The identification of vahlkampfiid amoebae by ITS sequencing

We have determined the internal transcribed spacer (ITS) sequences (including the 5.8S ribosomal DNA) of 30 strains of 14 species belonging to eight vahlkampfiid genera. Each previously described species has a specific ITS sequence, except for Tetramitus aberdonicus, Tetramitus thorntoni, and Tetramitus jugosus, which have identical ITS sequences. The latter three may therefore constitute a single species despite their apparent phenotypic differences. The ITS sequence appears to be conserved within a species. The species Willaertia magna appears to be ubiquitous. The 5.8S rDNA sequences of Singhamoeba horticola and Learamoeba waccamwensis indicate that they do not represent different genera, but both belong to the genus Tetramitus. The ITS sequences of 16 undescribed vahlkampfiid isolates were determined. Based on these sequences, seven isolates were identified as belonging to described species, while nine probably represent seven new species. Five of these presumed new species belong to the genus Tetramitus, and one each to the genera Vahlkampfia and Paravahlkampfia.     

基于ITS和matK基因对牡丹组序列分析及其亲缘关系的研究

以芍药属牡丹组全部9个野生种、5个紫斑牡丹栽培品种及3个中原牡丹品种为试材,进行核糖体内转录间隔区（ITS）和叶绿体成熟酶K （matK）基因片段测序分析,探讨ITS和matK序列为牡丹组所有野生种种间关系提供分子证据。从GeneBank中选取了1个牡丹及3个外类群芍药、川赤芍和草芍药的ITS及matK序列。对试验样品进行DNA提取、PCR扩增并双向测序得到44条序列,人工校正后将所得44条序列进行比对;计算碱基组成频率、变异位点、简约信息位点数、转换/颠换比率、种内及种间遗传距离,以邻接法进行系统发育分析。结果表明,牡丹组所有个体ITS序列长度在750~800 bp,含有86个多态位点,74个简约信息位点,转换/颠换比率（R）为1.2;而matK序列含有20个简约信息位点,转换/颠换比率（R）为1.7。ITS序列分析将牡丹组野生种分为两大枝,稷山牡丹、紫斑牡丹、卵叶牡丹和杨山牡丹聚为一枝,狭叶牡丹、滇牡丹、黄牡丹和大花黄牡丹聚为另一枝,这两枝分别与革质花盘亚组和肉质花盘亚组相对应,而四川牡丹位于革质花盘亚组最底端,支持前人研究将四川牡丹归为革质花盘亚组。matK序列分析的牡丹组野生种间遗传距离结果不理想,未能清晰的表明野生种之间的亲缘关系。由此说明,ITS序列更适合牡丹组野生种间亲缘关系的研究分析。     

Identifying Pseudo-nitzschia species in natural samples using genus-specific PCR primers and clone libraries

The diatom genus Pseudo-nitzschia contains a number of toxic and non-toxic species that are difficult to distinguish using light microscopy (LM) and at times even with electron microscopy (EM). In order to investigate the actual diversity and seasonal occurrence of Pseudo-nitzschia species, we developed genus-specific ribosomal DNA LSU primers to be used in PCR reactions with environmental DNA samples. Using this approach, we constructed clone libraries from samples collected in the Gulf of Naples (Mediterranean Sea) on six dates between April and October 2004 and compared molecular results with those obtained from counts using LM on the same dates. Thirteen distinct genotypes could be distinguished by their LSU sequence, against five species discriminated using the light microscope. Despite the limited number of samples, 10 out of 14 LSU genotypes known in the area were recovered. In addition, three new genotypes were retrieved, two of which were from within the P. galaxiae clade and one possibly corresponding to an undescribed P. delicatissima-like morph. Molecular results matched LM findings in the case of P. multistriata, whereas they provided a much higher resolution for morphs such as P. delicatissima- and P. pseudodelicatissima-like, which include several pseudo-cryptic species. Overall, the direct amplification with the primers developed proved to be an effective and useful tool to assess Pseudo-nitzschia diversity in the natural environment.     

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, and Pgk1) and one chloroplast region (trnL-F)

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.     

基于DNA条形码技术对浙江省外来入侵福寿螺进行分子鉴定

外来入侵福寿螺对我国农业生产和水生生态系统平衡等造成严重危害。2010年, 种类鉴定研究首次揭示我国外来入侵福寿螺包括Pomacea canaliculata和P. maculata两个种, 而浙江省仅见P. canaliculata一种报道。P. canaliculata和P. maculata种间形态近似, 且受环境、食物源等因素影响, 同种内外壳形态特征多样, 因而基于形态特征进行种类的准确鉴定极为困难。本研究在采集浙江省7个区县的福寿螺样本的基础上, 利用DNA条形码技术扩增了101个不同个体的COI序列, 并从BOLD数据库下载了“P. canaliculata种团”的5个近缘种的55条COI序列用于分析, 其中包括P. lineata, P. dolioides和P. paludosa所有已发表序列, 以及P. canaliculata和P. maculata的南美洲样品的序列等。序列相似度比对、DNA条形码间隙和系统发育树等分析表明, COI序列可以实现近缘福寿螺的有效鉴别。待测的浙江省福寿螺样品中, 杭州江干区检测到P. canaliculata和P. maculata两种, 而舟山普陀区、绍兴上虞区和新昌县、温州瓯海区及杭州西湖区仅检测到P. canaliculata, 表明P. canaliculata在浙江省具有更广的分布范围。P. canaliculata和P. maculata分别形成4种和2种单倍型, 各区县样点分别包含1-3种单倍型, 浙江省各发生地呈现较低的遗传多样性。依据系统发育关系推测, 浙江省分布的P. canaliculata和P. maculata分别可能来源于阿根廷和巴西。     

Cartographie de restriction comparée de la séquence d''ADN hautement répétée coupée par Bam HI chez Papio papio et P. cynocephalus

Highly repeated DNA sequences from two baboon species (Papio papio and P. cynocephalus) have been compared using restriction endonucleases. The two species share a 343 base pairs tandemly repeated DNA, that is cut once by Bam HI. Papio cynocephalus differs from P. papio by loss of an EcoRI star site in the repeated sequence.     

Breeding systems and phylogeny in Poa,with special attention to Northeast Asia: The problem of Poa shumushuensis and sect. Nivicolae (Poaceae)

Poa sect. Poa subsect. Nivicolae (Prob.) Tzvelev was circumscribed to include four species of the Soviet Union: Poa shumushuensis, Poa caucasica, Poa irkutica, and Poa veresczaginii. Bayesian phylogenetic analyses of plastid and nuclear‐ribosomal DNA revealed that it is polyphyletic, none of these species are closely related. Poa shumushuensis, type of sect. Nivicolae, or its ancestor, likely displayed the nrDNA genotype characteristic of the higher polyploid P. sect. Malacanthae. Genotype codes are designated for each species: Hx, C c, Php, and Shp. Poa sect. Nivicolae s.s. is restricted to P. shumushuensis; P. sect. Irkuticae is restricted to P. irkutica; P. caucasica is moved to P. subg. & sect. Caucasicae nov.; and P. sect. Dschungaricae is resurrected for P. veresczaginii and two other species. Although diclinous breeding systems are known in many western hemisphere species of Poa, dicliny is infrequent and little studied in Asian Poa. Poa shumushuensis is judged to be either sequentially gynomonoecious or gynodioecious. A ratio of 2 perfect‐, to 2 mixed‐, to 1 pistillate‐flowered inflorescences from different plants in P. shumushuensis is suggestive of a recessive allele for stamen suppression, and this is associated with subtle sexual‐dimorphism. Poa irkutica is diclinous with a breeding system between simple gynomonoecy and sequential gynomonoecy; P. caucasica is perfectly flowered; and P. veresczaginii has infrequent abortive anthers, indicative of limited dicliny, or sterility for other reasons possibly related to its reticulate origin. In total, 23 Asian species are here reported to be diclinous and their breeding systems are characterized. A lectotype is designated for P. fauriei.     

Molecular characterization and mitochondrial sequence variation in two sympatric species of Proechimys (Rodentia: Echimyidae) in French Guiana

Variations in mitochondrial DNA characters were used to characterize two morphologically similar and sympatric species of Neotropical terrestrial rodents of the genus Proechimys (Mammalia: Echimyidae). We sequenced both cytochrome b (1140 pb) and part of the control region (445 pb) from four individuals of P. cuvieri and five of P. cayennensis from French Guiana, which allowed us to depict intra- and inter-specific patterns of variation. The phylogenetic relationships between the nine sequences evidence the monophyly of each species, and illustrate that more polymorphism might exist within P. cuvieri than within P. cayennensis. By developing species-specific primers to amplify a fragment of the cytochrome b gene, we were able to identify 50 individuals of Proechimys spp. caught in two localities of French Guiana. In both sites of primary rainforests, we showed that the two species live in syntopy, and this observation emphasizes the need to document ecological differences which should exist in order to diminish inter-specific competition.     

长柄山蚂蝗属三个种的核型分析及山蚂蝗属两个种的染色体数

长柄山蚂蝗属Podocarpium(Benth.)Yang et Huang属蝶形花科,间断分布于东亚和中北美洲,广布种分布到非洲和大洋洲。北美有4种,亚洲约有14种.我国约有该属植物11种,以西南和长江以南地区分布种类最多。国外已有人做过本属一半以上的种的染色体记数和核型。本文对本属的三个种.长柄山蚂蝗P.podocarpum(DC.)Yang et Huang,大苞长柄山蚂蝗P.williamsii(Pamp.)Yang et Huang和云南长柄山吗蝗P.du-clouxii(Pamp.)Yang et Huang进行了染色体的记数和核型描述,其中后两个种的工作属于首次。此外,本文还首次报道了山蚂蝗属两个种:Des-modium caudatum(Thunb.)DC.和D.yunnanense Franch.的染色体数目。     

基于叶绿体DNA atpB-rbcL片段的典型樱亚属部分种的亲缘关系及分类地位探讨

蔷薇科典型樱亚属植物（Subg.Cerasus Koehne）（樱花类）具有重要的观赏价值,深入研究其种间亲缘关系及分类地位,对于国产樱属植物系统发育与种质资源创新具有重要的理论指导意义。基于PCR扩增与测序技术研究了从云南、江西、福建采集的典型樱亚属3个种（含变种）的叶绿体DNA非编码区atpB-rbcL片段,结合GenBank数据库已经提交的其它4个种的同源序列,共获得7个种的30条序列矩阵,以此构建了单倍型中介网络图与系统发育树,分析和探讨了它们的亲缘关系与分类地位。（1）在atpB-rbcL序列矩阵中,774个有效位点中共发现15个多态性位点,占分析序列的1.94%,（A+T）含量为70.50%,存在明显的碱基偏好;（2）DNASP 5共检测到9个单倍型,物种间平均单倍型多样性（H_d=0.880 5±0.026）,平均核苷酸多态性（π=0.007 11±0.000 54）,除尾叶樱桃（Prunus dielsiana）外（Hap5~Hap7）,其余物种拥有各自独特的1个单倍型,具有较丰富的遗传多样性;（3）综合Network中介图与系统发育重建结果：推测磐安樱桃（P.pananensis）处于较原始的进化阶段,相比尾叶樱桃,与浙闽樱桃（P.schneideriana）亲缘关系较近;长柱尾叶樱桃（P.dielsiana var.longistyla）与尾叶樱桃互为姊妹支,并共同构成独立进化单元。综上,叶绿体atpB-rbcL片段在典型樱亚属下种间的适用效果较好,可以优先选为DNA条形码;分子证据结合形态学特征支持将长柱尾叶樱桃作为尾叶樱桃变种的处理意见,而磐安樱桃的分类地位则需要更多的证据。     

Revision of the genus Noculacia Mayer, 1903 (Crustacea: Amphipoda: Caprellidea) with the description of two new species

The genus Noculacia Mayer, 1903 is reviewed. Two new species, N. africana n. sp. and N. australiensis n. sp., are described based on material collected from southeast Africa and western-southern Australia, respectively. Noculacia bullata Mayer, 1903, the type species of the genus, is redescribed. Noculacia bogisa Mayer, 1903 is transferred to the genus Pseudoprotella Mayer, 1890 mainly on the basis of the presence of a well developed molar, the structure of pereopods 3 and 4, and the setal formula of the mandibular palp being 2-x-1. The genus Noculacia is presently composed of three species: N. africana n. sp., N. australiensis n. sp, and N. bullata Mayer, 1903. The genus Pseudoprotella is composed of P. bogisa (Mayer, 1903), P. inermis Chevreux, 1927, and P. phasma (Montagu, 1804).     

Evidence for conspecificity of Piper methysticum forst. f. and Piper wichmannii C. DC

Morphological, chemical, cytological and genetic evidence demonstrating the absence of taxonomic distinction between Piper methysticum and Piper wichmannii are reviewed. Piper methysticum is not a separate species, but rather a group of sterile cultivars selected from somatic mutants of P. wichmannii. As P. methysticum was described first (1786), it has priority and P. wichmannii (1910) is superfluous. A new subspecific classification is suggested that makes a distinction between the sterile cultivars (P. methysticum var. methysticum) and the wild populations (P. methysticum var. Wichmannii).     

A genetic diversity study of endangered Psiadia species endemic from Mauritius Island using PCR markers

The genus Psiadia Jacq. represents the most important indigenous genus, by the number of species present, in the Mascarene archipelago (Mauritius, Reunion, Rodrigues), and is a typical example of adaptive radiation in oceanic islands. The Mauritius species are used in traditional pharmacopoeia for their expectorant properties, and most of them are heavily threatened. Molecular genetic relationships between representatives of eight endangered endemic Psiadia species from Mauritius, conserved in Le Mondrain Reserve, and P. dentata (Cass.) DC, endemic from Reunion island, were studied. The absence of length variations of the 5s rDNA non-transcribed spacer demonstrated the recent common origin of all the species surveyed. RAPD analysis revealed a relatively high intra-specific variability in accordance with the outcrossing mode of reproduction of Psiadia species. Moreover, RAPD analysis showed the existence of four major phenetic groups: (A) P. arguta (Pers.) Voigt, P. dentata, (B) P. penninervia D. C., P. terebinthina A.J. Scott, P. lithospermifolia (Lam.) Cordem, (C) P. viscosa (Lam.) A.J. Scott, P. canescens A.J. Scott, P. cataractae A.J. Scott, and (D) P. pollicina A.J. Scott. These groups were consistent with the chemical composition of the essential oils of the species as well as with their floral characteristics, based on literature. A molecular germplasm database for Psiadia species was established, which will allow further characterisation of new samples being introduced in Le Mondrain Reserve for conservation purpose.     

Sporobolomyces magnisporus sp. nov., a new yeast species in the Erythrobasidium cluster isolated from plants in Taiwan

Two strains of yeasts that contain Q-10 as the major ubiquinone, lack cellular xylose and produce large bilaterally symmetrical ballistoconidia were isolated from plants collected in a protected subtropical rain forest in Taiwan and were found to represent a new species. The taxonomic properties of this species coincide with the genus Sporobolomyces, so it is described as Sporobolomyces magnisporus sp. nov. In phylogenetic trees based on the nucleotide sequences of 18S ribosomal DNA and D1/D2 domain of 26S ribosomal DNA, this species is located in the Erythrobasidium cluster.     

中国冬青卫矛叶斑上的假尾孢菌

卫矛科Celastraceae植物上已报道尾孢类真菌10种,其中包括假尾孢属Pseudocercospora真菌7种。在对中国尾孢类真菌的调查研究中,采集到寄生在冬青卫矛Euonymus japonicus上的3种假尾孢菌,其中2个为新种,即冬青卫矛假尾孢Pseudocercospora euonymi-japonici和北京假尾孢P. beijingensis。本文对这2个新种和Pseudocercospora cf. destructiva提供了形态描述、图及与近似种区别的讨论。采用ITS、tef1-α、act和rpb2 4个片段的序列构建了系统发育树。     

Microbial colonization in the seagrass Posidonia spp. roots

The pattern of colonization by microorganisms on root surfaces from three species of seagrass belonging to the genus Posidonia was assessed. Microbial abundance on roots was measured by two electronic microscope techniques. Trends in microbial colonization between species and root order were defined. In addition, eutrophication status of the sampling sites and physiological status of Posidonia oceanica (L.) Delile roots have been taken into account. Our results show high microbial abundance in the Mediterranean species P. oceanica, in comparison with the low rates of colonization found in the Australian species P. australis Hook f. and P. sinuosa Cambridge et Kuo. Microbial density tended to decrease as root order increased, and living roots always showed higher microbial abundance than dead ones. Colonization of P. oceanica roots at the three sites with different environmental status follows different trends according to root order. It is suggested that root age influences the rate of microbial colonization of seagrass roots and that colonization of root surface by microorganisms is associated with organic exudates from the roots rather than with decaying root tissues.