Organization of the Mitochondrial Genome of a Deep-Sea Fish, Gonostoma gracile (Teleostei: Stomiiformes): First Example of Transfer RNA Gene Rearrangements in Bony Fishes

We determined the complete nucleotide sequence of the mitochondrial genome (except for a portion of the putative control region) for a deep-sea fish, Gonostoma gracile. The entire mitochondrial genome was purified by gene amplification using long polymerase chain reaction (long PCR), and the products were subsequently used as templates for PCR with 30 sets of newly designed, fish-universal primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products showed that the genome contained the same 37 mitochondrial structural genes as found in other vertebrates (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes), with the order of all rRNA and protein-coding genes, and 19 tRNA genes being identical to that in typical vertebrates. The gene order of the three tRNAs (tRNA^Glu, tRNA^Thr, and tRNA^Pro) relative to cytochrome b, however, differed from that determined in other vertebrates. Two steps of tandem duplication of gene regions, each followed by deletions of genes, can be invoked as mechanisms generating such rearrangements of tRNAs. This is the first example of tRNA gene rearrangements in a bony fish mitochondrial genome. Received August 5, 1998; accepted February 19, 1999.     

Complete mitochondrial DNA sequence of the Japanese spiny lobster,Panulirus japonicus (Crustacea: Decapoda)

We determined the complete nucleotide sequence of the mitochondrial genome for a Japanese spiny lobster, Panulirus japonicus (Crustacea: Decapoda). The entire genome was amplified using long polymerase chain reaction, and the products were subsequently used as templates for direct sequencing using a primer-walking strategy. The genome (15,717 base pairs) contained the same 37 genes (two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) plus the putative control region as found in other arthropods, with the gene order identical to that of typical arthropods. Preliminary phylogenetic analyses of selected arthropods using concatenated amino acid sequences of the 13 protein-coding genes strongly supported monophyly of Decapoda species and confidently rejected "Macroura", a conventional taxon that shares an elongated abdominal body.     

The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes

We determined the whole mitochondrial genome sequence for spotted green pufferfish, Tetraodon nigroviridis (Teleostei: Tetraodontiformes). The genome (16,488 bp) contained 37 genes (two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes) plus control region as found in other vertebrates, with the gene order identical to that of typical vertebrates. The sequence was used to estimate phylogenetic relationships and divergence times among major lineages of fishes, including representative model organisms in fishes. We employed partitioned Bayesian approaches for these two analyses using two datasets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding the ND6 gene) and concatenated nucleotide sequences from the 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The resultant trees from the two datasets were well resolved and largely congruent with those from previous studies, with spotted green pufferfish being placed in a reasonable phylogenetic position. The approximate divergence times between spotted green pufferfish and model organisms in fishes were 85 million years ago (MYA) vs. torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records.     

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.     

中华鳖线粒体基因组序列分析

参照近源物种线粒体基因组序列,设计17对特异引物,采用PCR产物直接测序法测得中华鳖线粒体基因组全序列.初步分析其基因组特点和各基因的定位,用pDRAW32软件预测12种限制性酶对其的酶切图谱.结果表明,中华鳖线粒体基因组全长17364bp,核苷酸组成为35.23%A、27.26%T、25.73%C、11.78%G,包括13个蛋白质编码基因、2个rRNA基因、22个tRNA基因和1个非编码控制区.基于线粒体基因组编码的13个蛋白质的氨基酸序列,用NJ法和MP法构建系统进化树,分析6种龟鳖类动物之间的亲缘关系,与传统的系统分类基本一致,初步确定淡水龟科与海龟科的亲缘关系比与龟科的亲缘关系要近.     

The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed.     

Complete Mitochondrial DNA Sequence of Conger myriaster (Teleostei: Anguilliformes): Novel Gene Order for Vertebrate Mitochondrial Genomes and the Phylogenetic Implications for Anguilliform Families

The complete nucleotide sequence of the mitochondrial genome was determined for a conger eel, Conger myriaster (Elopomorpha: Anguilliformes), using a PCR-based approach that employs a long PCR technique and many fish-versatile primers. Although the genome [18,705 base pairs (bp)] contained the same set of 37 mitochondrial genes [two ribosomal RNA (rRNA), 22 transfer RNA (tRNA), and 13 protein-coding genes] as found in other vertebrates, the gene order differed from that recorded for any other vertebrates. In typical vertebrates, the ND6, tRNA^Glu, and tRNA^Pro genes are located between the ND5 gene and the control region, whereas the former three genes, in C. myriaster, have been translocated to a position between the control region and the tRNA^Phe gene that are contiguously located at the 5′ end of the 12S rRNA gene in typical vertebrates. This gene order is similar to the recently reported gene order in four lineages of birds in that the latter lack the ND6, tRNA^Glu, and tRNA^Pro genes between the ND5 gene and the control region; however, the relative position of the tRNA^Pro to the ND6–tRNA^Glu genes in C. myriaster was different from that in the four birds, which presumably resulted from different patterns of tandem duplication of gene regions followed by gene deletions in two distantly related groups of organisms. Sequencing of the ND5–cyt b region in 11 other anguilliform species, representing 11 families, plus one outgroup species, revealed that the same gene order as C. myriaster was shared by another 4 families, belonging to the suborder Congroidei. Although the novel gene orders of four lineages of birds were indicated to have multiple independent origins, phylogenetic analyses using nucleotide sequences from the mitochondrial 12S rRNA and cyt b genes suggested that the novel gene orders of the five anguilliform families had originated in a single ancestral species. Received: 13 July 2000 / Accepted: 30 November 2000     

Complete sequence and gene organization of the mitochondrial genome of Siamensis Crocodile (<Emphasis Type="Italic">Crocodylus siamensis</Emphasis>)

The complete sequence of mitochondrial genome of Siamensis Crocodile (Crocodylus siamensis) is determined by using PCR amplification, clone and primer-walking sequencing methods. The genome is 16836 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. The mtDNA genome of Siamensis Crocodile is similar to most vertebrates in gene component, order, orientation, tRNA structure, low percentage of guanine and high percentage of thymine. The nonstandard stop codes (T) in two protein genes (Cox III and Cyt b) are more than those of most vertebrates. Transfer RNA genes range in length from 61 to 76 nucleotides, and their planar structure present characteristic clover leaf, except for tRNA-Ser (AGY) because of lacking the "DHU" arm.     

The complete mitochondrial genome sequence and gene organization of the mud crab (Scylla paramamosain) with phylogenetic consideration

The complete mitochondrial genome is of great importance for better understanding the genome-level characteristics and phylogenetic relationships among related species. In the present study, we determined the complete mitochondrial genome DNA sequence of the mud crab (Scylla paramamosain) by 454 deep sequencing and Sanger sequencing approaches. The complete genome DNA was 15,824 bp in length and contained a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). Of 37 genes, twenty-three were encoded by the heavy strand (H-strand), while the other ones were encoded by light strand (L-strand). The gene order in the mitochondrial genome was largely identical to those obtained in most arthropods, although the relative position of gene tRNA^His differed from other arthropods. Among 13 protein-coding genes, three (ATPase subunit 6 (ATP6), NADH dehydrogenase subunits 1 (ND1) and ND3) started with a rare start codon ATT, whereas, one gene cytochrome c oxidase subunit I (COI) ended with the incomplete stop codon TA. All 22 tRNAs could fold into a typical clover-leaf secondary structure, with the gene sizes ranging from 63 to 73 bp. The phylogenetic analysis based on 12 concatenated protein-coding genes showed that the molecular genetic relationship of 19 species of 11 genera was identical to the traditional taxonomy.     

Complete mitochondrial genome of the Chinese spiny lobster <Emphasis Type="Italic">Panulirus stimpsoni</Emphasis> (Crustacea: Decapoda): genome characterization and phylogenetic considerations

The genetics and molecular biology of the commercially important Chinese spiny lobster, Panulirus stimpsoni are little known. Here, we present the complete mitochondrial genome sequence of P. stimpsoni, determined by the long polymerase chain reaction and primer walking sequencing method. The entire genome is 15,677 bp in length, encoding the standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The overall A + T content of the genome is 65.6%, lower than most malacostracan species. The gene order is consistent with the pancrustacean ground pattern. Several conserved elements were identified from P. stimpsoni control region, viz. one [TA(A)]n-block, two GA-blocks and three hairpin structures. However, the position of [TA(A)]n-block and number of hairpin structure are different from those in the congeneric P. japonicus and other decapods. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes do not support the monophyly of suborder Pleocyemata, which is in contrast to most morphological and molecular results. However, the position of Palinura and Astacidea is unstable, as represented by the basal or sister branches to other Reptantia species. P. stimpsoni, as the second species of Palinura with complete mitochondrial genome available, will provide important information on both genomics and conservation biology of the group.     

Organization of the Mitochondrial Genome of Antarctic Krill <Emphasis Type="Italic">Euphausia superba</Emphasis> (Crustacea: Malacostraca)

We determined the nearly complete DNA sequence of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca), one of the most ecologically and commercially important zooplankters in Antarctic waters. All of the genome sequences were purified by gene amplification using long polymerase chain reaction (PCR), and the products were subsequently used as templates for either direct sequencing using a primer-walking strategy or nested PCR with crustacea-versatile primers. Although we were unable to determine a portion of the genome owing to technical difficulties, the sequenced position, 14,606 bp long, contained all of the 13 protein-coding genes, 19 of the 22 transfer RNA genes, and the large subunit as well as a portion of the small subunit ribosomal RNA genes. Gene rearrangement was observed for 3 transfer RNA genes (tRNA^Cys, tRNA^Tyr, and tRNA^Trp) and the 2 leucine tRNA genes.     

The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar.

The complete sequence of the Atlantic salmon (Salmo salar) mitochondrial genome has been determined. The entire sequence is 16665 base pairs (bp) in length, with a gene content (13 protein-coding, two ribosomal RNA [rRNA] and 22 transfer RNA [tRNA] genes) and order conforming to that observed in most other vertebrates. Base composition and codon usage have been detailed. Nucleotide and derived amino acid sequences of the 13 protein-coding genes from Atlantic salmon have been compared with their counterparts in rainbow trout. A putative structure for the origin of L-strand replication (O(L)) is proposed, and sequence features of the control region (D-loop) are described.     

The complete mitochondrial genome and phylogenetic analysis of Nyctereutes procyonoides

The complete mitochondrial genome sequence of the raccoon dog (Nyctereutes procyonoides) was determined by using the long and accurate polymerase chain reaction. The entire mitochondrial genome sequence is 16,713 bp in length contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 control region. Most mitochondrial genes are encoded on the H strand, except for the ND6 gene and 8 tRNA genes. The base compositions of mitochondrial genomes present clearly A–T skew. All the transfer RNA genes can be folded into the typical cloverleaf-shaped structure except tRNA-Ser (AGY), which lacks the dihydrouridine arm. Protein-coding genes mainly initiate with ATG and terminate with TAA. Some reading frame intervals and overlaps are found in the mitochondrial genome. The control region can be divided into three domains: the extended termination associated sequences (ETASs) domain, the central conserved domain and the conserved sequence blocks (CSBs) domain. Three conserved sequence blocks (CSBs) and one extended termination associated sequences (ETAS-1) is found in the control region. The phylogenetic analysis based on the concatenated data set of 14 genes in the mitochondrial genome of Canidae shows that the raccoon dog has close phylogenetic position with the red fox (Vulpes vulpes) and they constitute a clade which has an equil evolutionary position with the clade formed by the genera Canis and Cuon.     

The Complete Mitochondrial Genomes of Three Bristletails (Insecta: Archaeognatha): The Paraphyly of Machilidae and Insights into Archaeognathan Phylogeny

The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.     

Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.     

The first mitochondrial genome for Brahmin moths (Brahmaeidae) and implications for the higher phylogeny of Bombycoidea

Bombycoidea comprises 10 families and 4723 species, and the phylogenetic relationships among families are still in debate. In this study, we have determined the complete mitochondrial genome (mitogenome) of Brahmaea porphyria. The 15,429-bp mitogenome contains a common set of 37 mitochondrial genes including 13 protein-coding genes, 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and an inferred control region, and shares the conserved gene rearrangement (trnM-trnI-trnQ) in most ditrysian mitogenomes. Moreover, we analysed the secondary structure for all the tRNA genes of B. porphyria and the preference of codon usage in the PCGs of B. porphyria. The putative 373-bp control region (CR) possesses three types of conserved elements, including ATAGA, Ploy-T stretch, and microsatellite-like elements. A phylogenetic analysis among available Bombycoidea mitogenomes using the concatenated 37 mitochondrial genes appears to support the hypothesis of (Sphingidae+Bombycidae)+Saturniidae and the relatively basal phylogenetic position of Brahmaeidae within Bombycoidea.     

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。     

Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences

Although adequate resolution of higher-level relationships of organisms apparently requires longer DNA sequences than those currently being analyzed, limitations of time and resources present difficulties in obtaining such sequences from many taxa. For fishes, these difficulties have been overcome by the development of a PCR-based approach for sequencing the complete mitochondrial genome (mitogenome), which employs a long PCR technique and many fish-versatile PCR primers. In addition, recent studies have demonstrated that such mitogenomic data are useful and decisive in resolving persistent controversies over higher-level relationships of teleosts. As a first step toward resolution of higher teleostean relationships, which have been described as the "(unresolved) bush at the top of the tree," we investigated relationships using mitogenomic data from 48 purposefully chosen teleosts, of which those from 38 were newly determined during the present study (a total of 632,315 bp), using the above method. Maximum-parsimony and maximum-likelihood analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and third codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) from the 48 species. The resultant two trees from the two methods were well resolved and largely congruent, with many internal branches supported by high statistical values. The tree topologies themselves, however, exhibited considerable variation from the previous morphology-based cladistic hypotheses, with most of the latter being confidently rejected by the mitogenomic data. Such incongruence resulted largely from the phylogenetic positions or limits of long-standing problematic taxa, which were quite unexpected from previous morphological and molecular analyses. We concluded that the present study provided a basis of and guidelines for future investigations of teleostean evolutionary mitogenomics and that purposeful higher-density taxonomic sampling, subsequent sequencing efforts, and phylogenetic analyses of their mitogenomes may be decisive in resolving persistent controversies over higher-level relationships of teleosts, the most diversified group of all vertebrates, comprising over 23,500 extant species.     

Complete mitochondrial genome of Pycnonotus xanthorrhous (Passeriformes,Pycnonotidae) and phylogenetic consideration

The complete mitochondrial genome (mitogenome) of Pycnonotus xanthorrhous was sequenced via next generation sequencing. The full length of the circular genome is 16,952 bp. It consists of 37 typical animal mitochondrial genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) and 2 ribosomal RNA (rRNA) genes. P. xanthorrhous also contains one control region (CR) and one pseudo-control region, and shares the identical gene arrangements with sequenced Pycnonotus spp. which differs from the typical vertebrates gene order. Phylogenetic analyses indicates that Passerida sensu stricto contains three major clades and the core Sylvioidea form a monophyletic group. Furthermore, we investigated the evolution of control region within this lineage and revealed the multiple independent origins of duplicate control region.