红足壮异蝽Urochela quadrinotata Reuter线粒体基因组的测定与分析

研究测定并分析了红足壮异蝽Urochela quadrinotata Reuter的线粒体基因组全序列。该线粒体基因组全长16585bp(GenBank登录号为JQ743678),A+T含量为75.4%,共编码35个基因,包括13个蛋白质基因、20个tRNA基因(两个tRNA基因,即tRNAIle和tRNAGln未被检测到)、2个rRNA基因及一段较长的非编码区(控制区,亦称A+T富含区)。基因排序与大部分昆虫的线粒体基因排列方式相同,没有发生基因重排。除tRNASer(AGN)的DHU臂无法形成典型的茎环结构,其余tRNA基因均能稳定形成典型的三叶草二级结构。预测了红足壮异蝽16S和12S rRNA的二级结果,分别包括6个结构域43个茎环和3个结构域27茎环。控制区含一个长1652bp的串联重复区域,由16个串联重复单元组成。     

Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei)

The complete mitochondrial genome (mitogenome) of Oxuderces dentatus was determined first. The genome was 17,116?bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [the control region (CR) and the origin of the light strand replication], the gene composition and order of which was similar to most other vertebrates. The overall base composition of the heavy strand was T 27.9%, C 26.8%, A 30.2%, and G 15.1%, with a slight A+T bias of 58.1%. In addition to the discrete and conserved sequence blocks, unusual long tandem repeat unit (three 150-bp tandem repeat units and an incomplete copy of 146?bp) was also detected within CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

Mitochondrial genome of the cockscomb pearl mussel Cristaria plicata (Bivalvia, Unionoida, Unionidae)

The complete mitochondrial genome sequence of the cockscomb pearl mussel Cristaria plicata, which is an endangered species in South Korea, was sequenced. The circle genome (15,708 bp in size) consists of 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. There were 26 noncoding regions (NCs) found throughout the mitogenome of C. plicata, ranging in size from 2 to 327 bp, and the two largest NC regions, NC286 and NC326, were found between ND5 and tRNA(Gln) (286 bp) and between tRNA(Glu) and ND2 (326 bp), respectively. The 13 mitochondrial protein-coding genes of a female individual of C. plicata collected from Korea (15,708 bp) were compared to those of the Chinese individual (15,712 bp) published before. The result showed that ND3 is the most conserved with 100% nucleotide similarity, and each of the other protein-coding genes has ca. 99%, respectively. The two largest NCs among 26 NCs have totally 98% nucleotide similarity between Korean and Chinese ones.     

Complete mitochondrial genome of the marine medaka Oryzias melastigma (Beloniformes, Adrianichthyidae)

The complete mitochondrial genome was obtained from the assembled genome data sequenced by next-generation sequencer from the marine medaka Oryzias melastigma. The mitochondrial genome sequence was 16,864 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), 4 genes (CO3, ND3, ND4, and Cytb) had incomplete stop codons. The base composition of O. melastigma mitogenome showed high A+T (59.65%) and anti-G bias (8.73%) on the 3rd position of PCGs.     

The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL(1), trnL(2), and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of K(a)/K(s) in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 x 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda.     

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.     

A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.)

ABSTRACT: BACKGROUND: Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138. RESULTS: Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the largest unique region. Blast analysis performed to assign the unique regions showed that about 80% of the region was covered by short homologous sequences to the mitochondrial sequences of normal-type radish or other reported Brassicaceae species, although no homology was found for the remaining 20% of sequences. CONCLUSIONS: Ogura-type mitochondrial genome was highly rearranged compared with the normal-type genome by recombination through one large repeat and multiple short repeats. The rearrangement has produced four unique regions in Ogura-type mitochondrial genome, and most of the unique regions are composed of known Brassicaceae mitochondrial sequences. This suggests that the regions unique to the Ogura-type genome were generated by integration and shuffling of pre-existing mitochondrial sequences during the evolution of Brassicaceae, and novel genes such as orf138 could have been created by the shuffling process of mitochondrial genome.     

黄脸油葫芦线粒体基因组:一种新的基因排列方式

采用长距PCR扩增及保守引物步移法测定并注释了黄脸油葫芦（Teleogryllus emma）线粒体基因组全序列。结果表明,黄脸油葫芦的线粒体基因组全长15 660 bp,A+T含量为73.1%。谷氨酸、色氨酸及天冬酰胺的转运RNA基因由N链编码,形成了直翅目中的第三种基因排列顺序,其余结构与其它螽亚目昆虫的线粒体结构一致。基因间隔序列共计73 bp,间隔长度从1—24 bp不等;有14对基因间存在共54 bp重叠,重叠碱基数在1—11 bp之间。13个蛋白质编码基因中12个基因（除COⅠ基因外）的起始密码为标准的ATN组成,COI基因的起始密码子为TTA。有10个基因在基因3＇端能找到完全的TAA或TAG终止密码子,而有三个基因（COII,ND5和ND4）终止密码子为不完整的T。除tRNASer（AGN）外,其余21个tRNA基因的二级结构均属典型的三叶草结构。黄脸油葫芦940bp的A+T富集区中存在一个被认为与复制起始有关的保守的二级结构,该结构不仅存在于直翅目昆虫中,而且也存在于双翅目、鳞翅目和膜翅目中,但是未见于昆虫纲的早期分化类群——弹尾目中。     

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.     

Complete sequence of the mitochondrial genome of Taenia saginata: comparison with T. solium and T. asiatica

The complete sequence of the Taenia saginata mitochondrial genome was determined, and its organization and structure were compared to other human-tropic Taenia tapeworms for which complete mitochondrial sequence data were available. The mitochondrial genome was 13,670 bp long, contained 12 protein-coding genes, two ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). It did not encode the atp8 gene. Overlapping regions were found between nad4L and nad4, nad1 and trnN, and cox1 and trnT. The ATG initiation codon was used for 10 protein-coding genes, and the GTG initiation codon was used for the remaining 2 genes (nad4 and atp6). The size of the protein-coding genes of the three human Taenia tapeworms did not vary, except for Taenia solium nad1 (891 aa) and nad4 (1212 aa) and Taenia asiatica cox2 (576 aa). The tRNA genes were 57-75 bp long, and the predicted secondary structures of 18 of these genes had typical clover-leaf shapes with paired dihydrouridine (DHU) arms. The genes in all human Taenia tapeworms for the two mitochondrial rRNA subunits rrnL and rrnS are separated by trnC. The putative T. saginata rrnL and rrnS are 972 and 732 bp long, respectively. The non-coding regions of the mt genome of T. saginata consisted of 2 regions: a short non-coding region (SNR, 66 nucleotides) and a long non-coding region (LNR, 159 nucleotides). The overall sequence difference in the full mitochondrial genome between T. saginata and T. asiatica was 4.6%, while T. solium differed by 11%. In conclusion, the complete sequence of the T. saginata mitochondrial genome will serve as a resource for comparative mitochondrial genomics and systematic studies of the parasitic cestodes.     

The complete mitochondrial genome of Solen strictus (Bivalvia: Solenidae)

In this paper, we determined the complete mitochondrial genome of Solen strictus (Bivalvia: Solenidae). The whole mitogenome of S. strictus is 16,535?bp in length with a base composition of 21.7% A, 41.0% T, 25.6% C, and 11.7% G and contains 12 protein-coding genes (atp8 is missing), 2 ribosomal RNA genes, 22 transfer RNA genes, and a major non-coding region (MNR). Some peculiar patterns including tandem repeats and microsatellite-like elements are found in the MNR of S. strictus.     

Sequence and comparative analysis of the maize NB mitochondrial genome

The NB mitochondrial genome found in most fertile varieties of commercial maize (Zea mays subsp. mays) was sequenced. The 569,630-bp genome maps as a circle containing 58 identified genes encoding 33 known proteins, 3 ribosomal RNAs, and 21 tRNAs that recognize 14 amino acids. Among the 22 group II introns identified, 7 are trans-spliced. There are 121 open reading frames (ORFs) of at least 300 bp, only 3 of which exist in the mitochondrial genome of rice (Oryza sativa). In total, the identified mitochondrial genes, pseudogenes, ORFs, and cis-spliced introns extend over 127,555 bp (22.39%) of the genome. Integrated plastid DNA accounts for an additional 25,281 bp (4.44%) of the mitochondrial DNA, and phylogenetic analyses raise the possibility that copy correction with DNA from the plastid is an ongoing process. Although the genome contains six pairs of large repeats that cover 17.35% of the genome, small repeats (20-500 bp) account for only 5.59%, and transposable element sequences are extremely rare. MultiPip alignments show that maize mitochondrial DNA has little sequence similarity with other plant mitochondrial genomes, including that of rice, outside of the known functional genes. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly three-fourths of the maize NB mitochondrial genome is still of unknown origin and function.     

Complete mitochondiral genome of the Korean red fox Vulpes vulpes (Carnivora, Canidae)

The complete mitochondrial genome sequence of Vulpes vulpes consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (CR). CR is located between the tRNA-Pro and tRNA-Phe genes and is 1173?base pairs (bp) in length. It consists of a short non-repetitive sequence followed by 8-bp 5'-ACACACGT-3' tandem repeat between conserved sequence black I and conserved sequence black II.     

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.     

斑翅草螽线粒体基因组序列测定与分析

已经测定的昆虫线粒体基因组中, 直翅目草螽亚科的疑钩额螽Ruspolia dubia线粒体控制区长度最短, 仅70 bp。为此, 本研究采用L-PCR结合二次PCR扩增策略对另一种草螽亚科昆虫斑翅草螽Conocephalus maculates线粒体基因组序列进行了测定。序列注释发现: 斑翅草螽线粒体基因组序列全长15 898 bp, A+T含量为72.05%, 基因排列与典型的节肢动物线粒体基因组一致。全部蛋白质编码基因以典型的ATN作为起始密码子, 9个蛋白质编码基因具有完整的终止密码子, 其余4个以不完整的T作为终止信号。除trnS^AGN外, 其余21个tRNAs均可折叠形成典型的三叶草结构, 依照Steinberg等(1997)线粒体特殊tRNA结构类型-9, trnS^AGN的DHU臂形成一个7 nt环, 反密码子臂则长达9 bp, 含1个突起碱基, 而不是正常的5 bp。斑翅草螽与其他直翅目昆虫线粒体基因组的主要区别在于, 在trnS^UCN和nad1, nad1和trnL^CUN基因间各存在一段罕见的、大段的基因间隔序列, 长度分别为78 bp和360 bp。其中, 位于nad1和trnL^CUN之间的基因间隔序列N链可形成一个包含完整起始、终止密码子(ATT/TAA)、编码103个氨基酸的未知开放阅读框。同义密码子使用偏好与线粒体基因组编码的tRNA反密码子匹配情况无关, 但与密码子第3位点的碱基组成紧密相关; 相对密码子使用频率(relative synonymous codon usage, RSCU)大于1的密码子, 其第3位点全部是A或T。在已经测定的直翅目昆虫线粒体基因组tRNAs中, 均存在一定数量的碱基错配, 且以G-U弱配对为主, 表明G-U配对在线粒体基因组中可能是一种正常的碱基配对形式。本研究测定的斑翅草螽线粒体基因组序列, 和先前已经测定的直翅目线粒体基因组序列一起, 可以为重建直翅目的进化历史提供数据资源。     

短额负蝗线粒体基因组及其lrRNA和srRNA二级结构分析

采用长距PCR扩增及保守引物步移法测定并注释了短额负蝗的线粒体基因组全序列。结果表明,短额负蝗的线粒体基因组全长15558bp,A T含量为74.3%,37个基因位置与飞蝗的一致,基因间隔序列共计11处64bp,间隔长度从1～16bp不等;有15对基因间存在51bp重叠,重叠碱基数在1～8bp之间。13个蛋白质编码基因中找到6种可能的起始密码子,有12个基因在基因3'端能找到完全的TAA或TAG终止密码子,只有ND5基因终止密码子为不完整的TA。除tRNASer(AGN)外,其余21个tRNA基因的二级结构均属典型的三叶草结构。tRNASer(AGN)的DHU臂缺失,在相应的位置上只形成一个环。预测的lrRNA二级结构总共有6个结构域(结构域Ⅲ缺失),49个茎环结构。预测的srRNA的二级结构包含3个结构域,33个茎环结构。A T丰富区中存在一个被认为与复制及转录起始有关的Ploy(T)(T-stretch)结构。     

Complete mitochondrial genome of the Amur stickleback Pungitius sinensis (Gasterosteiformes, Gasterosteidae)

The complete mitochondrial genome was sequenced from the Amur stickleback Pungitius sinensis. The genome sequence was 16,581 bp in size, and the gene order and contents were identical with those of previously reported fish mitochondrial genomes. Of 13 protein-coding genes (PCGs), four genes (ND2, CO2, ND4, Cytb) had incomplete stop codons. The base composition of P. sinensis showed anti-G bias (9.53%) on the third position of PCGs.