the 16s rRNA gene fragment here seems suitable for examining phylogenetic relationships at the species or genus levels in Crustaceans. Our time estimates suggest that Penaeus and Metapenaeus might have separated about 6.38 x 10(6)-7.98 x 10(6) years BP in the post-Miocene, and the species separation within Metapenaeus and Penaeus might occur 0.08 x 10(6)-0.4 x 10(6) years BP in the late Pleistocene.     

猕猴属6个种的rDNA变异及其系统进化关系

以人２８Ｓ,１８Ｓ,ｒＤＮＡ为探针,用１５种限制性内切酶构建了猕猴属６个种（Ｍ．ｍｕｌａｔｔａ,Ｍ．ｆａｃｓｉｃｕｌａｒｉｓｆＭ．ａｒｃｔｏｉｄｅｓ,Ｍ．ａｓｓａｍｅｎｓｉｓ．Ｍ．ｔｈｉｂｅｔａｎａ．Ｍ。ｎｅｍｅｓｔｒｉｎａ）和滇金丝猴Ｒｈｉｎｏｐｉｔｈｅｃｕｓｂｉｅｔｉ）,白颊长臂猿（Ｈｙｌｏｂａｔｅｓｌｅｕｃｏｇｅｎｙｓ）核糖体ＤＮＡ重复单位的限制性内切酶图谱,红面猴（Ｍ．ａｒｃｔｏｉｅｓ）与