熊超科的分子系统发生研究

有关熊超科的系统发生与演化存在很多争议。本工作测定了黑足鼬、南方海狮和非洲猎犬线粒体细胞色素ｂ、１２ＳｒＲＮＡ、ｔＲＮＡｔｈｒ和ｔＲＮＡＰｒｏ基因片段的ＤＮＡ序列。结合我们过去确定的熊超科其他动物的ＤＮＡ序列,我们采用简约法和距离法构建了较为系统的熊超科分子系统树。结果表明：浣熊科与鼬科、熊科与大熊猫科分别具有较近的共同祖先;鳍脚类不是一个独立的目,它们应归入熊超科;鳍脚类可能是单起源的,它们与浣熊科和鼬科的关系较与其他科更紧密;小熊猫科与其他科的关系并不密切。     

Sequence analysis of a soilborne wheat mosaic virus isolate from Italy shows that it is the same virus asEuropean wheat mosaic virus andSoilborne rye mosaic virus

The complete sequence of the two RNAs of a furovirus isolate from durum wheat in Italy was determined. Sequence comparisons and phylogenetic analysis were done to compare the Italian virus withSoilborne wheat mosaic virus (SBWMV) from the USA and with furovirus sequences recently published asEuropean wheat mosaic virus (EWMV), from wheat in France, andSoilborne rye mosaic virus (SBRMV), from rye and wheat in Germany. Over the entire genome, the Italian isolate RNA1 and RNA2 had respectively 97.5% and 98.6% nucleotide identity with EWMV, 95.5% and 85.8% with SBRMV-G and 70.6% and 64.5% with SBWMV. The Italian isolate was therefore clearly distinct from SBWMV The European isolates all appear to belong to the same virus and the nameSoilborne cereal mosaic virus may resolve earlier ambiguities.     

Sequence analysis of a soil-borne wheat mosaic virus isolate from Italy shows that it is the same virus as European wheat mosaic virus and Soil-borne rye mosaic virus

The complete sequence of the two RNAs of a furovirus isolate from durum wheat in Italy was determined. Sequence comparisons and phylogenetic analysis were done to compare the Italian virus with Soil-borne wheat mosaic virus (SBWMV) from the USA and with furovirus sequences recently published as European wheat mosaic virus (EWMV), from wheat in France, and Soil-borne rye mosaic virus (SBRMV), from rye and wheat in Germany. Over the entire genome, the Italian isolate RNA1 and RNA2 had respectively 97.5% and 98.6% nucleotide identity with EWMV, 95.5% and 85.8% with SBRMV-G and 70.6% and 64.5% with SBWMV. The Italian isolate was therefore clearly distinct from SBWMV. The European isolates all appear to belong to the same virus and the name Soil-borne cereal mosaic virus may resolve earlier ambiguities.     

Morphology and Molecular Phylogeny of Trimyema koreanum n. sp., a Ciliate from the Hypersaline Water of a Solar Saltern

ABSTRACT. A new ciliate, Trimyema koreanum n. sp., isolated from hypersaline water (salinity of 293‰) from a solar saltern in Korea, was investigated using live observation, protargol impregnation, and gene sequencing. Trimyema koreanum is about 30 × 13 μm in vivo, has usually 23 longitudinal ciliary rows forming two distinct ciliary girdles visible both in vivo and in protargol impregnation. A third indistinct ciliary girdle as well as a girdle of mucocysts is distinguishable only in impregnated cells. We suggest T. koreanum as a new species, differing from the most similar species, T. marinum, by the presence of two distinct ciliary girdles (T. marinum usually has six ciliary girdles clearly visible in living cells and three anterior spirals that encircle the cell completely). Although the number of known 18S rRNA sequences in the genus Trimyema was limited, the Trimyema group including T. koreanum forms a strong clade. The phylogenetic position confirms that the isolate belongs to the genus Trimyema and is different from previously sequenced species. Trimyema koreanum is able to consume both prokaryotes and small eukaryotes (specifically, the alga Dunaliella sp.).     

Molecular approaches to the study of evolution and phylogeny of the Nemertina

Molecular biological tools currently available to us are revolutionizing the way in which we can address questions in evolutionary biology. The purpose of this article is to provide an overview of molecular techniques and applications available to biologists who are interested in evolutionary studies but who have little acquaintance with molecular biology. In evolutionary biology, techniques designed to determine degree of nucleic acid similarity are in common use and will be dealt with first. Another approach, namely gene expression studies, has strong implications for evolutionary biology but generally requires substantial familiarity with molecular biological tools. Expression studies provide powerful tools for discerning processes of speciation, as in the selection of genetic variants, as well as discerning lineages, e.g., expression of specific homeobox genes during segment formation. For investigations where either nucleic acid identity or gene expression are the ultimate goal, detailed information, protocols and appropriate controls are beyond the scope of this work but, where possible, recent review articles are cited.     

A Molecular Study of Euglenoid Phylogeny using Small Subunit rDNA

The euglenoids are an ancient and extremely diverse lineage of eukaryotic flagellates with unclear relationships among taxa. Synapomorphies for the euglenoids include a surface pellicle and a closed mitosis with a series of separate sub-spindles. The taxonomy currently in use is inconsistent with the available data and needs revision. Most euglenoid phylogenies are largely intuitive reconstructions based on a limited number of morphological characters. Therefore, we have added molecular characters from the Small Subunit (SSU) rDNA to generate an overall phylogenetic framework for the euglenoids. SSU rDNA sequences from photosynthetic, osmotrophic, and phagotrophic euglenoids were aligned based on secondary structure. Phylogenetic analysis using the conserved areas of the sequence was performed using parsimony, maximum likelihood, and distance methods. Trees derived using different criteria are in agreement. The euglenoids form a distinct monophyletic clade with phagotrophic members diverging prior to the phototrophic and osmotrophic members. Among photosynthetic members, the biflagellate form diverged prior to the uniflagellate form. Additionally, the genus Euglena appears to be paraphyletic, with osmotrophic taxa, such as Astasia and Khawkinea, diverging independently within the clade containing the photosynthetic genus Euglena.     

Molecular, morphological, and experimental evidence support the synonymy of Perkinsus chesapeaki and Perkinsus andrewsi

Diverse analytical and experimental results confirm that two protistan parasites, Perkinsus chesapeaki and Perkinsus andrewsi, described separately as parasites of Mya arenaria and Macoma balthica clams sympatric in Chesapeake Bay, USA, represent a single species. Ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions, rRNA large subunit (LSU) gene, and actin gene sequences were obtained from clonal Perkinsus spp. cultured in vitro. Although multiple polymorphic sequences were found in DNA from clonal cultures at each locus, identical ITS region and actin gene sequences were found in the P. andrewsi holotype culture and in Perkinsus sp. clonal cultures from M. arenaria and Tagelus plebius. All sequences determined from cultures of P. chesapeaki and P. andrewsi at each locus grouped together in monophyletic clades with high support values in phylogenetic analyses. In vitro isolates of Perkinsus spp. from M. arenaria and M. balthica were reciprocally infective for each other's cognate host. Lesions and histozoic parasite cell morphologies were consistent with those described for the original host/parasite interactions. In vitro isolate cell cycles and cell types of both parasites were indistinguishable. In accordance with the International Code of Zoological Nomenclature rules of priority, P. andrewsi is declared a junior synonym of P. chesapeaki.     

Molecular Phylogeny of the Papilionoideae (Family Leguminosae): RbcL Gene Sequences versus Chemical Taxonomy

Total DNA was extracted from 67 species (30 genera) of the subfamily Papilionoideae (family Leguminosae). The rbcL gene was amplified by polymerase chain reaction (PCR) and sequenced directly. RbcL sequences were evaluated with character-state (maximum parsimony; PAUP) and distance methods (neighbour-joining; MEGA). Morphology-based classifications of tribes and subtribes are mostly congruent with rbcL phylogeny. Differences occur for members of the genus Sophora and for intratribal relationships within the Genista/Cytisus complex: Sophora appears in two clades; one clade with S. japonica at the base of the Papilionoideae and a second more advanced group (with S. davidii, S. jaubertii, and S.flavescens) which represents a sister clade of the Thermopsideae. The Cytisus complex includes the genera Cytisus, Chamaecytisus, Calicotome and Spartocytisus but not Cytisophyllum which appears as a distinct member of the Genista complex. Chamaespartium sagittale is very close to Genista supporting the view that it does not represent an independent genus but should be treated as Genista sagittalis. Close to Genista are Teline and Spartium, whereas Argyrolobium, Retama, Cytisophyllum, Ulex, Petteria, Adenocarpus, Chamaespartium tridentatum and Laburnum can be considered as “outliers” of the Genista-group sensu stricto. RbcL phylogeny is compared with profiles of alkaloids and other natural products. First results indicate that secondary metabolite profiles, if compared with morphology or rbcL sequences, are of limited value as a taxonomic marker.     

獐牙菜亚族植物的系统发育分析

獐牙菜亚族(subtribe Swertiinae)是龙胆科(Gentianaceae)中分类处理较困难的一个亚族。为探讨该亚族各属之间和属内的系统关系,选取了该亚族86种及变种,采用ML和BI方法对样本的叶绿体基因mat K和rbc L片段进行分析,构建了该亚族的系统发育树,用马尔科夫蒙特卡洛算法(MCMC)的分子序列贝叶斯分析推算了该亚族的关键演化时间点。结果显示:①龙胆亚族和獐牙菜亚族各自为单系,且互为姐妹类群;②獐牙菜属、假龙胆属、肋柱花属和喉毛花属均不是单系群,各属的种在系统发育树上互有交叉,特别是獐牙菜属的多个种分别聚到不同的支上,与其它属是并系关系;③獐牙菜亚族49个种在约4 Ma开始形成;④分子数据支持何廷农分类系统对于獐牙菜亚属和多枝亚属的属间划分,部分支持多枝亚属下多枝组和宽丝组的划分;⑤异型花属、獐牙菜属、假龙胆属、喉毛花和肋柱花属的属间分类以及獐牙菜属肉根亚属密花组的系统位置仍需进一步讨论。     

猪伪狂犬病毒蛋白激酶基因的序列测定与分析

对伪狂犬病毒湖北株（ＰＲＶ ＨＢ株）蛋白激酶（ＰＫ）基因进行了克隆和序列测定。分析比较了该序列与ＰＲＶＮＩＡ－３株、Ｋａ株以及ＨＳＶ－１、ＶＺＶ ＰＫ基因的同源性。结果显示,在测定全长１３１２ｂｐ的ＤＮＡ序列中,包括着一个１００２核苷酸的开放读框,可编码３３４个氨基酸组成的多肽。ＰＲＶ－ＨＢ株ＰＫ与ＰＲＶ－ＮＩＡ３、ＰＲＶ－Ｋａ、ＨＳＶ－１、ＶＺＶ ＰＫ基因比较,核苷酸的同源性分别为９８．７％、９     

Phylogeny and species delimitation of the C-genome diploid species in Oryza

The diploid Oryza species with C-genome type possesses abundant genes useful for rice improvement and provides parental donors of many tetraploid species with the C-genome (BBCC,CCDD).Despite extensive studies,the phylogenetic relationship among the C-genome species and the taxonomic status of some taxa remain controversial.In this study,we reconstructed the phylogeny of three diploid species with C-genome (Oryza officinalis,O.rhizomatis,and O.eichingeri) based on sequences of 68 nuclear single-copy genes.We obtained a fully resolved phylogenetic tree,clearly indicating the sister relationship of O.officinalis and O.rhizomatis,with O.eichingeri being the more divergent lineage.Incongruent phylogenies of the C-genome species found in previous studies might result from lineage sorting,introgression/hybridization and limited number of genetic markers used.We further applied a recently developed Bayesian species delimitation method to investigate the species status of the Sri Lankan and African O.eichingeri.Analyses of two datasets (68 genes with a single sample,and 10 genes with multiple samples) support the distinct species status of the Sri Lankan and African O.eichingeri.In addition,we evaluated the impact of the number of sampled individuals and loci on species delimitation.Our simulation suggests that sampling multiple individuals is critically important for species delimitation,particularly for closely related species.     

Phylogeny and Molecular Evolution of the Green Algae

The green lineage (Viridiplantae) comprises the green algae and their descendants the land plants, and is one of the major groups of oxygenic photosynthetic eukaryotes. Current hypotheses posit the early divergence of two discrete clades from an ancestral green flagellate. One clade, the Chlorophyta, comprises the early diverging prasinophytes, which gave rise to the core chlorophytes. The other clade, the Streptophyta, includes the charophyte green algae from which the land plants evolved. Multi-marker and genome scale phylogenetic studies have greatly improved our understanding of broad-scale relationships of the green lineage, yet many questions persist, including the branching orders of the prasinophyte lineages, the relationships among core chlorophyte clades (Chlorodendrophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae), and the relationships among the streptophytes. Current phylogenetic hypotheses provide an evolutionary framework for molecular evolutionary studies and comparative genomics. This review summarizes our current understanding of organelle genome evolution in the green algae, genomic insights into the ecology of oceanic picoplanktonic prasinophytes, molecular mechanisms underlying the evolution of complexity in volvocine green algae, and the evolution of genetic codes and the translational apparatus in green seaweeds. Finally, we discuss molecular evolution in the streptophyte lineage, emphasizing the genetic facilitation of land plant origins.     

Molecular typing of meningococci: recommendations for target choice and nomenclature

The diversity and dynamics of Neisseria meningitidis populations generate a requirement for high resolution, comprehensive, and portable typing schemes for meningococcal disease surveillance. Molecular approaches, specifically DNA amplification and sequencing, are the methods of choice for various reasons, including: their generic nature and portability, comprehensive coverage, and ready implementation to culture negative clinical specimens. The following target genes are recommended: (1) the variable regions of the antigen-encoding genes porA and fetA and, if additional resolution is required, the porB gene for rapid investigation of disease outbreaks and investigating the distribution of antigenic variants; (2) the seven multilocus sequence typing loci-these data are essential for the most effective national, and international management of meningococcal disease, as well as being invaluable in studies of meningococcal population biology and evolution. These targets have been employed extensively in reference laboratories throughout the world and validated protocols have been published. It is further recommended that a modified nomenclature be adopted of the form: serogroup: PorA type: FetA type: sequence type (clonal complex), thus: B: P1.19,15: F5-1: ST-33 (cc32).     

Molecular Comparison of Dengue Type 1 Mochizuki Strain Virus and Other Selected Viruses Concerning Nucleotide and Amino Acid Sequences of Genomic RNA: A Consideration of Viral Epidemiology and Variation

Dengue-1 (D1) Mochizuki strain was examined for its nucleotide and amino acid sequences of genomic RNA and the data obtained were compared with those of other selected virus strains reported previously. Genomic regions corresponding to C, preM and M proteins were the major subjects of study. Parts of E protein were additionally examined. Among the D1 viruses investigated, the Mochizuki virus which was isolated in 1943 in Japan was shown to be close to Philippine 836-1 strain isolated in 1984 and Nauru Island strain isolated in 1974 at the respective places, in contrast with Thai AHF 82-80 strain isolated in 1980 and Caribbean CV1636/77 strain isolated in 1977. At the same time, a difference was noted between the Mochizuki and Philippine/Nauru strains at the cleavage site of preM/M junction: Mochizuki possessed RRGKR/S sequence whereas the Philippine/Nauru had RRDKR/S. The glycosylation site in preM and hydrophobic regions at the carboxyl termini of M and E were well conserved. Significances of the data are discussed in connection with viral epidemiology and variation.     

The nucleotide sequence of the gene encoding the K99 subunit of enterotoxigenic Escherichia coli

Abstract The nucleotide sequence of the gene encoding the K99 fimbrial subunit of enterotoxigenic Escherichia coli was determined. It appeared that the subunit is composed of 159 amino acid residues preceded by a N-terminal signal sequence of 22 amino acid residues. The secondary structure of the mature K99 polypeptide and the location of potential antigenic determinants were predicted. A comparison was made between the amino acid sequence of the K99 subunit and the subunits of other fimbrial adhesins.     

麝属分子系统进化地位的再分析

对麝Moschus spp.的分子系统进化地位进行了再研究.结果 表明,不同的基因及序列长度、分析中不同的物种数目、不同的分析方法对研究结果产生明显影响.在用线粒体Cyt b、16S rRNA基因及二者的连接序列分别构建的NJ、MP树中,都支持麝与鹿有更近的亲缘关系.在使用γ干扰素核基因的编码序列构建的NJ树中,显示麝与鹿也有较近的亲缘关系;而MP树则暗示麝与牛科有更近的亲缘关系.当选用包括林麝在内的18个物种,使用线粒体基因组重链上12个蛋白编码基因的核苷酸串连序列构建系统发生树时,在NJ、MP、ML和BI树中都支持麝与鹿有更近的亲缘关系,与选用23个物种得到的支持麝为鹿科/牛科二者共同姐妹群的结果存在明显差异.这可能是因为麝科与鹿科和牛科的亲缘关系较近,分歧时间较短,其分子片段所累积的进化信息较少,而且不同的分子片段进化速率不一致等造成的.因此,要彻底解决麝在偶蹄目中的进化地位必须要找到更适合的分子标记.