Complete mitochondrial genome of the boreal digging frog Kaloula borealis (Anura, Microhylidae)

We sequenced the complete mitochondrial genome from the boreal digging frog Kaloula borealis. The genome sequence was 17,173 bp in size, and the gene order and contents were identical to those of previously reported amphibian mitochondrial genomes. Of 13 protein-coding genes (PCGs), 5 genes (CO2, ATPase 6, CO3, ND3, and ND4) had incomplete stop codons. Also ND1 gene used GTG as a start codon, while CO1 and ND5 genes used AGG as a stop codon. The base composition of K. borealis mitogenome showed a strong anti-G bias (6.11%) on the 3rd position of PCGs.     

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.     

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。     

Complete mitochondrial genome sequence of the Korean water deer Hydropotes inermis argyropus (Cervidae, Capreolinae)

The complete mitochondrial genome sequence of Hydropotes inermis argyropus consists of 13 protein-coding, 22 tRNA, and two rRNA genes, and 1 control region (CR). Three overlaps among the 13 protein-coding genes were found: ATP8/ATP6, ND4L/ND4, and ND5/ND6. The CR was located between the tRNA-Pro and tRNA-Phe genes and is 928 bp in length. The typical conserved domains, such as TAS and CSB, were identified in the CR.     

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 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.     

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.     

Complete mitochondrial genome of the Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae) and related phylogenetic analyses

In this study, we sequenced the complete mitochondrial genome of Teinopalpus aureus guangxiensis (Lepidoptera: Papilionidae), which is considered as an endemic species in China. It is listed as a vulnerable species by International Union for Conservation of Nature and Natural Resources Red List and also a first class endangered species in China. The complete mtDNA from T. aureus guangxiensis was 15,235 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. The T. aureus guangxiensis genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species. All PCGs of T. aureus guangxiensis mitogenome start with a typical ATN codon and terminate in the common stop codon TAA, except that ND1 gene uses TTA, ND3 gene uses ATT, and ND4 and ND4L gene use TAA. The phylogenetic relationships were reconstructed with the concatenated sequences of the 13 PCGs of the mitochondrial genome, and phylogenetic results confirmed that Nymphalidae, Lycaenidae, Papilionidae, Pieridae are monophyletic clades.     

Mitochondrial genome of <Emphasis Type="Italic">Pteronotus personatus</Emphasis> (Chiroptera: Mormoopidae): comparison with selected bats and phylogenetic considerations

We described the complete mitochondrial genome (mitogenome) of the Wagner’s mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes. The order of protein-coding and rRNA genes was highly conserved in all mitogenomes. All protein-coding genes started with an ATG codon, except for ND2, ND3, and ND5, which initiated with ATA, and terminated with the typical stop codon TAA/TAG or the codon AGA. Phylogenetic trees constructed using Maximum Parsimony, Maximum Likelihood, and Bayesian inference methods showed an identical topology and indicated the monophyly of different families of bats (Mormoopidae, Phyllostomidae, Vespertilionidae, Rhinolophidae, and Pteropopidae) and the existence of two major clades corresponding to the suborders Yangochiroptera and Yinpterochiroptera. The mitogenome sequence provided here will be useful for further phylogenetic analyses and population genetic studies in mormoopid bats.     

Mitochondrial genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis

We determined the complete mitochondrial (mt) genome sequences of the striped field mice Apodemus agrarius coreae and Apodemus agrarius chejuensis. The mt genomes of A. a. coreae and A. a. chejuensis are 16,260 and 16,261 base pairs in length, respectively. The general features of the 13 protein-coding genes of the two species are similar to those of other rodents. The TAG termination codon for NADH dehydrogenase subunit (ND) 3 is unique to Apodemus in the Muroidea. The L-strand replication origin has the potential to form a stable stem-loop structure. Within the control region, a termination-associated sequence and several conserved sequence blocks were observed. The diversity of the 13 protein-coding genes, 2 rRNAs, and 1 control region between the two species ranged between 0.005 (ATP8) and 0.027 (ND4L).     

大豆蚜线粒体基因组序列测定与分析

采用LongPCR和引物步移法测得大豆蚜Aphis glycines Matsumura线粒体基因组约90%的序列,并与蚜总科Aphidoidea已报道的3种蚜虫进行了比较。结果表明:已测得的序列长度为13696bp,AT含量为83.3%;蛋白质编码基因起始密码子都为ATN,COI、ND4、CYTB、ND2使用不完整终止密码子T,其余都使用常见终止密码子TAA;15个tRNA基因除tRNA-W外都能折叠成典型的三叶草二级结构。比较大豆蚜、豌豆蚜Acyrthosiphon pisum(Harris)、麦二叉蚜Schizaphis graminum(Rondani)和葡萄根瘤蚜Daktulosphaira vitifoliae(Fitch)的线粒体基因组,结果表明4个种均具有后生动物线粒体基因组中常见的基因,基因顺序与假想昆虫祖先的排列方式相同,但豌豆蚜包含3个tRNA-M;蛋白质编码基因的起始密码子都为ATN,除葡萄根瘤蚜外,其他3种蚜虫的COⅠ、ND4使用不完整终止密码子T;tRNA-W的二级结构中都存在TψC臂中"茎"的结构缺失,只有环的结构;而蛋白质编码基因使用最频繁的氨基酸略有不同,大豆蚜为Leu,豌豆蚜和麦二叉蚜为Ile;大豆蚜和麦二叉蚜的ND4/ND4L都存在7bp的重叠序列,而豌豆蚜和葡萄根瘤蚜没有发现此现象。     

中华雏蝗（Chorthippus chinensis Tarb）线粒体基因组分析

采用Lon-PCR扩增线粒体全基因组和保守引物步移法结合克隆方法测定并拼接获得了中华雏蝗（Chorthippus chinensis Tarb）线粒体基因组全序列．序列的注释和分析结果表 明,中华雏蝗线粒体基因组序列全长15 599 bp,共有13个编码蛋白质基因、22个tRNA基因、2个rRNA基因和1个A+T富集区．基因顺序与非洲飞蝗（Locusta migratoria）相同,也发生了2个 tRNA Asp(D)和tRNALys(K)的倒置．13个编码蛋白质基因都使用了ATN作为起始密码子．除ND1以TAG和ND5的终止密码子为不完全的T外,其余11个编码蛋白质基因的终止密码子都为完整的TAA．6种直翅类昆虫13个蛋白质的氨基酸序列的联合数据集构建的系统树与形态分类系统一致,中华雏蝗与非洲飞蝗为姐妹群,并与东方蝼蛄构成一单系群．     

褶纹冠蚌线粒体基因组全序列分析

采用LA-PCR(Long amplification polymerase chain reaction )扩增方法首次获得褶纹冠蚌(Cristaria plicata)线粒体基因组全序列。分析表明:序列全长15 712 bp, 包括13个蛋白质基因、22个tRNA基因、2个rRNA基因和26个长度为2~328 bp的非编码区。A、T、C、G碱基组成分别为36.54%、27.22%、23.22%、13.02%。大部分基因在L链编码, 其中ND3~ND5、ND4L、COI~COIII、ATP6、ATP8、tRNA^Asp和tRNA^His在H链编码。基因排列与同科的射线佩饰真珠蚌(Lampsilis ornata)一致, 与三角帆蚌(Hyriopsis cumingii)在COII和12S rRNA之间存在差异。13个蛋白质基因具有I(AUU、AUC)、V(GUG)、M (AUA、AUG)3种起始密码子, 除ND2终止密码子为不完整的T, 其余基因均为典型的UAA或UAG。22个tRNA中, 除tRNA^Thr、tRNA^Lys、tRNA^Ser(UCN)、tRNA^Asp、tRNA^Arg、tRNA^Tyr和tRNA^Met之外, 其他15个tRNA都具有典型三叶草结构。与其他淡水双壳贝类一样, 褶纹冠蚌具有ATP8基因, 该基因可能与细胞质的渗透压平衡有关。     

云斑车蝗线粒体基因组全序列测定与分析

采用长距 PCR 扩增及保守引物步移法并结合克隆测序测定并注释了云斑车蝗 Gastrimargus marmoratus （Thunberg）的线粒体基因组全序列。结果表明：云斑车蝗线粒体基因组全序列为15 904 bp（GenBank登录号为EU527334）,A+T含量略高于非洲飞蝗Locusta migratoria,为76.04%,包括13个蛋白质编码基因,22个tRNA 基因,2个rRNA基因和一段1 057 bp的A+T富集区。蛋白质基因的起始密码子中,除COⅠ和ND5为TTG以外,均为昆虫典型的起始密码子ATN。ND5基因使用了不完全终止密码子T,其余基因均为典型的TAA或TAG。预测了22个tRNA基因的二级结构,发现tRNA^Ser（AGN）缺少DHU臂, tRNA^Ser（UGY）的反密码子环上有9个碱基。预测了云斑车蝗12S和16S rRNA二级结构,分别包括3个结构域30个茎环和6个结构域44个茎环。A+T富集区含有3个串联重复序列。     

Mitochondrial genome of the Guizhou snub-nosed monkey (Rhinopithecus brelichi)

The Guizhou snub-nosed monkey (Rhinopithecus brelichi) is an endangered species which is endemic to a small region in the fanjing mountain national nature reserve in Guizhou province, China. In this study, we determined the complete mitochondrial genome of R. brelichi. The results showed that the total length of the mitogenome was 16,548 bp and contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region. Overall base composition of the complete mitochondrial DNA was 32.35% A, 29.28% T, 25.54% C and 12.83% G. All the genes in R. brelichi were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.     

Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships

For the first step toward resolution of the higher-level relationships of the order Aulopiformes (Teleostei: Eurypterygii) using longer DNA sequences, we determined the complete mitochondrial DNA sequence for Aulopus japonicus (Aulopodidae). The entire genome was purified by gene amplification using a long PCR technique, and the products were subsequently used as templates for PCR with 63 fish-versatile and 3 species-specific primers that amplify contiguous, overlapping segments of the entire genome. Direct sequencing of the PCR products demonstrated that the genome (16 653 base pairs [bp]) contained the same 37 mitochondrial genes (2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes) as found in other vertebrates, with the gene order identical to that in typical vertebrates. Maximum-parsimony analysis using nucleotide sequences from the concatenated 12 protein-coding genes (no third codon positions and excluding the ND6 gene) plus 22 tRNA genes (stem regions only) from eight teleosts placed A. japonicus in a reasonable phylogenetic position; those from individual protein-coding genes and the concatenated 22 tRNA genes alone, however, did not reproduce the expected phylogeny with few exceptions, probably owing to insufficient phylogenetic information in these smaller data sets. This result suggests that further taxonomic sampling and sequencing efforts may clarify limits and intra- and interrelationships of this morphologically and ecologically diverse group of fishes using mitochondrial genomic (mitogenomic) data. Received: August 31, 2000 / Revised: December 20, 2000 / Accepted: January 23, 2001     

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.     

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。     

Maxicircle (mitochondrial) genome sequence (partial) of Leishmania major: gene content, arrangement and composition compared with Leishmania tarentolae

We report 8420 bp of DNA sequence data from the maxicircle (mitochondrial) genome of Leishmania major (MHOM/SU/73/5ASKH), a much larger portion of this genome than has been reported previously from any Leishmania species infecting humans. This region contains 10 partial and complete genes: 5 protein-encoding genes (COII, COIII, ND1, ND7 and Cyt b); two ribosomal RNA subunits (12S and 9S) and three unidentified open reading frames (MURF1, MURF4 (ATPase6) and MURF5), as in the lizard-infecting species L. tarentolae. The genes from L. major exhibit 85-87% identity with those of L. tarentolae at the nucleotide level and 71-94% identity at the amino acid level. Most differences between sequences from the two species are transversions. The gene order and arrangement within the maxicircle of L. major are similar to those in L. tarentolae, but base composition and codon usage differ between the species. Codons assigned for initiation for protein-coding genes available for comparison are similar in five genes in the two species. Pre-editing was identified in some of the protein-coding genes. Short intergenic non-coding regions are also present in L. major as they are in L. tarentolae. Intergenic regions between 9S rRNA and MURF5, MURF1 and ND1 genes are G+C rich and considered to be extensive RNA editing regions. The RNA editing process is likely to be conserved in similar pattern in L. major as in L. tarentolae.