锦葵科植物DNA条形码通用序列的筛选

对锦葵科植物样品的ITS、ITS2、rbcL、matK和psbA-trnH序列进行PCR扩增和测序,比较各序列的扩增效率、测序成功率、种内和种间变异的差异以及barcoding gap图,使用BLAST1和Nearest Distance方法评价不同序列的鉴定能力,进而从这些候选序列中筛选出较适合锦葵科植物鉴别的DNA条形码序列。结果表明,ITS序列在采集的锦葵科植物11个种26个样品中的扩增成功率较高,其种内、种间变异差异和barcoding gap较ITS2、psbA-trnH及rbcL序列具有更明显的优势,且纳入60个属316个种共1228个样品的网上数据后,其鉴定成功率可达89.9%。psbA-trnH序列的扩增和测序成功率最高,其鉴定成功率为63.2%,并能鉴别一些ITS序列无法鉴别的种。实验结果表明,ITS和psbA-trnH是较适合鉴别锦葵科植物的DNA条形码序列组合。     

Xylodon subflaviporus sp. nov. (Hymenochaetales,Basidiomycota) from East Asia

Xylodon subflaviporus (Hymenochaetales, Basidiomycota) is described as a new species collected from tropical and subtropical regions of East Asia. This new species is characterized by resupinate basidiocarps, a poroid hymenophore, pseudodimitic hyphal system, nodose-septate hyphae, four types of cystidia (capitate, acicular to cylindrical, subulate to ventricose, and apically-encrusted), and thin-walled, colorless, smooth and ellipsoid basidiospores. Bayesian, Maximum Likelihood and Maximum Parsimony algorithms were used to construct phylogenies inferred from the internal transcribed spacer (ITS) region of rDNA. Morphological and molecular studies, along with intercompatibility tests, confirmed the independent status of this species. Also, based on morphological and molecular evidence, six new combinations of Xylodon are proposed to accommodate species originally classified under Hyphodontia s.l., i.e. X. bubalinus, X. chinensis, X. mollissimus, X. nongravis, X. reticulatus and X. subtropicus. A key to known species of Hyphodontia s.l. with poroid, irpicoid or raduloid hymenophores is provided for the convenience in identification.     

Molecular phylogeny of Osmanthus(Oleaceae)based on non-coding chloroplast and nuclear ribosomal internal transcribed spacer regions

The phylogenetic relationships of Osmanthus Lour.were investigated using the nuclear ribosomal internal transcribed spacer(ITS)regions and non-coding chloroplast regions(psbA-trnH,trnL-F).The two datasets support the conclusion that Osmanthus is polyphyletic.with some species of the subtribe Oleinae nested within Osmanthus.Osmanthus didymopetalus P S.Green is nested within the clade formed by species of section Osmanthus in two trees.Osmanthus attenuatus P.S.Green.O.Funnanensis P.S.Green,and O gracilinervis R.L.Lu of traditional section Osmanthus are clearly divergent from other accessions,and do not form a monophyletic group with other Osmanthus accessions.Osmanthus marginatus Hemsl.is embedded in the clade formed by species of section Osmanthus in the ITS tree.In cpDNA trees all species of section Osmanthus are placed in the large clade and all species of section Leiolea formed a group.The taxonomic incongruence among trees for ITS and cpDNA indicate hybridization.as introgression may have occurred among some species of sections Osmanthus and Leiolea.Phylogeny of Osmanthus is discussed in light of molecular and morphological data,and a revised infrageneric classification with three sections(Leiolea,Siphosmanthu,and Osmanthus)is presented.The section Linocieroides is abandoned and united with section Osmanthus.     

堇菜属组间的系统发育与亲缘关系：基于trnL-trnF、psbA-trnH、rpL16、ITS序列,细胞学以及形态学证据

以鼠鞭草（Hybanthus enneaspermus）、鳞隔堇（Scyphellandra pierrei）、雷诺木（Rinorea benga-lensis）作为外类群,对堇菜属（Viola）20个类群的trnL-trnF序列,17个类群的psbA-trnH、rpL16序列以及1个类群的nrDNAITS序列进行了测定,并从GenBank下载相应的序列,运用最大简约法以及贝叶斯推论法进行系统分析,构建系统发育树。结果表明：堇菜亚属（subgen. Viola）不是一个单系类群,并明确了堇菜属部分组间类群的亲缘关系。本文还结合形态与细胞学证据对堇菜属进行性状演化的推测。结果表明：1）直立茎较匍匐茎、莲座状茎（叶基生）原始;2）托叶边缘长流苏状与托叶1/2～3/4合生分别是鸟嘴柱头堇菜组（sect. Trigonocarpae）和合生托叶组（sect. Adnatae）演化路线的重要性状标志;3）花柱样式从柱头无喙演化至柱头有喙,并由柱头简单演化至柱头复杂,再趋向于柱头简化。     

堇菜属组间的系统发育与亲缘关系：基于trnL-trnF、psbA trnH、rpL16、ITS序列，细胞学以及形态学证据

以鼠鞭草(Hybanthus enneaspermus)、鳞隔堇(Scyphellandra pierrei)、雷诺木(Rinorea bengalensis)作为外类群,对堇菜属(Viola)20个类群的trnL trnF序列,17个类群的psbA trnH、rpL16序列以及1个类群的nrDNA ITS序列进行了测定,并从GenBank下载相应的序列,运用最大简约法以及贝叶斯推论法进行系统分析,构建系统发育树。结果表明：堇菜亚属(subgen.Viola)不是一个单系类群,并明确了堇菜属部分组间类群的亲缘关系。本文还结合形态与细胞学证据对堇菜属进行性状演化的推测。结果表明：1）直立茎较匍匐茎、莲座状茎（叶基生）原始;2）托叶边缘长流苏状与托叶1/2~3/4合生分别是鸟嘴柱头堇菜组（sect.Trigonocarpae）和合生托叶组（sect.Adnatae）演化路线的重要性状标志;3）花柱样式从柱头无喙演化至柱头有喙,并由柱头简单演化至柱头复杂,再趋向于柱头简化。     

Lophodermium pini-mugonis sp. nov. on needles of Pinus mugo from the Alps based on morphological and molecular data

Lophodermium pini-mugonis, collected on needles of Pinus mugo from German Alps, is described as a species new to science. It is characterized by subcuticular ascomata with a wrinkled surface and a somewhat untidy outline, a complex structure of lip cells, and ellipsoidal conidia. An analysis of the internal transcribed spaces of rDNA showed that Lophodermium pini-mugonis is, sister to Lophodermium autumnale and distantly related to other Lophodermium species on pines. The hypothesis of cospeciation of Lophodermium species with members of the Pinaceae is discussed.     

基于DNA条形码的柳属植物系统发育研究

对黑龙江省柳属不同植物ITS2和psbA-trnH基因间隔区序列进行系统发育分析,探索柳属植物的遗传多样性和亲缘关系。提取柳属植物和柽柳样品基因组DNA,通过PCR扩增法,获得各样品ITS2和psbA-trnH序列并测序。通过对序列种内种间遗传距离及邻接法构建系统发育树进行分析。基于ITS2序列的DNA条形码鉴定方法能将五蕊柳、粉枝柳、筐柳、蒿柳与其他物种区分开,柳组物种仅可鉴定到组级别。在以psbA-trnH基因片段序列建立的系统发育树中,柳属各种之间的序列聚类较为混乱,并不能各自独立聚为一支。因此,ITS2序列在柳属植物分类鉴定上具有一定的优势,为柳属植物的开发利用提供参考依据。     

水霉菌的形态及ITS区分子鉴定

研究利用形态学和分子生物学相结合的方法, 对从患病黄颡鱼病灶处分离的水霉菌株(HSY)的分类地位进行了研究。结果显示, 该菌在18—23℃均能形成游动孢子囊, 但只在20℃才大量释放游动孢子; 在15℃培养约3 周出现大量的藏卵器, 多数顶生, 形态与Saprolegnia litoralis 和Saprolegnia ferax 的均非常相似。序列比对分析显示, HSY 菌株与S. litoralis、S. bulbosa、S. oliviae、S. longicaulis、S. ferax、S. mixta 和S.anomalies 的ITS 区(包括5.8S rDNA)序列相似性均高于99%。系统发育分析显示, 所选的真菌分为3 个群,HSY 落于第一个群, MP 树显示HSY 菌株与S. litoralis、S. bulbosa、S. oliviae、S. longicaulis、S. ferax 以及S. mixta 枝系均互相平行, 而NJ 树显示其与S. ferax 和S. mixta 更近。综合形态学、ITS 区序列及系统发育分析, 将HSY 菌株暂定为多子水霉(Saprolegnia ferax)。     

Species identification in the genus Saprolegnia (Oomycetes): Defining DNA-based molecular operational taxonomic units

The lack of a robust taxonomy in the genus Saprolegnia is leading to the presence of incorrectly named isolates in culture collections and of an increasing number of misassigned sequences in DNA databases. Accurate species delimitation is critical for most biological disciplines. A recently proposed approach to solve species delimitation (taxonomic diagnosis system) of difficult organisms is the definition of molecular operational taxonomic units (MOTUs). We have used 961 sequences of nrDNA ITS from culture collections (461 sequences) and GenBank (500 sequences), to perform phylogenetic and clustering optimization analyses. As result, we have identified 29 DNA-based MOTUs in agreement with phylogenetic studies. The resulting molecular clusters support the validity of 18 species of Saprolegnia and identify 11 potential new ones. We have also listed a number of incorrectly named isolates in culture collections, misassigned species names to GenBank sequences, and reference sequences for the species. We conclude that GenBank represents the main source of errors for identifying Saprolegnia species since it possesses sequences with misassigned names and also sequencing errors. The presented taxonomic diagnosis system might help setting the basis for a suitable identification of species in this economically important genus.     

Asterostroma species (Basidiomycota) from mangrove forests in Japan

A new homobasidiomycete, Asterostroma macrosporum, was found in mangrove forests of Iriomote Island, Japan. This species is morphologically characterized by having resupinate basidiomata, a monomitic (asterodimitic) hyphal system, simple septate generative hyphae, dextrinoid asterosetae, four sterigmate basidia and globose, tuberculate and amyloid basidiospores measuring 8.5–11 × 7.5–9 μm. It is similar to A. muscicola, but basidiospores in the latter are smaller (7–8 × 5.5–7 μm). Furthermore, phylogenetic analysis using internal transcribed spacer (ITS) region revealed that A. macrosporum is distinctly separated from A. muscicola. In Japan, A. muscicola is widely distributed in warm-temperate to subtropical regions, growing on a variety of broadleaved trees including mangroves, while A. macrosporum has been found only on mangroves.     

DNA条形码在中国金合欢属中的应用

根据形态特征难以准确地辨别金合欢属植物,DNA条形码技术提供了一种准确地鉴定物种的方法。本文利用条形码技术对中国金合欢属物种的序列(psbA trnH、matK、rbcL和ITS)及其不同组合进行比较,通过计算种内和种间变异进行barcoding gap分析,运用Wilcoxon秩和检验比较不同序列的变异性,构建系统树。结果表明：4个片段均存在barcoding gap,ITS序列种间变异率较psbA trnH、rbcL和matK序列有明显优势,单片段ITS正确鉴定率最高,ITS+rbcL片段联合条码的正确鉴定率最高,因此我们认为ITS片段或条形码组合ITS+rbcL是金合欢属的快速鉴别最理想的条码。     

中国柽柳属和水柏枝属的分子系统学研究

对中国柽柳科 3属 2 1种植物的核糖体DNA中的内转录间隔区 (ITS)序列及 5 8SrRNA基因的 3′端序列进行测定。结果表明 ,ITS - 1片段的长度范围在 2 5 4bp～ 2 6 9bp之间 ,ITS - 2片段的长度范围在 2 2 5bp～ 2 5 3bp之间。以Reaumuriasongarica作为功能性外类群 ,运用PAUP软件分析仅得到一个最简约树。简约树步长为 4 6 6步 ,一致性指数CI =0 85 84 ,保持性指数RI=0 86 2 2。系统发育分析表明 :秀丽水柏枝不应从水柏枝属中分出。另外 ,研究分析为目前分类上存有争议的白花柽柳、短毛柽柳及甘蒙柽柳的划分提供了分子生物学证据     

Cortinarius sect. Brunnei (Basidiomycota, Agaricales) in North Europe

The section Brunnei was extensively studied based on material from North Europe. To stabilise the nomenclature we studied the relevant types of taxa included in this section. Phylogenetic relationships and species limits were investigated using rDNA ITS sequences and the results were compared with the morphological data. We recognised 11 species: Cortinarius brunneus, C. clarobrunneus comb. nov., C. coleoptera, C. ectypus, C. gentilis, C. glandicolor (neotypified), C. pseudorubricosus, and four species described as new C. caesiobrunneus, C. albogaudis, C. carabus, and C. cicindela. They are described here and their taxonomy, ecology, distribution, and relationships are discussed. In addition, a key to species of the section Brunnei is provided. A total of 77 new sequences of 11 species are published including nine type sequences. Also the taxonomic assignments of sequences in the public databases belonging to the section Brunnei are revised.     

Cystotheca tjibodensis (Erysiphaceae,Ascomycota): rediscovery in Java after 90 years and first finding of anamorph

Cystotheca tjibodensis, formerly known as Lanomyces tjibodensis (Perisporiales), is a fungus found in 1920 in Indonesia. This species, hitherto only known from its type collection, is now regarded as belonging to the Erysiphales. However, molecular data are still required to verify the taxonomic affinity. In March 2011, we rediscovered this fungus at Cibodas Botanical Garden, Java. Detailed characterizations of this tropical powdery mildew are reported in this study based on morphological and molecular examinations. The anamorph of this species that was not found in the type specimen is also reported in this study.