基于rDNA-ITS序列的散斑壳属系统发育学初步研究

对散斑壳属Lophodermium 22个种的40个rDNA-ITS序列进行分析,研究了该属种间系统发育关系。对以简约法构建的系统进化树分析表明,散斑壳属种间亲缘关系与其寄主有很大的相关性,针叶树和阔叶树上的散斑壳可能是亲缘关系较远的两大类群,寄主和产地的不同导致了L.agathidis、L.australe和L.conigenum等种内遗传变异。同时,子囊果的开口机构和唇细胞的有无及特征在种水平分类上具有重要意义,而rDNA-ITS序列系统学分析并不能证实子囊果埋生位置在散斑壳属分类上的重要性。     

松树上的七种散斑壳*

本文报道松树上散斑壳属(Lophodermium Chev)的7个种,其中3个新种:安徽散斑壳(L.anhuiense Y.R.Lin sp.nov.)、白皮松散斑壳(L.pini—bungeanae Y.R.Lin sp.nov.)及奇异散斑壳(L.mirabile Y.R.Lin sp.nov.);2个我国新记录种:针叶树散斑壳(L.conigenum(Brunaud)Hilitz.)和南方散斑壳(L.australe Dearn.);2个国内已记载的种:松针散斑壳(L.pinastri(schrad.)Chev.)和乔松散斑壳(L.pini-excelsae Ahmad)。文中列出了分种检索表,对新种作了拉丁文和汉文描述,对新记录种的主要特点以及已知种的寄主新记录和地理新分布分别作了记载。     

松树上的七种散斑壳

本文报道松树上散斑壳属(Lophodermium Chev)的7个种,其中3个新种:安徽散斑壳(L.anhuiense Y.R.Lin sp.nov.)、白皮松散斑壳(L.pini—bungeanae Y.R.Lin sp.nov.)及奇异散斑壳(L.mirabile Y.R.Lin sp.nov.);2个我国新记录种:针叶树散斑壳(L.conigenum(Brunaud)Hilitz.)和南方散斑壳(L.australe Dearn.);2个国内已记载的种:松针散斑壳(L.pinastri(schrad.)Chev.)和乔松散斑壳(L.pini-excelsae Ahmad)。文中列出了分种检索表,对新种作了拉丁文和汉文描述,对新记录种的主要特点以及已知种的寄主新记录和地理新分布分别作了记载。     

散斑壳属Lophodermium spp.ITS区的序列分析

在国内首次对散斑壳属两个代表种的rRNA基因内转录间区(ITS区)进行了克隆测序,并与Genbank中已有的有关序列进行了比较。发现散斑壳属种间的遗传差异明显高于种内的遗传差异,这与形态学分类相符合,表明ITS区序列分析与形态学鉴定相结合的方法用于散斑壳属的分类研究是可行的。     

基于3个DNA序列的不同形态类型诸葛菜的遗传关系分析及后代性状观察

选择4种形态类型(花紫色-果实光滑、花紫色-果实密生毛、花白色-果实光滑和花白色-果实密生毛)诸葛菜[Orychophragmus violaceus (L. ) O. E. Schulz]共11个单株为实验材料,在进行ITS、trnL-F和psbA-trnH序列分析的基础上,采用邻接法(NJ)构建系统发育树,并对各形态类型的后代性状进行观察和分析.结果表明,诸葛菜的ITS、trnL-F和psbA-trnH序列长度分别为704、767和216 bp,合并序列长度为1 687 bp,G+C含量为43.5%;共有7个变异位点和7个信息位点,变异率0.41%.4个形态类型诸葛菜的trnL-F序列完全一致,ITS和psbA-trnH序列略有差异.其中,花紫色和花白色的果实密生毛类型中各有1个单株的ITS序列第519位碱基为C,其他单株为T;花紫色和花白色的果实光滑类型中各有1个单株的psbA-trnH序列第68位至第73位碱基依次为CAAAAA,其他单株均为TTTTTG.NJ系统发育树显示,4个类型诸葛菜之间没有完全清晰的界限,亲缘关系很近.后代性状观察结果表明,诸葛菜白色花为特化现象,果实光滑和密生毛是不稳定的性状.研究结果支持将毛果诸葛菜(O. violaceus var. lasiocarpus Migo)并入诸葛菜的分类处理.     

中国东北地区壳囊孢属真菌分类和系统发育研究

对采自中国东北地区不同寄主植物上的壳囊孢属真菌标本进行了形态学观察,依据其子实体顶盘、腔室、分生孢子以及子囊壳、子囊、子囊孢子的形态特征,并结合其培养性状等划分为5个形态学类群;利用ITS序列分析构建了系统发育树,结果显示这5个类群的划分均得到了分子证据的支持。腔室特征、孔口数量、中柱以及黑色基线的有无、分生孢子大小等可作为壳囊孢属分类的主要依据。     

中国南部地区松树上的散斑壳菌Ⅰ.

近年作者对我国南部地区松树上的散斑壳属(Lophodermium Chev.)真菌进行了调查和研究。本文报道8个种,其中椭圆散斑壳(L.ellipticum Y.R.Lin)是新种,喜马拉雅散斑壳(L.himalayense P.F.Cannon & Minter)和库曼散斑壳(L.kumaunicum Minter &M.P.Sharma)为我国新记录种,南方散斑壳(L.australe Dearn.)等5种为国内已记载种。对新种作了拉丁文、汉文描述和图解,对新记录种进行了简要记述。另外,记载了已知种的寄主新记录和地理新分布。     

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。     

基于ITS和trnL-trnF序列的草木樨种群遗传多样性研究

以白花草木樨(Melilotus alba)和黄花草木樨(Melilotus officinalis)18个地理种群植物为材料,用ITS序列和trnL-trnF序列研究了2种草木樨不同种群间的遗传多样性。结果表明:(1)trnL-trnF序列对位后长度为459bp,其中包括6个变异位点,6个简约信息位点,G+C含量为33.1%;ITS序列对位后长度为714bp,其中包括5个变异位点,3个简约信息位点,G+C含量为48.9%。(2)在基于trnL-trnF序列构建的系统发育树中,2种草木樨能够形成单系分支,说明trnL-trnF序列在草木樨中的鉴别能力较强。(3)单倍型多样性以及核苷酸多样性分析表明,黄花草木樨的遗传多样性高于白花草木樨。     

基于ITS序列分析豹子花属与5种百合的亲缘关系

以滇蜀豹子花和多斑豹子花为材料,采用PCR直接测序法测定其ITS序列,结合GenBank中其它3种豹子花和5种百合的ITS序列,构建了这10种植物的系统发育树.结果表明:(1)10种植物的ITS序列长度在625bp～627 bp之间,总G C含量在60.38%～61.12%之间,5.8S的G C含量除大理百合为45.4%外,其余9种植物为55.01%或54.60%,说明ITS序列在进化上保守性较强,同属不同种甚至不同属间的长度差异不明显;(2)NJ、MP、ME聚类树的分支趋势一致,都是豹子花属植物先聚在一起再和5种百合相聚,滇西豹子花和豹子花在3种聚类树中都以99%以上的支持率聚成一支,说明这2个种的亲缘关系最近;(3)在10种植物中,形态相似且分布海拔和区域重叠的种类先相聚,说明这些物种的亲缘关系密切.     

干酪乳杆菌的近缘种及亚种部分看家基因的系统发育分析

【背景】16S rRNA基因序列分析已广泛应用于细菌的分类鉴定,但是存在一定局限性,而使用看家基因作为分子标记在近缘种及亚种间的系统发育分析中具有其独特的优势。【目的】研究16S rRNA、uvr C (核酸外切酶ABC,C亚基)和mur E (UDP-N-乙酰胞壁酰三肽合酶)基因序列对干酪乳杆菌的近缘种及亚种的区分能力。【方法】采用分离自传统发酵乳中的6株干酪乳杆菌为研究对象,选取uvr C和mur E基因片段,通过PCR扩增、测序,结合已公布的干酪乳杆菌的近缘种或亚种的相应序列计算遗传距离、构建系统发育树,并与16S rRNA基因序列分析技术进行比较。【结果】研究发现Lactobacilluscasei及相近种间的uvr C、mur E和联合基因(uvr C-mur E)构建的系统发育树拓扑结构与16S rRNA基因结果基本一致,区别在于相似性的不同,其分别为79.00%-99.16%、89.08%-99.20%、76.56%-99.69%和99.58%-100%。基于16S rRNA基因不能区分干酪乳杆菌的近缘种及亚种,而看家基因uvr C和mur E基因序列能够很好地区分干酪乳杆菌的近缘种及亚种,并且将uvr C和mur E基因串联使用后,试验菌株与参考菌株的分类关系更加清晰。【结论】联合基因(uvr C-mur E)可作为16SrRNA基因的辅助工具用于干酪乳杆菌的近缘种及亚种的快速准确鉴定。     

Molecular phylogeny of Corynosoma Lühe, 1904 (Acanthocephala), based on 5.8S and internal transcribed spacer sequences

Species of Corynosoma (Acanthocephala) are distributed worldwide as parasites of marine mammals and sea birds. Species diagnosis is based on morphological characters, including the size and number of hooks in the proboscis and the number of spines in the dorsal and ventral regions of the body. We inferred the phylogenetic relationships of 10 nominal species of Corynosoma through analysis of internal transcribed spacers (ITS-1, ITS-2) and 5.8S ribosomal RNA sequences. Nucleotide distances between species of Corynosoma ranged from 0.4 to 11% for ITS sequences. Maximum parsimony and likelihood analyses indicated that species of Corynosoma that inhabit hosts in the marine environment form a monophyletic assemblage, but yielded conflicting hypotheses for the relationship of Corynosoma cetaceum to other members of the genus. However, parsimony and likelihood analyses were consistent for many Corynosoma sister species relationships of (e.g., C. australe plus C. bullosum, C. validum plus C. villosum, C. caspicum plus C. magdaleni, and C. enhydri plus C. strumosum). This phylogenetic framework was used to evaluate taxonomic controversies concerning C. cetaceum and C. caspicum.     

Patchy distributions belie morphological and genetic homogeneity in rosy-finches

DNA sequence data often appear to contradict low-level avian taxonomy, which is usually based on patterns of external phenotypic similarity. We examined such an apparent contradiction in the Nearctic rosy-finches. On the basis of several phenotypic characters the finches were divided into three species congeneric with three Asian species. When Nearctic taxa were analyzed in a principal components analysis, 66.9% of phenotypic variation was explained by differences between the Bering Sea and continental populations, sexual dimorphism and a latitudinal cline. Our phylogenetic analysis of mitochondrial ND2 sequences revealed four clades among six species of rosy-finches. Three clades corresponded to three Asian species. The fourth clade included all three Nearctic species. Their haplotypes were not reciprocally monophyletic and the combined genetic variability of all Nearctic taxa was lower than in two of their Asian congeners. A Z-specific intron (ACO1I9) and an autosomal coding locus (MC1R) provided little additional phylogenetic information, most likely because of the longer coalescence times relative to ND2. Phylogeographic analyses of ND2 data revealed significant gene flow among neighboring localities regardless of their taxonomic assignment. Our analyses showed that DNA and phenotypic data are not in conflict, but rather complement each other, and together help clarify species limits. Our data are consistent with a single species in North America, not three.     

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.     

Comparative morphology and molecular phylogeny of aplanochytrids (Labyrinthulomycota)

Aplanochytrids comprise one of three major subgroups within the Labyrinthulomycota. We have surveyed the diversity of aplanochytrids and have discovered that most isolates are difficult to identify to species because of character plasticity and ambiguity. Ten isolates were studied using molecular phylogenies based on small subunit ribosomal gene sequences (SSU rDNA) and morphological characters derived from light microscopy, SEM and TEM (e.g., colony size, colony shape, colony pattern, agar penetration, cell shape, cell surface patterns, cell inclusion characteristics and ectoplasmic net morphology). Of these isolates, we could positively identify two of them to species, namely Aplanochytrium yorkensis (Perkins, 1973) Leander and Porter, 2000 and A. minuta (Watson and Raper, 1957) Leander and Porter, 2000. We used standardized conditions for growing aplanochytrid isolates in order to minimize environmentally induced phenotypic plasticity in our comparative studies of morphology. By mapping the morphological characters listed above onto a conservative phylogenetic topology derived from SSU rDNA sequences, we were able to identify several synapomorphies (e.g., gross colony characteristics and cell surface patterns) that serve as valuable taxonomic characters for the identification of species and specific clades of aplanochytrids.     

The new species Lecanora bicinctoidea, its position and considerations about phenotypic evolution in the Lecanora rupicola group

A phylogenetic analysis of the Lecanora rupicola group based on combined nITS rDNA and beta-tubulin sequences and a combined dataset of ITS, beta-tubulin and partial sequences of polyketide synthase genes reveals a previously unrecognized species, which here is introduced under the name Lecanora bicinctoidea. The new species is a sister group of the L. swartzii complex (including L. swartzii and L. lojkaeana), which is characterized by eucorticate ascomata, and a morphological diversity that includes also a dwarf-fruticose lineage. The preferential occurrence on vertical to overhanging siliceous rocks corresponds more closely to L. swartzii. A detailed investigation of phenotypic characters reveals that the new species differs from the superficially similar morphospecies L. bicincta in several ways, such as a thallus of comparatively small areoles and broadly sessile ascomata and the development of an amphithecial cortex devoid of algal remnants (i.e. an eucortex). L. bicinctoidea contains methyl 3alpha-hydroxy-4-O-demethylbarbatate, a chemical compound not known from other members of the L. rupicola group. We also discuss the importance of eucortex formation as one of several factors that are involved in the evolution of substrate-detached thallus structures.     

Molecular phylogenetics and delimitation of species in Cortinarius section Calochroi (Basidiomycota, Agaricales) in Europe

Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to different taxonomic schools. Here, we evaluated species delimitation within this taxonomically difficult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identified species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identified, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.