拟迷误裂孔苔虫18S rDNA的序列测定及系统学分析

对我国沿海常见的一种污损苔藓动物--拟迷误裂孔苔虫的18S rRNA基因进行了PCR扩增、全序列测定及分析.同时通过获取已有的苔藓动物和其它触手冠动物的18S rDNA序列资料,经CLUSTAL软件对位排列后,用MEGA分子进化遗传分析软件构建了分子系统树, 并结合形态学资料探讨了它们的系统发生关系.     

红豆杉科及相关类群叶绿体rbcL基因与trnL-trnF间隔区序列的分支分析

运用对PCR产物克隆后测序和对PCR产物直接测序的方法对红豆杉科，三尖杉科和罗汉松科16种植物的叶绿体rbcL基因和trnL-trnF基因间隔区序列进行了测定，选用PAUP软件分别对rbcL基因，trnL-trnF间隔区和rbcL基因－trnL-trnF间隔区联合数据矩阵进行分支分析，结果：（1）穗花杉属以置于红豆杉科内为宜，将穗花杉属独立成科的意见未得到支持；（2）三尖杉属内篦子三尖杉地位特殊，赞同成立篦子三尖杉组；（3）罗汉松科属单系群，竹柏类应归属罗汉松，不同意将其从该科中分离出来成立新科竹柏科；（4）不支持红豆杉科独立成目，其单生单轴球果可能是由复合双轴球果减化而来。     

The eukaryotic Pso2p/Snm1p family revisited: in silico analyses of Pso2p A, B and Plasmodium groups

The eukaryotic family of Pso2/Snm1 exo/endonuclease proteins has important functions in repair of DNA damages induced by chemical interstrand cross-linking agents and ionizing radiation. These exo/endonucleases are also necessary for V(D)J recombination and genomic caretaking. However, despite the growing biochemical data about this family, little is known about the number of orthologous/paralogous Pso2p/Snm1p sequences in eukaryotes and how they are phylogenetically organized. In this work we have characterized new Pso2p/Snm1p sequences from the finished and unfinished eukaryotic genomes and performed an in-depth phylogenetic analysis. The results indicate that four phylogenetically related groups compose the Pso2p/Snm1p family: (i) the Artemis/Artemis-like group, (ii) the Pso2p A group, (iii) the Pso2p B group and (iv) the Pso2p Plasmodium group. Using the available biochemical and genomic information about Pso2p/Snm1p family, we concentrate our research in the study of Pso2p A, B and Plasmodium groups. The phylogenetic results showed that A and B groups can be organized in specific subgroups with different functions in DNA metabolism. Moreover, we subjected selected Pso2p A, B and Plasmodium proteins to hydrophobic cluster analysis (HCA) in order to map and to compare conserved regions within these sequences. Four conserved regions could be detected by HCA, which are distributed along the metallo-β-lactamase and β-CASP motifs. Interestingly, both Pso2p A and B proteins are structurally similar, while Pso2p Plasmodium proteins have a unique domain organization. The possible functions of A, B and Plasmodium groups are discussed.     

Phylogeny of SARS-CoV as inferred from complete genome comparison

SARS-CoV, as the pathogeny of severe acute respi-ratory syndrome (SARS), seems to be the first coronavirus that is lethal to humans. Coronavirus (family Coronaviri-dae, genus Coronavirus) is an enveloped, single-stranded plus sense RNA virus whose genome has approximately 30 kb size. Whereas coronaviruses may cause severe dis-ease in animals, coronaviruses human strains only cause mild diseases until SARS-CoV was discovered. To date, SARS-CoV genomes from 12 isolates have been comp…     

8种唇口目苔藓动物的分子系统发生--基于28S rRNA基因的证据

对我国沿海较为常见的8种唇口目苔藓动物的28S rRNA基因的部分序列进行了PCR扩增和序列测定。用排序软件进行序列比对后，以腕足动物为外组群，运用MEGA遗传分析软件以邻接法（NJ）和最大似然法（MP）构建了系统发生树。结果表明，有囊亚目的4种苔藓动物（刺轴拟缘孔苔虫、假缘孔苔虫、拟迷误裂孔苔虫、仿分胞苔虫）构成一个单系群；无囊亚目则是一个复系数，其中2种草苔虫（匍茎草苔虫、多室草苔虫）为单系发生，而大室膜孔苔虫和艳丽琥珀苔虫的系统发生位置尚需进一步探讨。     

Molecular phylogeny of the specialized schizothoracine fishes （Teleostei： Cyprinidae）,with their implications for the uplift of the Qinghai-Tibetan Plateau

Molecular phylogeny of three genera containing nine species and subspecies of the specialized schizothoracine fishes are investigated based on the complete nucleotide sequence of mitochondrial cytochrome b gene. Meantime relationships between the main cladogenetic events of the specialized schizothoracine fishes and the stepwise uplift of the Qinghai-Tibetan Plateau are also conducted using the molecular clock, which is calibrated by geological isolated events between the upper reaches of the Yellow River and the Qinghai Lake. Results indicated that the specialized schizothoracine fishes are not a monophyly. Five species and subspecies of Ptychobarbus form a monophyly. But three species of Gymnodiptychus do not form a monophyly. Gd.integrigymnatus is a sister taxon of the highly specialized schizothoracine fishes while Gdo pachycheilus has a close relation with Gd. dybowskii, and both of them are as a sister group of Diptychus maculatus. The specialized schizothoracines fishes might have originated during the Miocene(about 10 MaBP), and then the divergence of three genera happened during late Miocene (about 8 MaBP). Their main specialization occurred during the late Pliocene and Pleistocene (3.54-0.42 MaBP). The main cladogenetic events of the specialized schizothoracine fishes are mostly correlated with the geological tectonic events and intensive climate shift happened at 8, 3.6, 2.5 and 1.7 MaBP of the late Cenozoic.Molecular clock data do not support the hypothesis that the Qinghai-Tibetan Plateau uplifted to near present or even higher elevations during the Oligocene or Miocene, and neither in agreement with the view that the plateau uplifting reached only to an altitude of 2000 m during the late Pliocene(about 2.6 MaBP).     

Molecular biological research on Foraminifera

As one of the most important groups in micropaleontology, Foraminifera is traditionally described to have a membranous, agglutinated or carbonate shell according to its morphology, which resembles the marine granuloreticuloseans. However, recent molecular analyses on its ribosomal RNA gene have disclosed the existence of the naked, and also freshwater and terrestrial species. Foraminiferal SSU rDNA sequence suggests that this group is positioned at the base of the Eukaryotes phylogenetic trees, between Euglenoida and Diplomonadida. Existence of a large amount of genetic types in planktonic foraminifera suggests an underestimation of the biodiversity for the nearly 50 species in world oceans and their close relationship with the ocean environment, such as bio-geographic distribution and water currents. This provides a more reliable proxy for future paleoenvironmental study.     

Comparison between phylogeny of introns and exons in primate

Introns and exons of 7 genes (epsilon globin, gamma-1 globin, gamma-2 globin, delta globin, beta globin, Immunoglobulin andprepro-insulin) in primates have been separated out and used to infer phylogeny respectively. For each gene, results based on these two parts have been compared and showed that: (i) the topology of introns is almost consistent with that of exons in each gene, while the branch length of them varies, because of the dierent mutation rate; (ii) there is evidence that the substitution rate of exons would decrease inhominoids, but that of introns would not; (iii) divergence time of orangutan deduced from different genes based on exons is various, while that based on introns is much similar, and consistent with fossil records; (iv) there is a relationship between the G + C content and the substitution rate. When the substitution rate of introns is higher than exons in a gene, the G + C content of introns is less. The above results suggest that introns could provide useful evolutionary information among closety related species.     

基于随机聚类方法建模的序列分析

大数据下的系统发育估计是一个组合优化问题,在有限计算时间内,现有算法很难为大量序列数据的分析提供最优解.基于前人启发式算法,提出了一种系统发育树随机聚类建树方法,可在较短时间内为系统发育过程产生的大规模序列数据提供所有具有进化意义的解及最优解,以揭示发育过程中的序列进化关系.实验结果表明,该随机聚类方法是行之有效的,对生物计算及系统发育相关领域研究具有积极意义.