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 mitochondrial genome of the dotted gizzard shad Konosirus punctatus (Teleostei, Clupeidae)

The complete mitochondrial genome of the dotted gizzard shad Konosirus punctatus (Teleostei, Clupeidae) has been determined. The entire sequence is 16,706 bp in length, with a gene content (13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 1 control region) and organization similar to that observed in most other vertebrates. Overall base composition of the light strand was represented as 25.8% of A, 29.0% of C, 25.1% of T and 20.1% of G. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Tandem repeat sequences were observed in the control region, indicating a useful marker for population genetic studies.     

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.     

Complete mitochondrial genome of Trypauchen vagina (Perciformes, Gobioidei)

The complete mitochondrial genome of Trypauchen vagina was determined first. The genome is 16,686 bp in length and consists 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 T. vagina is T 27.6%, C 27.6%, A 29.5%, and G 15.3%, with a slight A+T bias of 57.1%. In addition to the discrete and conserved sequence blocks, an incomplete tandem repeat unit is detected within the CR. This mitogenome sequence data would play an important role in population genetics and phylogenetic analysis of the Gobioidei.     

麦穗鱼线粒体基因组序列测定及分析

利用麦穗鱼Pseudorasbora parva和相关鱼类的部分线粒体基因序列,设计出2对长批引物和30对短批引物,采用基于长PCR的2次PCR扩增法测定并注释麦穗鱼线粒体基因组全序列。结果表明,麦穗鱼线粒体基因组长16600bp,A+T含量为58.9%,37个基因位置及组成与其它硬骨鱼一致,均由13个蛋白编码基因、22个tRNA、2个rRNA基因和1个控制区(D-loop)组成。其中L链仅含8个tRNA(Pro、T yr、Ser、Ala、Asn、Cys、Glu、Gln)及ND6基因,其余基因皆由H链编码。基因排列紧密,间隔序列共计13处64bp,长度从1～32bp不等;基因重叠区7处23bp,重叠碱基数在1～7bp之间。13个蛋白编码基因中,除COI起始密码子为GTG外,其余均以ATG为起始密码子;有8个基因(ND1、ND2、COI、ATP6、ATP8、ND4L、ND5、ND6)3’端有完全的TAA或TAG终止密码子,其它5个基因终止密码子为不完整的TA(ND3和ND4)或T(COⅡ,COⅢ,Cyt b)。除tRNASer(AGY)外,其余21个tRNA基因的二级结构均为典型的三叶草结构。预测的lrRNA二级结构共有6个结构域,53个茎环结构,srRNA二级结构包含43个茎环结构。控制区(D-loop)存在3个结构区:终止序列区(TAS)、中央保守区(CSB-F、CSB-D)和保守序列区(CSB-1、CSB-2、CSB-3),其中TAS与DNA复制终止相关,出现茎环结构。     

眼镜王蛇线粒体基因组全序列分析

参照近缘物种线粒体基因序列共设计和合成了8对引物, 结合Ex Taq-PCR、TA克隆和步移测序技术, 文章首次获得眼镜王蛇线粒体基因组全序列(GenBank登录号: EU_921899)。该基因组全长17 267 bp, 共编码13个蛋白、2个rRNA、23个tRNA-- 其中tRNA-Ile基因发生了复制, 属于一种新的蛇类物种线粒体基因排列模式, 另外还含有2个非编码的富含AT的控制区。除了8个tRNA基因和1个蛋白基因由L链编码外, 其余均由H链编码, 其中H链编码基因的A和T含量接近, 而L链上A的含量则明显高于T。基于21种蛇合并的“12S＋16S”rRNA基因序列的系统发育分析表明, 眼镜王蛇属与眼镜蛇属亲缘关系较近, 两者与环蛇属共同构成一个单系群。作为国内外眼镜王蛇线粒体基因组全序列的首次报道, 上述结果对于蛇类物种分子系统发育和进化研究具有重要意义。     

Complete mitochondrial genome of Oxya chinensis （Orthoptera, Acridoidea）

The complete sequence of Oxya chinensis （0. chinensis） mitochondrial genome is reported here. It is 15,443 bp in length and contains 75.9% A＋T. The protein-coding genes have a similar A＋T content （75.2%）. The initiation codon of the cytochrome oxidase subunit I gene in the mitochondrial genome of O. chinensis appears to be ATC, instead of the tetranucleotides that have been reported in Locusta migratoria （L migratoria） mitochondrial genome. The sizes of the large and small ribosomal RNA genes are 1319 and 850 bp, respectively. The transfer RNA genes have been modeled and showed strong resemblance to the dipteran transfer RNAs, and all anticodons are identical to those of dipteran. The A＋T-rich region is 562 bp, shorter than that of other known Orthoptera insects. The six conserved domains were identified within the A＋T-rich region by comparing its sequence with those of other grasshoppers. The result of phylogenetic analysis based on the dataset containing 12 concatenated protein sequences confirms the close relation-ship of O. chinensis with L migratoria.     

鳙的线粒体基因组核苷酸全序列分析

对采集自我国长江的鳙的线粒体DNA全序列进行了测定.结果表明,鳙的线粒体DNA全长为166221 bp,其碱基因组成为A=31.6%;C=27.1%;G=16.0%;T=25.3%,A+T含量为56.9%.鳙线粒体基因组的排列、结构和组成与其它鲤科鱼类相似,包括37个基因,即13个蛋白质编码基因,2个rRNA基因,22个tRNA基因和一个非编码控制区(D-loop).在13个蛋白编码基因中,除ND6由轻链编码外,其余12个基因均由重链编码.COI基因的起始密码子为GTG,而其它12个蛋白编码基因的起始密码子均为ATG.     

The complete mitochondrial genome of sable, Martes zibellina

The complete mitogenome sequence of the Sable (NC_011579) was determined using long PCR (Polymerase Chain Reaction). The genome was 16,523?bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The gene composition and order of which was similar to most other mammals. The overall base composition of the heavy strand in descending order is A (32.0%), C (27. 6%), T (25.8%) and G (14.7%). The base compositions present clearly the A-C skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Sable. This mitogenome sequence data would play an important role in phylogenetics and systematics of Martes zibellina.     

Mitochondrial genome sequence of the shining catfish (Pelteobagrus nitidus)

The complete mitochondrial DNA sequence of Pelteobagrus nitidus was determined using a PCR-based method. The total length of mitochondrial DNA is 16,532 bp. The contents of the P. nitidus mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region. Base composition of the entire genome is A 31.72%, T 26.92%, C 26.45%, and G 14.91%, with an A+T (58.64%) rich feature as that of other vertebrate mitochondrial genome.     

The complete mitochondrial genome of the Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae)

We determined the complete nucleotide sequence of the mitogenome from Chinese oak silkmoth, Antheraea pernyi (Lepidoptera: Saturniidae). The 15,566 bp circular genome contains atypical gene organization and order for lepidopteran mitogenomes. The mitogenome contains the lowest A+T content (80.16%) among the known lepidopteran mitogenome sequences. An unusual feature is the occurrence of more Ts than As, with a slightly negative AT skewness (−0.021), in the composition of the major genome strand. All protein-coding genes are initiated by ATN codons, except for cytochrome oxidase subunit I, which is proposed by the TTAG sequence as observed in other lepidopterans. All transfer RNAs (tRNAs) have a typical clover-leaf structure of mitochondrial tRNA, except for tRNA ^Ser (AGN) , the DHU arm of which could not form a stable stem-loop structure. Two aligned sequence blocks with a length of more than 50 bp and 90% of the sequence identity were identified in the A+T-rich region of the Saturniidae and Bombycoidae species.     

Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.     

暗纹东方鲀线粒体基因组核苷酸全序列测定与分析

以暗纹东方鲀(Takifugu fasciatus)肝的线粒体DNA为模板,参照红鳍东方鲀(T.rubripes)等近源鱼类的线粒体基因组DNA序列,设计合成14对特异引物,进行PCR扩增并测序,首次获得了暗纹东方鲀线粒体基因组全序列。结果表明,暗纹东方鲀线粒体基因组序列全长16 444 bp(GenBank登录号为GQ409967),A+T含量为55.8%,其mtDNA结构与其他脊椎动物相似,由22个tRNA基因、2个rRNA基因、13个蛋白质编码基因和1段819 bp非编码的控制区(D-loop)所组成。蛋白质基因除COⅠ和ND6的起始密码子为GTG、CCT以外,均为典型的起始密码子ATG。ND1、ATPase8、COⅢ、ND4L、ND5、Cyt b使用典型的终止密码子TAA,其他的使用不完全终止密码子。除ND6和tRNAGln、tRNAAla、tRNAAsn、tRNACys、tRNATyr、tRNASer、tRNAGlu、tRNAPro在L-链上编码之外,其余基因均在H-链编码。基因排列顺序与已测定的鲀类一致,这显示了鲀类线粒体基因排列顺序上的保守性。tRNA基因核苷酸长度为64～73nt,预测了22个tRNA基因的二级结构,均呈较为典型的三叶草状。基于19种鲀类mtDNA全序列构建的进化树表明,暗纹东方鲀与红鳍东方鲀、中华东方鲀(T.chinensis)聚成一个姊妹群。结果还支持东方鲀属鱼类为一单系类群。     

Structure and evolution of the mitochondrial genome of Exorista sorbillans: the Tachinidae (Diptera: Calyptratae) perspective

The first complete mitochondrial genome (mitogenome) of Tachinidae Exorista sorbillans (Diptera) is sequenced by PCR-based approach. The circular mitogenome is 14,960?bp long and has the representative mitochondrial gene (mt gene) organization and order of Diptera. All protein-coding sequences are initiated with ATN codon; however, the only exception is Cox I gene, which has a 4-bp ATCG putative start codon. Ten of the thirteen protein-coding genes have a complete termination codon (TAA), but the rest are seated on the H strand with incomplete codons. The mitogenome of E. sorbillans is biased toward A+T content at 78.4?%, and the strand-specific bias is in reflection of the third codon positions of mt genes, and their T/C ratios as strand indictor are higher on the H strand more than those on the L strand pointing at any strain of seven Diptera flies. The length of the A+T-rich region of E. sorbillans is 106?bp, including a tandem triple copies of a13-bp fragment. Compared to Haematobia irritans, E. sorbillans holds distant relationship with Drosophila. Phylogenetic topologies based on the amino acid sequences, supporting that E. sorbillans (Tachinidae) is clustered with strains of Calliphoridae and Oestridae, and superfamily Oestroidea are polyphyletic groups with Muscidae in a clade.     

Complete mitochondrial DNA sequence of the sea-firefly, Vargula hilgendorfii (Crustacea, Ostracoda) with duplicate control regions

The primary structure of the mitochondrial genome of the bioluminescent crustacean, Vargula hilgendorfii, the sea-firefly (Arthropoda, Crustacea, Ostracoda), has sequenced using the transposon Tn5. The genome (15,923 bp) contains the same 37 genes (two ribosomal RNAs, 22 transfer RNAs, and 13 protein-coding genes) found in other Arthropoda. Interestingly, duplicate control regions (fragments of 778 and 855 bp) and triplicate short repeat sequences (fragments of 49 bp) occur. The AT composition of the protein-coding genes is lower than the published complete mitochondrial genomes within the Arthropoda. For gene arrangement, 13 transfer RNA genes and two protein-coding genes have moved and inserted directly or inversely relative to the typical Arthropoda order.     

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.     

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 grouse locust Tetrix japonica (Insecta: Orthoptera: Tetrigoidea)

We have determined the complete mitochondrial genome of a species of grouse locust, Tetrix japonica. The total length of the T. japonica mitogenome is 15,128 bp with 75.57% A+T content. It consists of 13 protein-coding, 22 transfer RNA (tRNA), and 2 ribosomal RNA (rRNA) genes, and an A+T-rich region. The A+T-rich region was located between the small rRNA and tRNA-Ile genes and is 531 bp in length.     

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.     

大紫蛱蝶线粒体基因组全序列分析

通过PCR步移法对大紫蛱蝶Sasakia charonda coreana线粒体基因组全序列进行了测定和分析。分析结果表明:大紫蛱蝶线粒体基因组全长15233bp,包括13个蛋白编码基因、22个tRNA基因、2个rRNA基因以及长度为381bp的非编码区。A、T、C、G碱基含量分别为39.7%、40.2%、12.2%、7.9%。9个蛋白编码基因和14个tRNA基因在J链编码,其余4个蛋白编码基因和8个tRNA基因在N链编码,基因排列顺序与其它已知鳞翅目昆虫相同。13个蛋白编码基因中除COⅠ以CGA作为起始密码外,其余蛋白质基因均以ATN作为起始密码子,终止密码子多数为典型的TAA、TAG,只有COⅡ和ND4以单独的T作为终止密码子。在所测得的22个tRNA基因中,除tRNA Ser(AGN)缺少DHU臂外,其余tRNA均能形成典型的三叶草结构。与其它多数鳞翅目昆虫一样,大紫蛱蝶的非编码区序列中散在着一些长短不一的串联重复单元,在与其近缘物种非编码区的比较当中并未发现共同的保守序列区。