Structure,DNA sequence variation and phylogenetic implications of the mitochondrial control region in horseshoe bats

There have been few studies of the structural and evolutionary characteristics of the mitochondrial control region (CR) in rhinolophids, yet this could have important consequences for the interpretation of phylogenetic relationships within this group. Here we sequenced and analyzed the CR of 37 individuals from 12 Rhinolophus species, including 2 species from GenBank. The length of the CR ranged from 1335 to 1514 bp, and the base composition was very similar among species. The CR of horseshoe bats, like that of other mammals, could be subdivided into a central conserved domain (CD) and two flanking variable domains, extended termination associated sequences (ETAS), and conserved sequence blocks (CSB). Besides the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2 and CSB3) found in 3 domains, an ETAS2-like and a CSB1-like element were also detected in the ETAS and CSB domains, respectively, in all individuals. Notwithstanding a short tandem repeat (11 or 13 bp) between CSB1 and CSB2 in all specimens, the base composition, copy number and arrays are all variable. A long tandem repeat (79 bp) was only identified in the ETAS domain in one individual of R. pusillus. Phylogenetic reconstructions based on the CR sequences indicated that the molecular phylogenetic relationships among some Rhinolophus species were inconsistent with the results of phenetic analyses, but similar to phylogenetic constructions using cytochrome b. An unidentified species R. sp and 3 species from the philippinensis-group that were clearly morphologically different comprised a monophyletic group, which could have resulted from morphological independent evolution.     

Cloning and characterization of a microsatellite in the mitochondrial control region of the African side-necked turtle,Pelomedusa subrufa

The nucleotide sequence of the African side-necked turtle mitochondrial control region and its flanking tRNA genes was determined. This 73% A+T-rich region is 1194 bp long. Several conserved motifs involved in the regulation of the mitochondrial genome replication process, including one conserved sequence block (CSB1), and three termination-associated sequences were identified. The most remarkable feature found in this control region was the presence of six microsatellite-containing tandem repeats between the CSB1 motif and the tRNA^Phe gene. The potential usefulness of this microsatellite sequence for population-level studies is enhanced by its unique localization in the maternally inherited mitochondrial molecule.     

简单重复DNA序列在哺乳动物mtDNA D-loop区的分布及进化特征

简单重复序列广泛分布于从原核到真核生物的基因组中, 其形成的分子机理目前尚不明确。对NCBI数据库中已有256种哺乳动物线粒体DNA (mtDNA) D-loop区进行序列比对分析, 根据其所含有的简单重复序列类型分为3组, 分别是53种哺乳动物含有六核苷酸重复序列; 104种哺乳动物含有非六核苷酸重复序列(＞6 bp); 99种哺乳动物不含有任何重复序列。通过碱基序列分析比对, 发现六核苷酸重复序列集中分布在CSB1-CSB2间隔区, 而非六核苷酸重复可以分布于终止区(TAS)、中央保守区(Central domain)以及CSB(Central sequence block)区。通过比较含有重复序列与不含重复序列的功能保守区发现, 简单重复序列的存在并不明确影响D-loop区内的中央保守区以及CSB1、CSB2、CSB3三个功能保守区的碱基序列保守性。在此基础上, 利用N-J法构建了256种哺乳动物的进化树, 分析了哺乳动物D-Loop区内重复序列在进化过程中的可能变化规律, 发现简单重复序列随着物种的进化地位的升高而呈现消失趋势。     

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein‐coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light‐strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA‐Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination‐associated sequence, six conserved sequence blocks (CSB‐1, CSB‐2, CSB‐3, CSB‐D, CSB‐E, CSB‐F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.     

A repeat complex in the mitochondrial control region of Adélie penguins from Antarctica.

We have determined the nucleotide sequence of the entire mitochondrial control region (CR) of the Adélie penguin (Pygoscelis adeliae) from Antarctica. Like in most other birds, this CR region is flanked by the gene nad6 and transfer (t)RNA trnE(uuc) at the 5' end and the gene rns and trnF(gaa) at the 3' end. Sequence analysis shows that the Adelie penguin CR contains many elements in common with other CRs including the termination associated sequences (TAS), conserved F, E, D, and C boxes, the conserved sequence block (CSB)-1, as well as the putative light and heavy strand promoters sites (LSP-HSP). We report an extraordinarily long avian control region (1758 bp) which can be attributed to the presence, at the 3' peripheral domain, of five 81-bp repeat sequences, each containing a putative LSP-HSP, followed by 30 tetranucleotide microsatellite repeat sequences consisting of (dC-dA-dA-dA)30. The microsatellite and the 81-bp repeat reside in an area known to be transcribed in other species.     

DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys)

The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 bp in length. Our data were compatible with the proposal of three domains (extended terminal associated sequences [ETAS], central, conserved sequence blocks [CSB]) within the control region. The most conserved region in the control region was the central domain (12% of nucleotide positions variable), whereas in the ETAS and CSB domains, 22% and 40% of nucleotide positions were variable, respectively. Tandem repeats were encountered only in the ETAS domain of Clethrionomys rufocanus. This tandem repeat found in C. rufocanus was 24 bp in length and was located at the 5' end of the control region. Only two of the proposed CSB and ETAS elements appeared to be supported by our data; however, a "CSB1-like" element was also documented in the ETAS domain.     

南蝠线粒体DNA控制区结构及贵州7个种群遗传多样性的分析研究

采用PCR技术获得了贵州7个南蝠(Ia io)自然种群42个个体的线粒体DNA控制区全序列,长度为1256～1340 bp.对控制区结构进行分析,识别了其延伸的终止结合序列区(包括ETAS1和ETAS2元件)、中央保守区(包括F、E、D、C、B元件)和保守序列区(包括CSB1、CSB2和CSB3元件);同时,在延伸的终止结合序列区还发现了若干能形成发夹结构的主体序列TACAT—ATGTA.在7个自然种群42个个体中共定义了16个单倍型.遗传多样性分析表明:贵州南蝠种群具有较高的单倍型多样性(h=0.945)和中等的核苷酸多样性(π=0.012).基因流、AMOVA和系统进化树分析表明贵州这7个南蝠自然群体间没有发生遗传分化.     

白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼(Anabarilius grahami)DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列(930bp)。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列(CSB-F、CSB-D、CSB-1、CSB-2、CSB-3)。同时运用DNA分析软件对白鱼一个驯养种群(中国科学院昆明动物研究所珍稀鱼类繁育中心)及两个自然地理种群(江川县明星鱼洞、江川县牛摩村)进行了遗传多样性分析。结果显示:两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。     

白鱼线粒体DNA控制区结构和种群遗传多样性分析

用特异性引物对白鱼（Anabarilius grahami）DNA进行PCR扩增,获得了白鱼线粒体DNA控制区基因全序列（930 bp）。控制区T、C、A和G碱基组成为29.8%、22.5%、33.0%和14.7%。对照其他已报道的鱼类控制区结构,对白鱼控制区结构进行了分析,识别了其终止序列区、中央保守区和保守序列区,找到了终止相关的序列TAS以及保守序列（CSB-F、CSB-D、CSB-1、CSB-2、CSB-3）。同时运用DNA分析软件对白鱼一个驯养种群（中国科学院昆明动物研究所珍稀鱼类繁育中心）及两个自然地理种群（江川县明星鱼洞、江川县牛摩村）进行了遗传多样性分析。结果显示：两个自然种群存在较强基因交流,未出现遗传分化;人工驯养种群遗传多样性最高,种群复壮程度较好。     

The conserved 3′ Angio‐domain defines a superfamily of short interspersed nuclear elements (SINEs) in higher plants

Repetitive sequences are ubiquitous components of eukaryotic genomes affecting genome size and evolution as well as gene regulation. Among them, short interspersed nuclear elements (SINEs) are non‐coding retrotransposons usually shorter than 1000 bp. They contain only few short conserved structural motifs, in particular an internal promoter derived from cellular RNAs and a mostly AT‐rich 3′ tail, whereas the remaining regions are highly variable. SINEs emerge and vanish during evolution, and often diversify into numerous families and subfamilies that are usually specific for only a limited number of species. In contrast, at the 3′ end of multiple plant SINEs we detected the highly conserved ‘Angio‐domain’. This 37 bp segment defines the Angio‐SINE superfamily, which encompasses 24 plant SINE families widely distributed across 13 orders within the plant kingdom. We retrieved 28 433 full‐length Angio‐SINE copies from genome assemblies of 46 plant species, frequently located in genes. Compensatory mutations in and adjacent to the Angio‐domain imply selective restraints maintaining its RNA structure. Angio‐SINE families share segmental sequence similarities, indicating a modular evolution with strong Angio‐domain preservation. We suggest that the conserved domain contributes to the evolutionary success of Angio‐SINEs through either structural interactions between SINE RNA and proteins increasing their transpositional efficiency, or by enhancing their accumulation in genes.     

银色裂腹鱼线粒体基因组序列特征与系统进化分析

银色裂腹鱼(Schizothorax argentatus)在我国仅分布于新疆地区的伊犁河流域,是我国裂腹鱼类中珍稀濒危品种之一,具有较高的科研和经济价值。本研究采用高通量测序技术获得了银色裂腹鱼长度为16580 bp的线粒体基因组全序列,其基因组成和排列顺序均与典型的脊椎动物相似,共有13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个非编码区(D-loop)。碱基组成分别为A(30.25%)、G(17.28%)、C(27.20%)和T(25.27%),呈现明显的AT偏好性和反G偏倚。tRNA基因中仅tRNA-Ser(GCU)因缺少二氢尿嘧啶茎而无法形成典型的三叶草结构。ND6基因的AT-skew和GC-skew值波动最大,揭示该基因经历的选择和突变压力可能与其他基因不同。银色裂腹鱼线粒体控制区包含了3个不同的结构域:终止序列区(ETAS)、中央保守区(CSB-F、CSB-E、CSB-D和CSB-B)和保守序列区(CSB1、CSB2和CSB3),且在CSB3下游约50 bp处识别到鲤形目(Cypriniformes)鱼类中普遍存在的保守序列片段TT(AT)nGTG。基于28种裂腹鱼属鱼类线粒体基因组全序列构建的系统发育关系表明银色裂腹鱼分化时间较早,与其他类群亲缘关系较远,这可能与其所生活的水域地理位置和水文环境有密切关系。     

Lineage Specificity of the Evolutionary Dynamics of the mtDNA D-Loop Region in Rodents

This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80 bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block (CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number, and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated; the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD, which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical support. Received: 26 February 2001 / Accepted: 6 June 2001     

Sequence and organization of the complete mitochondrial genomes of spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri).

In this work, the mitochondrial genomes for spotted halibut (Verasper variegatus) and barfin flounder (Verasper moseri) were completely sequenced. The entire mitochondrial genome sequences of the spotted halibut and barfin flounder were 17,273 and 17,588 bp in length, respectively. The organization of the two mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (2 rRNAs, 22 tRNAs and 13 protein-coding genes) and two non-coding regions (control region (CR) and WANCY region). In the CR, the termination associated sequence (ETAS), six central conserved block (CSB-A,B,C,D,E,F), three conserved sequence blocks (CSB1-3) and a region of 61-bp tandem repeat cluster at the end of CSB-3 were identified by similarity comparison with fishes and other vertebrates. The tandem repeat sequences show polymorphism among the different individuals of the two species. The complete mitochondrial genomes of spotted halibut and barfin flounder should be useful for evolutionary studies of flatfishes and other vertebrate species.     

大趾鼠耳蝠线粒体DNA控制区结构及变异

采用PCR产物直接测序法首次测定大趾鼠耳蝠(Myotis macrodactylus)10个个体的线粒体DNA(mtDNA)控制区全序列,并进行了结构和变异分析。结果表明,大趾鼠耳蝠的控制区结构与其他哺乳动物相似,可分为一个中央保守区(包括F、E、D、C、B元件)和两个外围结构域:延伸的终止结合序列区(包括ETAS1和ETAS2元件)和保守序列区(包括CSB1、CSB2和CSB3元件),其中最为保守的是中央保守区(核苷酸变异度为1.8%)。大趾鼠耳蝠控制区核苷酸全序列具有丰富的长度多态性(1778～2048bp),主要是由在碱基组成、重复数目和排列方式上异质的串联重复序列造成的。在ETAS内发现了TACAT及其反向互补序列ATGTA,支持滑移错配模式(slipped mispairing model)。本研究为该物种的进一步研究和保护提供基础遗传数据。     

Structure and variable numbers of tandem repeats (VNTRs) of the mitochondrial control region in mitten crab <Emphasis Type="Italic">Eriocheir</Emphasis> (Crustacean: Brachyura)

Mitochondrial control region was called “A + T-rich” region in invertebrate. In the study, the general organization of control region in mitten crab was divided into two major domains: high variable segment and conserved segment. Four conserved blocks (CSB1, CSB2, CSB3 and CSB4) and two tandem repeat sequences (RT1 and RT2) were defined in control region. There were 116 polymorphic sites and 84 parsimony information sites in 571 aligned sites of the high variable segment adjacent “tRNA-Gln”, in which 58 stable variable sites were defined between E. j. sinensis and E. j. hepuensis. Conserved domain contained more than two similar repeat units, and length polymorphism of control region was due to the number difference between the two repeat units (RT1 and RT2). And length polymorphism was a common phenomenon for tandem repeat in control region in the study. Furthermore, a novel result showed the core nucleotide of RT2 in control region tandem repeat was C in E. j. hepuensis, but G in E. j. sinensis. It might be a rapid and cost-effective measure of seedlings differentiation in aquaculture.     

Complete mitochondrial genome sequence of the Himalayan Griffon,Gyps himalayensis (Accipitriformes: Accipitridae): Sequence,structure, and phylogenetic analyses

This is the first study to describe the mitochondrial genome of the Himalayan Griffon, Gyps himalayensis, which is an Old World vulture belonging to the family Accipitridae and occurring along the Himalayas and the adjoining Tibetan Plateau. Its mitogenome is a closed circular molecule 17,381 bp in size containing 13 protein‐coding genes, 22 tRNA coding genes, two rRNA‐coding genes, a control region (CR), and an extra pseudo‐control region (CCR) that are conserved in most Accipitridae mitogenomes. The overall base composition of the G. himalayensis mitogenome is 24.55% A, 29.49% T, 31.59% C, and 14.37% G, which is typical for bird mitochondrial genomes. The alignment of the Accipitridae species control regions showed high levels of genetic variation and abundant AT content. At the 5′ end of the domain I region, a long continuous poly‐C sequence was found. Two tandem repeats were found in the pseudo‐control regions. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 13 protein‐coding genes indicated that the relationships at the family level were (Falconidae + (Cathartidae + (Sagittariidae + (Accipitridae + Pandionidae))). In the Accipitridae clade, G. himalayensis is more closely related to Aegypius monachus than to Spilornis cheela. The complete mitogenome of G. himalayensis provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of Gyps species.     

DNA sequence variation in the mitochondrial control region of subterranean mole rats,Spalax ehrenbergi superspecies,in Israel

The complete mitochondrial control region was sequenced for 60 individuals representing different populations for each of the four species of the subterranean mole rat Spalax ehrenbergi superspecies in Israel: Spalax galili (2n = 52), S. golani (2n = 54), S. carmeli (2n = 58), and S. judaei (2n = 60). The control region of all species and populations is very similar both in length (979 to 983 bp) and in base composition. As in agreement with previous surveys on mitochondrial control regions on mammals, the mole rat control region can be divided into a central domain and two flanking domains, ETAS (extended termination associated sequences) and CSB (conserved sequence blocks). Along with the common conserved blocks found in these domains (ETAS1, ETAS2, CSB1, CSB2, and CSB3), we have also detected in all individuals an ETAS1-like and a CSB1-like element, both in the ETAS domain. The most conserved region was the central domain, followed by the CSB and ETAS domains, showing important differences in the four species analyzed. Phylogenetic analysis supported the existence of two clades. One clade contained individuals belonging to Spalax galili (2n = 52) and S. golani (2n = 54), separated in two different branches depending on the species. The other clade contained individuals belonging to S. carmeli (2n = 58) and S. judaei (2n = 60) mixed together, suggesting a more recent event of speciation. Within species we have observed a southward trend of increasing variability. These results have been explained as a consequence of the adaptation of the species to ecological factors such as aridity and temperature stresses.     

鳜类鱼类的线粒体DNA控制区结构及其系统发育分析

鳜类为低等鲈形目鱼类,是东亚特有类群。然而,关于其系统位置、分类以及一些物种的有效性等尚有争议。采用PCR扩增直接测序的方法,获得了鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜、中国少鳞鳜线粒体DNA控制区基因的序列。对比其他已报道鱼类控制区的结构识别序列,对鳜类鱼类控制区的结构进行了分析,识别了终止序列区、中央保守区和保守序列区,并找到了DNA复制终止相关的序列ETAS和中央保守区的保守序列CSB-F、CSB-E、CSB-D以及保守序列区的保守序列CSB1、CSB2、CSB3。几种鳜鱼间共有191个变异位点,其中,终止序列区的变异最高,占总变异的61．3％,中央保守区和保守序列区占总变异的38．7％。这一结果可为全面了解鱼类线粒体DNA控制区的结构特征提供资料。同时,利用高度变异的控制区序列,以鲈科和错科作为外群,使用邻接法和最大简约法构建了这几种鳜鱼的系统发育树。结果表明：鳜类为一单系类群,鳜、大眼鳜、斑鳜、暗鳜、波纹鳜、长体鳜构成一支鳜鱼群,其中,鳜与大眼鳜为姐妹种;中国少鳞鳜为另一支少鳞鳜群;长体鳜未单独成一支,而是聚入鳜鱼群内,应更名为Siniperca roulei。研究结果支持将现生鳜类分为两个类群的观点。     

Structure of the Mitochondrial DNA Control Region of the Sinipercine Fishes and Their Phylogenetic Relationship

The mitochondrial DNA control region of Siniperca chuatsi, S. kneri, S. scherzeri, S. obscura, S. undulata, Coreosiniperca roulei and Coreoperca whiteheadi were amplified by PCR amplification and directly sequenced. The mtDNA control region of the sinipercine fishes could be separated into three domains, namely, the terminal associated sequence domain, the central conserved sequence domain and the conserved sequence block domain. The extended terminal associated sequence (ETAS), three conserved sequence blocks (CSB-F, CSB-E, CSB-D) in the central conserved sequence domain and three conserved sequence blocks (CSB1, CSB2, CSB3) in the conserved sequence block domain were also identified. The phylogenetic relationships among these sinipercine fishes were constructed through neighbor-joining and maximum parsimony methods using Percidae and Serranidae as outgroups. Results showed that sinipercine fishes were a monophyletic group, with Siniperca forming one group, and Coreoperca forming another group. Coreosiniperca roulei did not form an independent group but was merged into the genus Siniperca. Thus it should be renamed as Siniperca roulei.