大银鱼和小齿日本银鱼线粒体细胞色素b 和16S rRNA基因部分序列分析

　对大银鱼和小齿日本银鱼的线粒体细胞色素b 和16S rRNA 基因片段进行了扩增和序列测定,分析比较了2 种 间的序列差异。大银鱼2 个个体间细胞色素b 基因序列无差异,小齿日本银鱼3 个个体的序列出现了2 种单倍型;大银鱼 同小齿日本银鱼细胞色素b 序列(单倍型SB21) 之间存在86 个碱基差异(差异率21 %) ,变异较大。大银鱼、小齿日本银鱼 的16S rRNA 基因片段种内个体间无序列差异,两种间存在21 个碱基的差异(差异率5 %) ,有1 个碱基的插入/ 缺失。由 此可见,2 种银鱼间线粒体细胞色素b 基因的进化速率较快,约为16S rRNA 基因片段的4 倍。根据细胞色素b 序列数据, 推算出2 种银鱼大概在中新世晚期发生分化。

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals, collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058 bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML. and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species. (C) 2003 Elsevier Science (USA). All rights reserved.

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Phylogenetic relationships of the Chinese brown frogs (Genus rana) inferred from partial mitochondrial 12S and 16S rRNA gene sequences

Based on partial sequences of the 12S and 16S ribosomal RNA genes, we estimated phylogenetic relationships among brown frogs of the Rana temporaria group from China. From the phylogenetic trees obtained, we propose to include Rana zhengi in the brown frog

氨酰-tRNA合成酶的进化差异

下载PDF阅读器大量研究显示,细菌与真核生物中的许多氨酰-tRNA合成酶(aaRS)在一些细菌与真核生物中的基因进化机制与模式、氨酰化途径和结构与功能的进化模式等方面往往有着明显的差异.通过对这些差异的深入研究,对于理解蛋白质的结构与功能的进化将是非常有帮助的.虽然造成这些差异的机制目前仍不清楚,但是,所有的这些差异似乎提示,在细菌与真核生物的一些基本生命活动过程中的某些方面,可能还存在着目前尚未被人们所认识到的较大差异.

氨酰-tRNA合成酶专一性识别的进化

氨酰-tRNA合成酶(AARS)是一类在蛋白质合成过程中起着重要作用的酶,它通过与tRNA及其相应氨基酸的专一性识别作用,使得基因序列能够被精确地翻译成蛋白质序列。然而,氨酰-tRNA合成酶的这种识别作用既有专一性,也具有“兼容性”。氨酰-tRNA合成酶的这种双重性质不仅与其结构的进化有关,而且还与其所处的各类生物的不同进化阶段有关。AARS似乎经历了一个由“模糊专一性”(多重专一性)到“精确专一性”(单一专一性)的演变历程。

苯丙氨酰tRNA合成酶的进化与结构域丢失

基因的复制、融合以及基因的水平转移是许多蛋白质包括氨酚t RNA合成酶(aminoacyl-tRNA synthetase , AARS)进化过程中的常见事件。然而作者研究的结果显示，苯丙氨酚 t RNA合成酶( phenylalanyl-tRNA synthetase , PheRS)的进化主要表现为 一些结构域的丢失;并且这种结构域的丢失不影响Phe RS的功能或活性。通常在生物从细菌到真核生物的进化过程中，其基因组的大小和基因的数目都有所增加，然而有趣的是，真核生物中Phe RS的结构域类型和数目都明显少于细菌的Phe RS oPhe RS通过结构域的丢失而进化的现象，似乎与某些AARS功能由多重专一性向单一专一性的演化有着“异曲同工”之妙。

Evolution of structures and specific recognitions in aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AARS) are very important during the protein biosynthesis, which can make the gene sequence be accurately translated into the protein sequence by the specific recognition between AARS and tRNA/amino acids. However, the recog

Evolution of phenylalanyl-tRNA synthetase by domain losing

The gene duplication, fusion and horizontal transfer are the frequent events during evolution of many proteins, including the aminoacyl-tRNA synthetases (AARSs). However, in this work, it was shown that the main event during evolution of phenylalanyl-tRNA synthetase (PheRS) is a domain loss, and the function/activity of PheRS is not affected by domain losing. Generally, the size of genome and number of genes are increased during evolution from bacteria to eukaryote, but the interesting thing is that the type and number of PheRS domains in eukaryotae are obviously less than those in bacteria. The evolution of PheRS by domain losing seems to be related to the functional evolution of some AARSs from the multiple specificities to the single specificity.

Evolution of different oligorneric glycyl-tRNA synthetases

There are two oligomeric types of glycyl-tRNA synthetases (GlyRSs) in genome, the alpha(2)beta(2) tetramer and alpha(2) dimer. Here, we showed that the anticodon-binding domains (ABDs) of dimeric and tetrameric GlyRSs are non-homologous, although their catalytic central domains (CCDs) are homologous. The dimeric GlyRS_ABD is fused to the C-terminal of CCD in alpha-subunit, but the tetrameric GlyRS_ABD is to the C-terminal in beta-subunit during evolution. Generally, one species only contains one oligomeric type of GlyRS, but the both oligomeric GlyRSs with the multiple homologous domains can be observed in Magnetospirillum magnetotacticum genome, nevertheless, these homologous domains are probably from different genomes. (C) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Molecular dynamics simulation on the complex of the tobramycin and 16S rRNA a site

A 3. 6 ns molecular dynamics simulation was carried out on the complex system of tobramycin and 16S rRNA in order to understand the speciality recognition mechanism between tobramycin and 16S rRNA at the molecular level. The results demonstrate that two l

Phylogeny of fireflies (Coleoptera : Lampyridae) inferred from mitochondrial 16S ribosomal DNA, with references to morphological and ethological traits

We sequenced partial mitochondrial 16S ribosomal DNA (16S rDNA) of 18 firefly species from Southwest of China. Combined with homologous sequences previously reported, phylogenetic trees including Japanese, Korean and Chinese species were reconstructed by

Non-monophyly of Rhacophorus rhodopus,Theloderma and Philautus albopunctatus Inferred from Mitochondrial 16S rRNA Gene Sequences

测定了4个种(红蹼树蛙、黑蹼树蛙、白斑小树蛙和红吸盘小树蛙)共11个种群的16S rRNA基因片段.双斑树蛙、马来棱皮树蛙、越南棱皮树蛙以及日本溪树蛙的同源序列通过GenBank检索获得.去除所有插入、缺失及模糊位点后,比对序列长度为500 bp,其中变异位点115个,简约信息位点92个.以日本溪树蛙为外群,运用Bayesian法、MP法和ML法构建了系统发育树.结果表明红蹼树蛙和白斑小树蛙在种级水平上均不是单系.红蹼树蛙海南种群与双斑树蛙亲缘关系更近,并且来自云南不同地理种群的红蹼树蛙可以分为两大支系;越南棱皮树蛙与红吸盘小树蛙聚为一支,马来棱皮树蛙嵌套在白斑小树蛙不同地理种群中.进而认为白斑小树蛙是马来棱皮树蛙的同物异名,建议将红吸盘小树蛙并入棱皮树蛙属.

Phylogenetic and systematic study of the genus Bombina (Amphibia : Anura : Bombinatoridae): New insights from molecular data

Phylogenetic relationships and systematics of the eight currently recognized species of the genus Bombina were investigated using four mitochondrial gene fragments (16S rRNA, 12S rRNA, ND4-tRNA(LEU), and cytochrome b). We prepared two different concatenat