The complete mitochondrial genome of the bird schistosome Trichobilharzia regenti (Platyhelminthes: Digenea), causative agent of cercarial dermatitis

The complete mitochondrial (mt) genome of the neuropathogenic bird schistosome Trichobilharzia regenti was fully sequenced in order to develop molecular markers for future diagnostic, molecular ecological, population, and phylogenetic studies. The genome was 14,838 bp in length, with a 68.4% AT bias in protein coding regions. A repeat element (3 x 184 bp) between trnV and trnW distinguished a single short noncoding region. As 9 of 14 genera of schistosomes parasitize birds, future characterization of their mt genomes is desirable for species-specific and strain- or population-specific diagnostic markers; this concerns not only the nasal representatives, e.g., T. regenti characterized in this study, but also numerous species within the predominant group of visceral (blood dwelling) bird schistosomes.     

The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports classification of antipatharians within the subclass Hexacorallia

Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.     

Mitochondrial genome of the Komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements.

The mitochondrial genome of the Komodo dragon (Varanus komodoensis) was nearly completely sequenced, except for two highly repetitive noncoding regions. An efficient sequencing method for squamate mitochondrial genomes was established by combining the long polymerase chain reaction (PCR) technology and a set of reptile-oriented primers designed for nested PCR amplifications. It was found that the mitochondrial genome had novel gene arrangements in which genes from NADH dehydrogenase subunit 6 to proline tRNA were extensively shuffled with duplicate control regions. These control regions had 99% sequence similarity over 700 bp. Although snake mitochondrial genomes are also known to possess duplicate control regions with nearly identical sequences, the location of the second control region suggested independent occurrence of the duplication on lineages leading to snakes and the Komodo dragon. Another feature of the mitochondrial genome of the Komodo dragon was the considerable number of tandem repeats, including sequences with a strong secondary structure, as a possible site for the slipped-strand mispairing in replication. These observations are consistent with hypotheses that tandem duplications via the slipped-strand mispairing may induce mitochondrial gene rearrangements and may serve to maintain similar copies of the control region.     

The complete mitochondrial genome of the taimen, Hucho taimen, and its unusual features in the control region

The whole mitochondrial genome of Hucho taimen was firstly sequenced and characterized. The genome is 16,833 bp in length and contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region. Twelve protein-coding genes on the heavy strand showed that the content of A+T was higher than that of G+C, whereas the nd6 protein-coding gene on the light strand displayed an opposite pattern. We described the secondary structure of the origin of light strand (oriL) replication and found that the conserved 5'-GCCGG-3' sequence motif is variable in H. taimen and some other salmonids. We conclude that the control region is variable in length and represents the high A+T content, compared with other mitochondrial control regions available in Salmonidae and other non-salmonids. Additionally, another interesting feature of H. taimen mitogenome is that a T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region.     

The Mitochondrial Genome of Pseudocalotes microlepis (Squamata: Agamidae) and its Phylogenetic Position in Agamids

We describe the complete mitochondrial genome of a small-scaled forest agamid(Pseudocalotes microlepis), which is 17 873 bp in size, containing 13 PCGs, 2 r RNAs, 22 t RNAs and non-coding regions. The mitogenome has a typical gene order among squamates. 13 PCGs include 2 start codons(ATG and ATA), 3 stop codons(TAG, TAA and AGG), and an incomplete stop codon(T-). Codon usage analyses showed that CUA-Leu1 and CGG-Arg are the most frequently and rarely used codon, respectively. All 22 t RNAs were predicted to form canonical cloverleaf secondary structures, except for two t RNAs(t RNACys and t RNASer(AGY)) lacking the dihydorouridine(DHU) arm. The large noncoding region(control region) is 2 687 bp long(28.3% T, 18.2% C, 42.3% A, and 11.2% G), with four different types of repeating sequences. The phylogenetic tree resulting from BEAST analyses based on concatenated 2 r RNAs and 13 PCGs in sequence revealed that the newly sequenced P. microlepis, where the genus Acanthosaura were aggregated. Together with Calotes versicolor, they constitute the subfamily Draconinae.     

Molecular systematics of the western rattlesnake, Crotalus viridis (Viperidae), with comments on the utility of the D-loop in phylogenetic studies of snakes.

Crotalus viridis, the western rattlesnake, ranges throughout western North America and has been divided into at least eight subspecies. However, the validity of and relationships among these subspecies and the monophyly of C. viridis as a whole are questionable. We used mitochondrial DNA sequence data from the D-loop region and ND2 gene to examine the relationships among 26 populations of C. viridis and to test the monophyly of this species. These data were analyzed separately and combined using maximum-likelihood and maximum-parsimony. The C. viridis group was monophyletic in all combined analyses, consisting of two strongly divergent clades. We recommend that these clades be recognized as two distinct evolutionary species: C. viridis and C. oreganus. Crotalus viridis should be restricted to the subspecies viridis and nuntius and the remaining subspecies be assigned to the species C. oreganus. Our data do not allow strong evaluation of the validity of the subspecies. We found that the ND2 gene had greater sequence divergences among closely related individuals than the D-loop region, but this relationship reversed at higher levels of divergence. This pattern is apparently due to: (1) ND2 third positions evolving faster than the D-loop but becoming saturated at higher levels of divergence, and (2) the D-loop evolving faster than ND2 second (and possibly first) positions. Our results suggest that the ND2 gene is preferable for examining intraspecific relationships and the D-loop may better resolve relationships between species of snakes. The latter result is contrary to the common perception of the phylogenetic utility of the D-loop. Another unusual result is that the 145 bp spacer region, adjacent to the 5' end of the light strand of the D-loop, provides greater phylogenetic resolution than the 1030 bp D-loop.     

Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae).

We determined the complete nucleotide sequence of the mitochondrial genome for the rabbitfish Siganus fuscescens (Perciformes, Siganidae). This mitochondrial genome, consisting of 16,491 base pairs (bp), included 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region similar those found in other vertebrates; the gene order was identical to that of typical vertebrates. Most of the genes of S. fuscescens were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. The reading frames of ATPase 8 and 6 and those of ND4L and ND4 overlapped by ten and seven nucleotides, respectively. All mitochondrial protein-coding genes began with an ATG start codon, except for CO1, which started with GTG. Open reading frames of S. fuscescens ended with TAA (ND1, CO1, ATPase 8, ND4L, ND5 and ND6), and the remainder had incomplete stop codons, either TA (ATPase 6 and CO3) or T (ND2, CO2, ND3, ND4, and Cytb). The origin of L-strand replication in S. fuscescens was located in a cluster of five tRNA genes (WANCY) and was 34 nucleotides in length. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (828 bp) was considered to be the control region (D-loop). Within this sequence, we identified a conserved sequence block characteristic of this region. The rabbitfish was grouped with Siganus canaliculatus in most parsimony analyses, which showed 100% bootstrap support for their divergence. These findings are useful for inferring phylogenetic relationships and identification within the suborder Acanthuroidei.     

Body size variation among mainland populations of the western rattlesnake (Crotalus viridis)

In general, squamate reptiles follow the converse to Bergmann's rule, attaining smaller sizes in cooler environments, whereas other vertebrate groups follow Bergmann's rule, attaining larger sizes in cooler areas. Intensive studies of body size evolution for species of squamates are necessary to understand the processes responsible for this trend. Here I present data on body size variation among mainland populations of the western rattlesnake, Crotalus viridis. This species consists of two well-differentiated phylogenetic clades, therefore all analyses were performed for the C. viridis group as a whole and separately for each of the two clades within the C. viridis group. Although both phylogenetic and nonphylogenetic analyses were performed, the data did not show phylogenetic conservatism, and therefore the nonphylogenetic results are preferred. I found no significant relationships between mean adult female snout-vent length and any of the physical and climatic variables that were examined for the C. viridis group using simple linear regression analysis. Examined separately, I found that individuals of the western clade, C. oreganus, were smaller in cooler and more seasonal environments, whereas individuals of the eastern clade. C. viridis sensu stricto, were larger in cooler and more seasonal areas. Thus, the observed size trends were in opposite directions for the two clades. Multiple regression analysis revealed that seasonality was a stronger predictor of body size variation than was temperature for both clades. The differences in body size trends between these clades may be due to differences in mortality rates among populations.     

The complete mitochondrial genome of Microtus fortis calamorum (Arvicolinae, Rodentia) and its phylogenetic analysis

Microtus fortis is a special resource of rodent in China. It is a promising experimental animal model for the study on the mechanism of Schistosome japonicum resistance. The first complete mitochondrial genome sequence for Microtus fortis calamorum, a subspecies of M. fortis (Arvicolinae, Rodentia), was reported in this study. The mitochondrial genome sequence of M. f. calamorum (Genbank: JF261175) showed a typical vertebrate pattern with 13 protein coding genes, 2 ribosomal RNAs, 22 transfer RNAs and one major noncoding region (CR region).The extended termination associated sequences (ETAS-1 and ETAS-2) and conserved sequence block 1 (CSB-1) were found in the CR region. The putative origin of replication for the light strand (O(L)) of M. f. calamorum was 35bp long and showed high conservation in stem and adjacent sequences, but the difference existed in the loop region among three species of genus Microtus. In order to investigate the phylogenetic position of M. f. calamorum, the phylogenetic trees (Maximum likelihood and Bayesian methods) were constructed based on 12 protein-coding genes (except for ND6 gene) on H strand from 16 rodent species. M. f. calamorum was classified into genus Microtus, Arvcicolinae for the highly phylogenetic relationship with Microtus kikuchii (Taiwan vole). Further phylogenetic analysis results based on the cytochrome b gene ranged from M. f. calamorum to one of the subspecies of M. fortis, which formed a sister group of Microtus middendorfii in the genus Microtus.     

两种毛蚜线粒体基因组比较分析

【目的】线粒体基因组分析已被应用于昆虫系统发育研究。本研究以蚜科Aphididae重要类群毛蚜亚科物种为代表,测定并比较分析了该类蚜虫的线粒体基因组特征,探讨了基于线粒体基因组信息的蚜虫系统发育关系重建。【方法】以毛蚜亚科三角枫多态毛蚜Periphyllus acerihabitans Zhang和针茅小毛蚜Chaetosiphella stipae Hille Ris Lambers,1947为研究对象,利用长短PCR相结合的方法测定线粒体基因组的序列,分析了基因组的基本特征;基于在线t RNAscan-SE Search Server搜索方法预测了t RNA的二级结构;基于12个物种(本研究获得的2个物种和10个Gen Bank上下载的物种数据)的蛋白编码基因(PCGs)序列,利用最大似然法和贝叶斯法重建了蚜科的系统发育关系。【结果】两种毛蚜均获得了约94%的线粒体基因组数据,P.acerihabitans获得了14 908 bp,控制区为1 205 bp;C.stipae获得了13 893 bp,控制区为609 bp。两种毛蚜同时获得33个基因,包含接近完整的13个蛋白编码基因(PCGs)(nad5不完整),18个tRNA,2个rRNA基因;ka/ks值表明,C.stipae的进化速率更快。从基因组组成、基因排列顺序、核苷酸组成分析、密码子使用情况、t RNA二级结构等特征来分析,两种蚜虫线粒体基因组基本特征相似。系统发育重建结果表明毛蚜亚科、蚜亚科的单系性得到了支持,毛蚜亚科位于蚜科的基部位置。【结论】两种毛蚜线粒体基因组的基本特征相似,符合蚜虫线粒体基因组的一般特征,两种线粒体基因组的长度差异主要来自控制区长度的不同;系统发育重建支持毛蚜亚科与蚜亚科的单系性,毛蚜亚科位于蚜科较为基部的位置。研究结果为蚜虫类系统发育重建提供了参考。     

Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data

The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia, and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates.     

Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications

The mitochondrial genome is now widely used in the study of phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate, and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomic level, we sequenced and annotated the complete mitogenomes of 3 skippers: Ampittia virgata, Halpe nephele, and Onryza maga (new mitogenomes for 2 genera) with a total length of 15,333 bp, 15,291 bp, and 15,381 bp, respectively. The mitogenomes all contain 13 protein‐coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a noncoding A + T‐rich region and are consistent with other lepidopterans in gene order and type. In addition, we reconstructed the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the tribe Aeromachini in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + (Pyrginae + ((Eudaminae + Tagiadinae) + (Heteropterinae + ((Trapezitinae + Barcinae) + Hesperiinae))))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.     

Complete mitochondrial genome of the longtooth grouper Epinephelus bruneus (Perciformes, Serranidae)

We determined the complete nucleotide sequence of the mitochondrial (mt) genome for the longtooth grouper, Epinephelus bruneus (Perciformes, Serranidae). This mt genome, consisting of 16,686 base pairs (bp), encoded genes for 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a noncoding control region as those found in other vertebrates, with the gene order identical to that of typical vertebrates. A major noncoding region between the trnP and trnF genes (991 bp) was considered to be the control region (D-loop). Within this sequence, 22 copies of a 17-bp tandem repeat element, 5'-TGATATTACATATATGC-3', were identified in the control region unlike previous reported Epinephelus species.     

Fourteen complete mitochondrial genomes of butterflies from the genus Lethe (Lepidoptera,Nymphalidae, Satyrinae) with mitogenome-based phylogenetic analysis

The mitochondrial genome (mitogenome) can help us understand the phylogenetic relationships within the genus Lethe and the subfamily Satyrinae. In this study, we sequenced the complete mitogenomes of 14 Lethe species, which range in size from 15,225 to 15,271 bp, with both 37 genes (13 PCGs, 22 tRNAs, 2 rRNAs) and a noncoding A + T-rich region. The gene arrangement and orientation is similar to typical mitogenomes of Lepidoptera. The Ka/Ks ratio shows that cox1 has the slowest evolutionary rate. The secondary structure of trnN lacks the Pseudouracil loop (TψC loop) in most Lethe species. The inferred phylogenetic analyses show that Lethe is a well-supported monophyletic group, and reveal 2 major clades within the genus Lethe, which is consistent with previous morphological classifications.     

Complete mitochodrial genome of the crab spider Ebrechtella tricuspidata (Araneae: Thomisidae): A novel tRNA rearrangement and phylogenetic implications for Araneae

Mitochondrial genomes are widely used for phylogenetic and phylogeographic analyses among arthropods, but there is a lack of sufficient mitochondrial genome sequence data for spiders. Herein, we sequenced and characterized the complete mitochondrial genome of a crab spider Ebrechtella tricuspidata (Araneae: Thomisidae). The circular mitochondrial genome is 14,352 bp long, including a standard set of 37 genes and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (77.3%). A novel gene order rearrangement is detected by a tRNA (trnL1) translocation. Tandem repeats are not identified in the A + T-rich region. Most of the tRNAs are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. The phylogenetic analysis confirms that the mitochondrial genome sequences are useful in resolving higher-level relationship of Araneae. Overall, our data present in this study will elevate our knowledge on the architecture and evolution of spider mitochondrial genome.     

The complete mitochondrial genome of the small yellow croaker and partitioned Bayesian analysis of Sciaenidae fish phylogeny

To understand the phylogenetic position of Larimichthys polyactis within the family Sciaenidae and the phylogeny of this family, the organization of the mitochondrial genome of small yellow croaker was determined herein. The complete, 16,470 bp long, mitochondrial genome contains 37 mitochondrial genes (13 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes), as well as a control region (CR), as in other bony fishes. Comparative analysis of initiation/termination codon usage in mitochondrial protein-coding genes of Percoidei species, indicated that COI in Sciaenidae entails an ATG/AGA codon usage different from other Percoidei fishes, where absence of a typical conserved domain or motif in the control regions is common. Partitioned Bayesian analysis of 618 bp of COI sequences data were used to infer the phylogenetic relationships within the family Sciaenidae. An improvement in harmonic mean -lnL was observed when specific models and parameter estimates were assumed for partitions of the total data. The phylogenetic analyses did not support the monophyly of Otolithes, Argyrosomus, and Argyrosominae. L. polyactis was found to be most closely related to Collichthys niveatus, whereby, according to molecular systematics studies, the relationships within the subfamily Pseudosciaenidae should be reconsidered.     

绿眼赛茧蜂线粒体基因组全序列测定和分析

【目的】测定绿眼赛茧蜂Zele chlorophthalmus线粒体基因组全序列,分析其基因组结构及茧蜂科(Braconidae)部分类群的系统发育关系。【方法】利用Illumina MiSeq二代测序技术对绿眼赛茧蜂的线粒体基因组进行测序,对基因组序列进行拼装、注释,分析其结构特点和碱基组成;基于22种茧蜂科昆虫的COX1蛋白编码基因序列,应用最大似然法(ML)和邻接法(NJ)构建系统发育树,分析绿眼赛茧蜂与茧蜂科其他昆虫的系统发育关系。【结果】绿眼赛茧蜂线粒体基因组全长16 661 bp(GenBank登录号: MG822749),包含13个蛋白质编码基因、22个tRNA基因和2个rRNA基因,共37个基因,以及1个控制区。线粒体基因组有明显的核苷酸组成的偏倚,AT偏正,GC偏负,其A+T含量为82.83%。基因排列顺序与推测的昆虫祖先的序列不完全一致,tRNA基因7处发生重排。13个蛋白质编码基因均以ATN为起始密码子,以TAA为终止密码子。在22个tRNA基因二级结构中,除tRNA^His(H)缺失TΨC环和tRNA^Cys(C)仅剩二氢尿嘧啶(DHU)臂和反密码子臂外,其余tRNA基因均能形成典型的三叶草结构。基于COX1蛋白编码序列的系统发育分析结果显示,与绿眼赛茧蜂亲缘关系最近的是同属于赛茧蜂属的雪跗赛茧蜂Z. niveitarsis。【结论】本研究首次获得绿眼赛茧蜂线粒体基因组全序列。结果表明绿眼赛茧蜂隶属于优茧蜂亚科(Euphorinae)赛茧蜂属,并支持赛茧蜂属的单系性。     

First Sequenced Mitochondrial Genome from the Phylum Acanthocephala(Leptorhynchoides thecatus) and Its Phylogenetic Position Within Metazoa

The complete sequence of the mitochondrial genome of Leptorhynchoides thecatus (Acanthocephala) was determined, and a phylogenetic analysis was carried out to determine its placement within Metazoa. The genome is circular, 13,888 bp, and contains at least 36 of the 37 genes typically found in animal mitochondrial genomes. The genes for the large and small ribosomal RNA subunits are shorter than those of most metazoans, and the structures of most of the tRNA genes are atypical. There are two significant noncoding regions (377 and 294 bp), which are the best candidates for a control region; however, these regions do not appear similar to any of the control regions of other animals studied to date. The amino acid and nucleotide sequences of the protein coding genes of L. thecatus and 25 other metazoan taxa were used in both maximum likelihood and maximum parsimony phylogenetic analyses. Results indicate that among taxa with available mitochondrial genome sequences, Platyhelminthes is the closest relative to L. thecatus, which together are the sister taxon of Nematoda; however, long branches and/or base composition bias could be responsible for this result. The monophyly of Ecdysozoa, molting organisms, was not supported by any of the analyses. This study represents the first mitochondrial genome of an acanthocephalan to be sequenced and will allow further studies of systematics, population genetics, and genome evolution.Reviewing Editor: Dr. Rafael Zardoya The entire genome sequence has been deposited with the GenBank Data Libraries under-accession number AY562383.     

The complete mitochondrial genome of the Sichuan taimen (Hucho bleekeri): repetitive sequences in the control region and phylogenetic implications for Salmonidae

The complete mitochondrial DNA genome of the Sichuan taimen (Hucho bleekeri) was determined by the long and accurate polymerase chain reaction (LA-PCR) and primer walking sequence method. The entire mitochondrial genome of this species is 16,997 bp in length, making it the longest among the completely sequenced Salmonidae mitochondrial genomes. It consists of two ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and one control region (CR). The gene arrangement, nucleotide composition, and codon usage pattern of the mitochondrial genome are similar to those of other teleosts. A T-type mononucleotide microsatellite and an 82 bp tandem repeat were identified in the control region, which were almost identical among the three H. bleekeri individuals examined. Both phylogenetic analyses based on 12 concatenated protein-coding genes of the heavy strand and on just the control region show that H. bleekeri is a basal species in Salmoninae. In addition, Salmo, Salvelinus and Oncorhynchus all represent monophyletic groups, respectively. All freshwater species occupied basal phylogenetic positions, and also possessed various tandem repeats in their mitochondrial control regions. These results support established phylogenetic relationships among genera in Salmonidae based on morphological and molecular analyses, and are consistent with the hypothesis that Salmonidae evolved from freshwater species.     

Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: structural properties and cue for resolving teleostean relationships

We cloned and sequenced the complete mitochondrial genome of Japanese flounder (Paralichthys olivaceus). A circular 17,090 bp mitochondrial genome from the flounder contains 37 structural genes as in other vertebrates so far reported. This is the first report of the complete mitochondrial sequence from a higher teleostean fish (Acanthopterygii). The organization including gene order is quite similar to that of other teleostean fishes as well as placental mammals. The putative control region of the Japanese flounder mitochondrial genome contains a length variable region of about a 74 bp tandem repeat cluster. As a preliminary study we adopted the maximum likelihood and neighbor-joining inference methods to examine phylogenetic relationships among teleostean and related fishes. Comparisons of amino acid sequences of protein-coding genes and nucleotide sequences of tRNA genes resolved some middle to deep branches among some teleostean fishes. The flounder mitochondrial genome does not show an indication of evolutionary rate difference among teleosts leading to difficulty in phylogenetic analyses, and our data is useful for future evolutionary studies dealing with higher teleostean fishes.