Phylogenetic relations of Rhizoplaca Zopf. from Anatolia inferred from ITS sequence data

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.     

A study of the genetic variability of Rhizoplaca chrysoleuca using DNA sequences and secondary metabolic substances

Specimens of Rhizoplaca chrysoleuca from Mount Wuling can be divided into two distinct groups based on obvious differences in morphological characters. Here we investigated 26 specimens of R. chrysoleuca from Mount Wuling, 10 specimens of this species from other areas and seven specimens of other Rhizoplaca species by analyzing morphology, chemistry and genetics. Nine chemotypes were detected among the specimens of R. chrysoleuca from Mount Wuling, and five of them were reported for the first time. Based on the ITS phylogenetic analysis, the chemotypes and the insertion distribution patterns in SSU rDNA, the samples of R. chrysoleuca from Mount Wuling were grouped in two distinct clades corresponding to two phenotypic groups and no gene flow was detected between these two groups. Our results establish all individuals of Rhizoplaca chrysoleuca are conspecific although some populations have been isolated on Mount Wuling, indicating that they are in the process of speciation. Our study also reveals that the relationships between genotypes and chemotypes are complicated and should be avoided, and we instead recommend using single individuals or few individuals from the same site to represent the population or whole species in systematics study. The results also indicate that Rhizoplaca chrysoleuca might provide a good model for studying the speciation of saxicolous lichenized fungi.     

中国脐鳞属地衣的初步研究

在泛北极地区迄今已知的脐鳞属地衣共有三种:中国有记录的两种。本文报道了四种,其中之一为新种,另一种为中国新记录。此外,有一改级新组合。     

Determination of usnic acid in some Rhizoplaca species from Middle Anatolia and their antimicrobial activities

Three species of lichens, Rhizoplaca chrysoleuca (Sm.) Zopf, Rhizoplaca melanopthalma (DC.) Leuckert & Poelt and Rhizoplaca peltata Ramonds Leuckert, were collected from middle Anatolia, Erciyes Mountain (Kayseri) in Turkey. Their usnic acid amounts were determined by HPLC in acetone extracts. In addition, antimicrobial activities of these extracts were determined against Escherichia coli (ATCC 35218), Enterococcus faecalis (RSKK 508), Proteus mirabilis (Pasteur Ens. 235), Staphylococcus aureus, Bacillus subtilis, Bacillus megaterium and Pseudomonas aeruginosa. It was shown that, as the usnic acid amount increased, the antimicrobial activities increased too. The usnic acid contents of Rhizoplaca species varied between 0.19-4.0% dry weight.     

脐鳞属地衣一个新种(英文)

本文描述了脐鳞属地衣一个新种:褐脐鳞。这个新种类似红脐鳞,但地衣体上表面为灰褐色并且不合松萝酸。本种与泡状脐鳞的区别是不含富马原岛衣酸及地理分布的差异。     

Phylogenetic inference of the genus Bupleurum (Apiaceae) in Hengduan Mountains based on chromosome counts and nuclear ribosomal DNA ITS sequences

pleurum of Apiaceae in China. This paper reports chromosome numbers of six species and two varieties of Bupleurum, and for four species and two varieties their chromosome numbers are reported for the first time. The phylogeny of Bupleurum was investigated based on the ITS region of the nuclear ribosomal DNA (nrDNA) of 14 taxa from the Hengduan Mountains, 3 taxa from the North China (Hebei and Heilongjiang), and 16 taxa from Africa and the Mediterranean region. Varia-tions in chromosome numbers and the ITS sequences were used to infer phylogenetic relationships between Bupleurum species in Hengduan Mountains. The results showed that the Hengduan Mountains might represent one of the frequency and diversity centers for Bupleurum. The ancestors of Bupleurum species in the Hengduan Mountains may be related to the woody B. fruticosum in North Africa, or the species in the western Mediterranean region. It is postulated that the ancestral population migrated into Hengduan Mountains through the Middle East and the Caucasus. Furthermore, the neo-endemic B. mundtii in South Africa appeared to be a close relative of the species in the Hengduan Mountains. In the trend of basic chromosome number evolution, x = 8 should be regarded as the ancestral basic number, while x = 6, 7 as the derived ones. The Bupleurum species in the Hengduan Moun-tains have been undergoing changes in the basic chromosome numbers or the ploidy level. The ITS phylogenetic tree showed that the Chinese species were divided into two clades: one with the basic chromosome number x = 8, and the other with x = 6, 7. The results rejected the previous infrageneric classification of Bupleurum in China. We further suggested to raise B. marginatum var. stenophyllum to species rank based on the combined evidence from morphology, karyology, pollen morphology, and the ITS phylogenetic tree.     

基于染色体计数和ITS序列初步探讨横断山区柴胡属植物(伞形科)的系统发育

横断山区是中国柴胡属Bupleurum植物的分布中心。本文对横断山区6个种2变种进行了染色体记数报道,其中4个种2变种是首次报道。对横断山区的10个种4个变种、中国北方（河北和黑龙江）的3个种的nrDNA ITS进行测序,同时从GenBank里面下载同属的来自非洲和地中海西部的16个nrDNA ITS序列数据,结合染色体数目变化结果,初步探讨了横断山区柴胡属植物的系统发育。结果表明横断山区可能是现代柴胡属植物的频度中心和多样分布中心之一。它们的祖先种可能是非洲北部的木本柴胡属植物B.fruticosum,或者是地中海西部的柴胡属植物,推测是通过中东和高加索扩散而形成的,其中与非洲南部特有种B.mundtii的亲缘关系也较近;染色体基数演化趋势是：8是较原始基数,6和7是次生基数,其染色体异基数变异和多倍化可能是物种形成、进化以及向外扩散的主要方式;在ITS系统发育树中,中国柴胡属植物染色体基数为8的种类聚为一支,染色体基数为6和7的种类聚为了一支,不支持舒璞等（1998）关于中国柴胡属的属下分类系统。结合已有的形态学、细胞学、孢粉学证据和ITS系统发育树,建议窄竹叶柴胡B.marginatum var.stenophyllum独立成种。     

中国双缘衣属(双缘衣科)地衣一新种

现分类系统中,双缘衣属隶属于子囊菌门,茶渍纲,厚顶盘亚纲,文字衣目,双缘衣科。全世界有48种,被确认为单系类群的小属。利用形态学、解剖学、生物化学以及分子生物学方法,对采自天山西部的双缘衣属地衣标本进行分类学研究,发现了双缘衣属地衣1个新种：绿盘双缘衣Diploschistes viridis (属于双缘衣亚属)。基于最大似然分析(ML)和贝叶斯分析(BI)构建了基于ITS位点系统发育树,详细描述该种的形态特征、分布及栖息地等情况,并提供了地衣体的彩色图片。     

山西太行山地区铦囊蘑属两新种

铦囊蘑属Melanoleuca属于担子菌门Basidiomycota伞菌纲Agaricomycetes伞菌目Agaricales,因该属很多种类都是重要的食用菌而受到广泛关注。本文报道了在山西太行山地区发现的该属2个新种,即浅灰铦囊蘑Melanoleuca grisea和近白柄铦囊蘑M. subleucopoda。通过形态学特征、ITS和RPB2基因序列的分子系统发育分析结果,确定了其分类地位,并讨论了它们与铦囊蘑属内相关物种的形态学和系统发育关系。     

用rDNA的ITS序列探讨绵刺属的系统位置

绵刺属由于其特殊的形态特征,其系统位置至今仍存在争议。本文选定了蔷薇亚科6种植物和李亚科1种植物,扩增并测定了其核糖体DNA的ITS序列(不包括5.8S片断)。分析时又从GenBank中选取了蔷薇科另外5种植物的ITS序列共同分析。比较这12种植物的ITS1+ITS2,发现不同植物间序列长度变异较大。ITS1的长度范围为224~266 bp,ITS2的长度范围为202~221 bp。用PAUP 3.1.1软件对12种植物的ITS1+ITS2进行分析,结果表明蔷薇亚科中和绵刺属亲缘关系最近的属为金露梅属,其次为地蔷薇属,再次为山莓草属,而这4个属均具有花柱基侧生的特点,这与传统上依据花托杯状或坛状将绵刺属放在蔷薇属和龙牙草属附近的处理不符。系统树上李亚科的2种植物明显地聚为一个单系类群,说明绵刺与蒙古扁桃关系相对甚远。研究结果还表明绵刺这一蒙古高原旱生植物区系成分是由东亚中生植物区系成分的银露梅演化而来;绵刺的各种形态特征和生态习性是长期适应荒漠干旱气候环境的结果。这一植物起源及其迁移路线的发现,为深入研究亚洲中部荒漠植物区系和植被的形成提供了新的证据。     

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.     

基于形态特征和ITS序列对7个鹅膏菌属菌株的分类鉴定

以采自浙江省丽水地区的7个鹅膏菌属菌株作为研究材料,在基于形态特征进行初步鉴定的基础上,对7种鹅膏菌的rDNAITS区段进行克隆测序和序列特征比较分析。进一步对ITS序列进行核酸序列数据库GenBank同源性检索比对,将从GenBank检索获得的9个最相似物种的ITS序列连同7种鹅膏菌的ITS序列一起作系统发育分析。结果表明:基于ITS序列对f6、f9和f493个菌株的分子鉴定支持了基于形态特征的鉴定结果,对f5的分子鉴定不支持形态鉴定的结果,f8为鹅膏菌属内某种,f66为鹅膏菌属内某种,并与Amanitafulva,A.atrofusca,A.orientifulva3种鹅膏菌的亲缘关系较近,f7与另外6种鹅膏菌的亲缘关系相差甚远。研究结果提示基于分子水平上的ITS序列分析不能单方面作为大型真菌分类鉴定的可靠依据,可以作为基于传统形态学分类鉴定的辅助参考依据。     

大小兴安岭地区红菇属物种多样性及其地理成分

红菇属(Russula)真菌广泛分布于世界各地并与多种植物根系共生形成外生菌根, 对于森林生态系统的多样性维持与群落构建具有重要的作用。我国东北大小兴安岭地区是欧亚和美洲北温带地区生物群落交流的关键地区之一, 但该地区有关外生菌根真菌的区系研究较少。本研究对采自大小兴安岭的96份红菇标本进行了形态学鉴定和ITS序列分析, 通过结合世界范围内红菇属代表性物种(146个种)的ITS序列构建了红菇属系统发育图谱。结果表明, 大小兴安岭地区红菇属有46个分类单元, 其中包括37个种和9个未定种。对大小兴安岭地区37种红菇的地理成分分析表明, 北温带分布成分有13种、温带-热带共有成分8种、欧亚成分9种、世界广布成分7种。本研究表明大小兴安岭地区的红菇具有丰富的物种多样性, 而且具有明显的北温带区系特征, 同时也具有一定的区域特殊性。     

基于rDNA ITS序列探讨部分腐霉种的系统发育与其形态特征

基于对73株计58种腐霉和6种疫霉的核糖体DNA的ITS序列分析,以海生疫霉为外围群,按邻接法构建系统发育树,对腐霉的系统发育关系进行了研究。结果表明:在58种腐霉中,Pythium ostracodes,P.chamaehyphon,P.carbonicum,P.montanum和P.vexans归为同一组,介于其它腐霉和疫霉之间,这5种腐霉的孢子囊均为球形;现已归为疫霉属的P.undulatum 单独为一组,它与腐霉的亲缘关系比疫霉更近;其余52种腐霉聚成一大组,这52种腐霉基本上按孢子囊或菌丝膨大体形态分成Ⅰ、Ⅱ两组:第1组31种腐霉, 其中30种腐霉的孢子囊或菌丝膨大体为球形;第Ⅱ组21种腐霉,其中19种腐霉的孢子囊为丝状、瓣状或裂片状。基于ITS序列分析,腐霉属的其它性状如藏卵器壁是否光滑、卵孢子是否满器、雄器的着生方式和数量、异宗配合等呈多元演化。     

中国东北15种藓类植物RAPD分析及其分类学意义

本研究选用15 种东北藓类植物, 其中塔藓、赤茎藓、垂枝藓、拟垂枝藓、羽平藓、木藓、万年藓等为北半球广泛分布的大型藓类, 而褶叶藓、粗枝藓、球蒴金发藓等则是东亚特有种。在野外调查和采集的基础上, 进行RAPD 分析, 旨在从DNA 水平上对它们的亲缘关系和分类问题加以研究, 为它们的分类问题和亲缘关系提供分子证据。结果:从分子水平上进一步验证了15 种东北藓类植物形态分类的正确性。不同种类分别聚在金发藓目(Polytrichinales), 变齿藓目(Isobryales)和灰藓目(Hypnobryales)中, 与现采用分类系统一致。东北特产属褶叶藓属(Okamuraea)和粗枝藓属(Gollania)与垂枝藓科(Hyitidiaceae)植物关系较近, 而赤茎藓(Pleurozium)与绢藓(Entodon)有一定亲缘关系。因此, 将赤茎藓置于塔藓科(Hylocomiaceae)是合适的。     

野生食用菌“苇菇”的物种多样性及中华美味蘑菇适生区预测

“苇菇”是主产于新疆的野生食用菌,主要分布于我国西北内陆湖泊周边的芦苇或多枝柽柳林内,埋生或半埋生在土壤中。本研究共采集和收集相关标本91份,开展了形态学和分子系统学研究,结果表明这些宏观形态特征相似的“苇菇”标本并非一个物种,而是分属于蘑菇属Bivelares组的大肥蘑菇Agaricus bitorquis、中华美味蘑菇A. sinodeliciosus和亚托柄蘑菇A. subperonatus;及Nigrobrunnescentes组的帕达纳蘑菇A. padanus。本文对“苇菇”形态进行了描述,并提供了它们的分种检索表。其中大肥蘑菇、亚托柄蘑菇和帕达纳蘑菇在我国和欧洲等地均有分布,而中华美味蘑菇仅在我国有报道。据此,依据1950-2000年生物气候数据结合中华美味蘑菇的分布实地调查结果,利用最大熵模型(maximum entropy model,MaxEnt)开展了对中华美味蘑菇分布区的分析和预测,结果表明中华美味蘑菇适生区在我国主要为新疆天山山脉南北两侧、西藏西南部、青海海西州、甘肃西北部以及内蒙古西部地区;预测国外适生区域在中亚的哈萨克斯坦和蒙古国。物种分布模型涉及的环境变量对模型的贡献率显示,最湿月降水量、最暖季度降水量、最冷季度平均温度和最暖月最高温是影响中华美味蘑菇分布的主要环境因子。研究结果表明中华美味蘑菇适生区域狭窄,为狭域种,建议应加强相关资源的保护,并积极拓展其可持续利用途径以降低对野生中华美味蘑菇子实体的过度消耗。     

Phylogeny of Allium L. subg. Melanocrommyum (Webb et Berth.) Rouy based on DNA sequence analysis of the internal transcribed spacer region of nrDNA

 Sequence analysis of the ITS region of nuclear ribosomal DNA from subgeneric representatives of Allium L. produced phylogenetic trees which concurred with previous conclusions based on classical taxonomy. Phylogenetic analysis revealed a closer relationship between Nectaroscordum siculum and Allium cernuum (representing Amerallium) than between A. cernuum and the rest of the Allium species employed in this study. The phylogeny of subg. Melanocrommyum based on ITS sequences largely agreed with inferences made by previous researchers based on morphology or a restriction analysis of chloroplast DNA. However, the phylogenetic positions of Allium protensum and Allium macleanii based on ITS sequences did not correspond to their morphological similarity with Allium schubertii and Allium giganteum, respectively. Received: 15 February 1998 / Accepted: 12 March 1998     

Antrodia tropica sp. nov. from southern China inferred from morphological characters and molecular data

Antrodia tropica sp. nov. is described and illustrated on the basis of collections originating from Hainan, southern tropical China. Both the morphology and phylogenetic analysis of rDNA ITS sequences support this new species. Morphologically, it is characterized by resupinate basidiocarps, an annual growth habit, greyish to pinkish buff pore surface, a dimitic hyphal system with clamped generative hyphae, and cylindrical to subfusiform basidiospores. The hymenophoral trama is dominated by generative hyphae, whereas skeletal hyphae are dominant in the subiculum. Molecular phylogeny inferred from ITS sequence data suggested a close relationship between A. tropica and two other Antrodia species, including A. huangshanensis reported from China and A. ramentacea found mostly in boreal Eurasia.     

Characterization of biological ice nuclei from a lichen.

Biological ice nuclei (active at approximately -4 degrees C) were extracted from cells of the lichen Rhizoplaca chrysoleuca by sonication. Sensitivity to proteases, guanidine hydrochloride, and urea showed these nuclei to be proteinaceous. The nuclei were relatively heat stable, active from pH 1.5 to 12, and active without lipids, thereby demonstrating significant differences from bacterial ice nuclei.