Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis(McLachlan)(Insecta:Megaloptera:Corydalidae)

The complete mitochondrial genome of Acanthacorydalis orientalis(McLachlan)was determined and analyzed(GenBank accession number:KF840564).This paper represents the first mitochondrial(mt) genome of the dobsonfly genus Acanthacorydalis.The mt genome is a typical circular DNA of 15 753 bp composed of 37 genes with an A+T content of 76.7%.It has an ancestral gene arrangement of the insect mt genomes.Eleven of the 13 PCGs start with codon ATT and ATG,while several exceptions such as ATA and TTG respectively for atpS and nad\ are also present.Five protein-coding genes end with a single T,while others have a termination codon of TAA or TAG.Most tRNAs are folded into the typical clover-leaf structure except for the trnS 1 whose dihydrouridine arm was a simple loop.The secondary structure of rrnl consists of five structural domains and 50 helices,while the rrns includes three domains and 34 helices.The control region has a stretches of Ts with a length of 22 bp but lacks obvious tandem repeat region.Both Bayesian inference and maximum likelihood(ML) analyses,based on all 13 protein-coding genes and two rRNA genes of the mt genomes,confirm the monophyly of Corydalinae and suggest that Acanthacorydalis,together with Corydalus,which is an endemic dobsonfly genus from the New World,belong to a monophyletic lineage.     

Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications

In this study, we analyse the evolutionary dynamics and phylogenetic implications of gene order rearrangements in five newly sequenced mitochondrial (mt) genomes and four published mt genomes of isopod crustaceans. The sequence coverage is nearly complete for four of the five newly sequenced species, with only the control region and some tRNA genes missing, while in Janira maculosa only two thirds of the genome could be determined. Mitochondrial gene order in isopods seems to be more plastic than that in other crustacean lineages, making all nine known mt gene orders different. Especially the asellote Janira is characterized by many autapomorphies. The following inferred ancestral isopod mt gene order exists slightly modified in modern isopods: nad1, tnrL1, rrnS, control region, trnS1, cob, trnT, nad5, trnF. We consider the inferred gene translocation events leading to gene rearrangements as valuable characters in phylogenetic analyses. In this first study covering major isopod lineages, potential apomorphies were identified, e.g., a shared relative position of trnR in Valvifera. We also report one of the first findings of homoplasy in mitochondrial gene order, namely a shared relative position of trnV in unrelated isopod lineages. In addition to increased taxon sampling secondary structure, modification in tRNAs and GC-skew inversion may be potentially fruitful subjects for future mt genome studies in a phylogenetic context.     

The First Mitochondrial Genomes of Antlion (Neuroptera: Myrmeleontidae) and Split-footed Lacewing (Neuroptera: Nymphidae), with Phylogenetic Implications of Myrmeleontiformia

In the holometabolous insect order Neuroptera (lacewings), the cosmopolitan Myrmeleontidae (antlions) are the most species-rich family, while the closely related Nymphidae (split-footed lacewings) are a small endemic family from the Australian-Malesian region. Both families belong to the suborder Myrmeleontiformia, within which controversial hypotheses on the interfamilial phylogenetic relationships exist. Herein, we describe the complete mitochondrial (mt) genomes of an antlion (Myrmeleon immanis Walker, 1853) and a split-footed lacewing (Nymphes myrmeleonoides Leach, 1814), representing the first mt genomes for both families. These mt genomes are relatively small (respectively composed of 15,799 and 15,713 bp) compared to other lacewing mt genomes, and comprise 37 genes (13 protein coding genes, 22 tRNA genes and two rRNA genes). The arrangement of these two mt genomes is the same as in most derived Neuroptera mt genomes previously sequenced, specifically with a translocation of trnC. The start codons of all PCGs are started by ATN, with an exception of cox1, which is ACG in the M. immanis mt genome and TCG in N. myrmeleonoides. All tRNA genes have a typical clover-leaf structure of mitochondrial tRNA, with the exception of trnS1(AGN). The secondary structures of rrnL and rrnS are similar with those proposed insects and the domain I contains nine helices rather than eight helices, which is common within Neuroptera. A phylogenetic analysis based on the mt genomic data for all Neuropterida sequenced thus far, supports the monophyly of Myrmeleontiformia and the sister relationship between Ascalaphidae and Myrmeleontidae.     

The mitochondrial genome sequence analysis of Ophidascaris baylisi from the Burmese python (Python molurus bivittatus)

Ophidascaris species are parasitic roundworms that inhabit the python gut, resulting in severe granulomatous lesions or even death. However, the classification and nomenclature of these roundworms are still controversial. Our study aims to identify a snake roundworm from the Burmese python (Python molurus bivittatus) and analyze the mitochondrial genome. We identified this roundworm as Ophidascaris baylisi based on the morphology and cytochrome c oxidase subunit I (cox1) sequence. Ophidascaris baylisi complete mitochondrial genome was 14,784 bp in length, consisting of two non-coding regions and 36 mitochondrial genes (12 protein-coding genes, 22 tRNA genes, and two rRNA genes). The protein-coding genes used TTG, ATG, ATT, or TTA as start codons and TAG, TAA, or T as stop codons. All tRNA genes showed a TV-loop structure, except trnS1^AGN and trnS2^UCN revealed a D-loop structure. The mitochondrial large ribosomal subunit 16S (rrnL) and small ribosomal subunit 12S (rrnS) were 956 bp and 700 bp long, respectively. Phylogenetic analysis based on O. baylisi mitochondrial protein-coding genes demonstrated that O. baylisi clustered with the family Ascarididae members and was most closely related to Ophidascaris wangi. These results may enhance the nematode mitochondrial genome database and provide valuable molecular markers for further research on the taxonomy, phylogeny, and genetic relationships of Ophidascaris nematodes.     

The complete mitochondrial genome of yarrowia lipolytica

We here report the complete nucleotide sequence of the 47.9 kb mitochondrial (mt) genome from the obligate aerobic yeast Yarrowia lipolytica. It encodes, all on the same strand, seven subunits of NADH: ubiquinone oxidoreductase (ND1-6, ND4L), apocytochrome b (COB), three subunits of cytochrome oxidase (COX1, 2, 3), three subunits of ATP synthetase (ATP6, 8 and 9), small and large ribosomal RNAs and an incomplete set of tRNAs. The Y. lipolytica mt genome is very similar to the Hansenula wingei mt genome, as judged from blocks of conserved gene order and from sequence homology. The extra DNA in the Y. lipolytica mt genome consists of 17 group 1 introns and stretches of A+Trich sequence, interspersed with potentially transposable GC clusters. The usual mould mt genetic code is used. Interestingly, there is no tRNA able to read CGN (arginine) codons. CGN codons could not be found in exonic open reading frames, whereas they do occur in intronic open reading frames. However, several of the intronic open reading frames have accumulated mutations and must be regarded as pseudogenes. We propose that this may have been triggered by the presence of untranslatable CGN codons. This sequence is available under EMBL Accession No. AJ307410.     

The complete mitogenome of the Chinese bush cricket, Gampsocleis gratiosa （Orthoptera： Tettigonioidea）

The complete mitochondrial genome (mitogenome) of Gampsocleis gratiosa was determined. The 15, 929 bp in the size of G. gratiosa mitogenome contains a typical gene content, base composition, and codon usage found in metazoan. All 13 protein coding genes (PCGs) of the G. gratiosa mitogenome start with a typical ATN codon. The usual termination codons (TAA and TAG) were found from 10 PCGs. However, the atp6, nad4, and nad5 had incomplete termination codon (T). The anticodons of all tRNAs are identical to those observed in Drosophila yakuba and Locusta migratoria, and can be folded in the form of a typical clover leaf structure except for trnS (AGN). The secondary structure of trnS (AGN) was drawn according with the Steinberg-Cedergren tertiary structure. The A T content (67.4%) of the A T-rich region is relatively lower among the mitogenome regions, in contrast, it usually contains the highest A T content for most insects. Two isolated sequence repeat regions (202 bp) were found in the A T-rich region with mapping and secondary structure information.     

残锷线蛱蝶线粒体基因组全序列及其系统学意义(英文)

对残锷线蛱蝶(Parathymasulpitia)(鳞翅目:蛱蝶科)线粒体基因组全序列进行了测定。结果表明:残锷线蛱蝶线粒体基因组全序列全长为15268bp,除了在trnS1(AGN)和trnE基因之间有一段121bp长的基因间隔外,其基因的排列顺序及排列方向与大多数已测鳞翅目物种基本一致。在蛋白质编码基因中,除cox1以CGA作为其起始密码子之外,其余12个蛋白质编码基因都以标准的ATN作为起始密码子。此外,除nad4基因以单独的T为终止密码子,其余12个蛋白质编码基因都以TAA结尾。除trnS1(AGN)缺少DHU臂之外,22个tRNA基因都显示典型的三叶草形二级结构。除A+T富集区外的非编码序列中,线粒体基因组共含有11个基因间隔区。其中,最长的一个121bp的基因间隔区位于trnS1(AGN)和trnE之间,其A+T含量高达100%。另外,和其他鳞翅目物种一样,在其A+T富集区的3’端有一段长达18bp的poly-T结构。A+T富集区内部没有明显的小卫星样多拷贝重复序列,而含有一些微卫星样的重复结构。本研究基于13种蛋白编码基因序列的组合数据,用最大似然法和贝叶斯法对蛱蝶科几个主要亚科间共9个代表物种间的系统发生关系进行了分析。结果表明,本研究的结果与前人的分子系统学研究结论基本吻合(其中,线蛱蝶亚科和釉蛱蝶亚科互为姐妹群),而与形态学的研究结论不一致。     

Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae)

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.     

The mitochondrial genome of the plant bug Apolygus lucorum （Hemiptera： Miridae）＂ Presently known as the smallest in Heteroptera

The complete mitochondrial （mt） genome of the plant bug, Apolygus lucorum, an important cotton pest, has been sequenced and annotated in this study. The entire circular genome is 14 768 bp in size and represents the smallest in presently known heteropteran mt genomes. The mt genome is encoding for two ribosomal RNA （rRNA） genes, 22 transfer RNA （tRNA） genes, 13 protein coding genes and a control region, and the order, content, codon usage and base organization show similarity to a great extent to the hypothetical ancestral model. All protein coding genes use standard initiation codons ATN. Conventional stop codons TAA and TAG have been assigned to the most protein coding genes; however, COIII, ND4 and ND5 genes show incomplete terminator signal （T）. All tRNA genes possess the typical clover leaf structure, but the dihydrouridine arm of tRNAser（A6N） only forms a simple loop. Secondary structure models of rRNA genes are generally in accordance with the former models, although some differences exist in certain parts. Three intergenic spacers have never been found in sequenced mt genomes of Heteroptera. The phylogenetic study based on protein coding genes is largely congruent with previous phylogenetic work. Both Bayesian inference and maximum likelihood analyses highly support the sister relationship ofA. lucorum and Lygus lineolaris, and Miridae presents a sister position to Anthocoridae.     

Highly conserved gene arrangement of the mitochondrial genomes of 23 Plasmodium species

Mitochondrial (mt) genomes from diverse phylogenetic groups vary considerably in size, structure and organization. The genus Plasmodium, the causative agent of malaria, has the smallest mt genome in the form of a tandemly repeated, linear element of 6 kb. The Plasmodium mt genome encodes only three protein genes (cox1, cox3 and cob) and large- and small-subunit ribosomal RNA (rRNA) genes, which are highly fragmented with 19 identified rRNA pieces. The complete mt genome sequences of 21 Plasmodium species have been published but a thorough investigation of the arrangement of rRNA gene fragments has been undertaken for only Plasmodium falciparum, the human malaria parasite. In this study, we determined the arrangement of mt rRNA gene fragments in 23 Plasmodium species, including two newly determined mt genome sequences from P. gallinaceum and P. vinckei vinckei, as well as Leucocytozoon caulleryi, an outgroup of Plasmodium. Comparative analysis reveals complete conservation of the arrangement of rRNA gene fragments in the mt genomes of all the 23 Plasmodium species and L. caulleryi. Surveys for a new rRNA gene fragment using hidden Markov models enriched with recent mt genome sequences led us to suggest the mtR-26 sequence as a novel candidate LSU rRNA fragment in the mt genomes of the 24 species. Additionally, we found 22-25 bp-inverted repeat sequences, which may be involved in the generation of lineage-specific mt genome arrangements after divergence from a common ancestor of the genera Eimeria and Plasmodium/Leucocytozoon.     

基于太平洋甲胁虱裂化线粒体基因组推测甲胁虱属祖先线粒体核型

[目的]动物典型的单一染色体线粒体基因组在甲胁虱属Hoplopleura已裂化成多个线粒体微环染色体.本研究旨在通过测定太平洋甲胁虱Hoplopleura pacifica的线粒体基因组来推测甲胁虱属祖先线粒体核型.[方法]利用Illumina HiSeq X Ten高通量测序技术对太平洋甲胁虱裂化线粒体基因组进行测定...     

Contracaecum rudolphii B: gene content, arrangement and composition of its complete mitochondrial genome compared with Anisakis simplex s.l

In the present study, we sequenced the complete mt genome (14,022 bp) of parasitic nematode Contracaecum rudolphii B and its structure and organization compared with Anisakis simplex s.l. The mt genome of C. rudolphii B is slightly longer than that of A. simplex s.l. (13,916 bp). C. rudolphii B mt genome is circular, and consists of 36 genes, including 12 genes for proteins, 2 genes for rRNA and 22 genes for tRNA. This genome contains a high A+T (70.5%) content. The mt gene order for C. rudolphii B is the same as those for A. simplex s.l., but it is distinctly different from other nematodes compared. The start codons inferred in the mt genome of C. rudolphii B are TTG and ATT. Six protein-coding genes use TAA as a stop codon whereas five genes use T and one genes use TAG as a termination codon. This pattern of codon usage reflects the strong bias for A and T in the mt genome of C. rudolphii B. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes, with three different computational algorithms (Bayes, ML and MP), all revealed distinct groups with high statistical support, indicating that C. rudolphii B and A. simplex s.l. is distinct but closely related species. These data provide additional novel mtDNA markers for studying the molecular epidemiology and population genetics of the C. rudolphii B, and should have implications for the molecular diagnosis, prevention and control of anisakidosis in humans and animals.     

入侵害虫甘薯凹胫跳甲的鉴定及线粒体基因组分析

【目的】基于形态学鉴定和分子生物学技术确认甘薯凹胫跳甲Chaetocnema confinis是否入侵中国大陆,测定甘薯凹胫跳甲线粒体基因组序列,分析基因组结构及其系统发育关系。【方法】应用显微镜观察从广东不同地点采集的甘薯凹胫跳甲成虫的形态特征,并扩增cox1基因DNA序列进行分子鉴定;利用Illumina MiSeq测序平台对甘薯凹胫跳甲线粒体基因组进行测序、拼装、注释和特征分析;基于亲缘关系相近种属的线粒体基因组序列进行共线性分析和构建系统发育树,分析基因重排和系统发育关系。【结果】形态和分子鉴定结果表明大陆甘薯上发现的跳甲为甘薯凹胫跳甲。甘薯凹胫跳甲线粒体基因组序列大小为15 685 bp,包括有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;这37个基因之间排列紧凑,间隔总长度101 bp,排列顺序与模式昆虫Drosophila yakuba线粒体基因排列顺序相同。甘薯凹胫跳甲线粒体基因组A+T含量为77.3%,具有明显的AT偏向性。13个蛋白质编码基因的起始密码子均为ATN。在22个tRNA基因中除trnS1的DHU臂缺失,trnD, trnG, trnN和trnT的二级结构中缺少TψC环外,其余17个都能形成典型的三叶草式二级结构,另trnK的反密码子突变为UUU,trnS1的反密码子突变为UCU。甘薯凹胫跳甲的控制区片段长度仅有60 bp,是目前已报道的昆虫线粒体基因组中最短的控制区。基于线粒体基因组的系统发育分析表明,甘薯凹胫跳甲与跳甲亚科(Alticinae)黄曲条跳甲Phyllotreta striolata亲缘关系最近。【结论】甘薯凹胫跳甲已经入侵到中国大陆。本研究获得了甘薯凹胫跳甲的线粒体基因组序列,为防控甘薯凹胫跳甲和分析叶甲科(Chrysomelidae)各种属间的系统发育关系奠定了基础。     

The mitogenome of Paphia euglypta (Bivalvia: Veneridae) and comparative mitogenomic analyses of three venerids

Extraordinary variation has been found in mitochondrial (mt) genome inheritance, gene content and arrangement among bivalves. However, only few bivalve mt genomes have been comparatively analyzed to infer their evolutionary scenarios. In this study, the complete mt genome of the venerid Paphia euglypta (Bivalvia: Veneridae) was firstly studied and, secondly, it was comparatively analyzed with other venerids (e.g., Venerupis philippinarum and Meretrix petechialis) to better understand the mt genome evolution within a family. Though several common features such as the AT content, codon usage of protein-coding genes, and AT/GC skew are shared by the three venerids, a high level of variability is observed in genome size, gene content, gene order, arrangements and primary sequence of nucleotides or amino acids. Most of the gene rearrangement can be explained by the "tandem duplication and random loss" model. From the observed rearrangement patterns, we speculate that block interchange between adjacent genes may be common in the evolution of mt genomes in venerids. Furthermore, this study presents several new findings in mt genome annotation of V. philippinarum and M. petechialis, and hence we have reannotated the genome of these two species as: (1) the ORF of the formerly annotated cox2 gene in V. philippinarum is deduced by using a truncated "T" codon and a second cox2 gene is identified; (2) the trnS-AGN gene is identified and marked in the mt genome of both venerids. Thus, this study demonstrated a high variability of mt genomes in the Veneridae, and showed the importance of comparative mt genome analysis to interpret the evolution of the bivalve mt genome.     

Synthesis of a modified gene encoding human ornithine transcarbamylase for expression in mammalian mitochondrial and universal translation systems: a novel approach towards correction of a genetic defect

The mitochondrial (mt) genome is a potential means of gene delivery to human cells for therapeutic expression. As a first step towards this, we have synthesised a gene coding for mature human ornithine transcarbamylase (OTC) by recursive PCR using 18 oligodeoxyribonucleotides, each 70–80 nucleotides in length, with codons which should allow translation in accordance with both mammalian mt and universal codon usage. Flanking mt DNA sequences were incorporated which are designed to facilitate site-specific cloning into the mt genome. Expression of this human gene in Escherichia coli leads to an immunoreactive OTC product of the correct size and N-terminal amino-acid sequence, but which forms inclusion bodies and lacks enzymatic activity     

小长蝽线粒体基因组全序列测定与长蝽总科系统发育分析

为了解小长蝽Nysius ericae(Schilling)线粒体基因组结构及长蝽总科的分子系统发育关系。本试验采用Illumina MiSeq测序平台对小长蝽线粒体基因进行测序,对基因组序列进行拼装、注释和特征分析,利用最大似然法和贝叶斯法构建基于12种长蝽总科昆虫线粒体全基因组核苷酸序列的系统发育树。小长蝽线粒体基因组全长为16 330 bp(GenBank登录号：MW465654),基因组包括13个蛋白编码基因(PCGs),22个tRNA基因,2个rRNA基因和1段非编码控制区。11个蛋白质编码基因的起始密码子为典型的ATN;cox1,nad4l的起始密码子为TTG。cob的终止密码子为TAG,其余蛋白编码基因的终止密码子为TAA。只有trnS1缺少DHU臂,其余tRNA基因均能形成典型的三叶草结构。12种长蝽总科昆虫线粒体全基因组序列构建的昆虫系统发育树结果显示,小长蝽与Nysius plebeius具有更近的亲缘关系,且与传统形态学分类基本一致。小长蝽线粒体基因组符合长蝽总科线粒体基因组的一般特征。结果表明小长蝽与N.plebeius的亲缘关系更近。     

Evidence for maternal inheritance of mitochondrial DNA in allotetraploid.

The complete mitochondrial DNA (mtDNA) sequences of the allotetraploid and red crucian carp were determined in this paper. We compared the complete mtDNA sequences between the allotetraploid and its female parent red crucian carp, and between the allotetraploid and its male parent common carp. The results indicated that the complete mtDNA nucleotide identity (99.7%) between the allotetraploid and its female parent red crucian carp was higher than that (89.0%) between the allotetraploid and its male parent common carp. Moreover, the analysis on the start and stop codons, overlaps and spacers, and phylogeny of the mt genomes indicated the genetic relationship between the allotetraploid and its female parent red crucian carp was closer than that between the allotetraploid and its male parent common carp. Our results indicated that the allotetraploid mt genome was strictly maternally inherited. Through maternal inheritance, the mt genome in the F(11) allotetraploid displayed extremely high similarity to that in the female parent red crucian carp after 11 generations (from F(1) to F(11) hybrids). Such results indicated that the F(11) allotetraploid possessed the stable inheritance characteristic. Thus the tetraploid stocks possessed the good base to form a new tetraploid species in the future. Since the establishment of the new tetraploid stocks has the great significance in analyzing evolutionary theory of vertebrate and in improving aquaculture industry, analysis of the mt genome and the elucidation of the variation of the mt genome in the allotetraploid and its parents proved that it was a useful genetic marker to monitor the variations in the progeny of the crosses.     

The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora,Camaenidae): the first complete sequence in the family Camaenidae

The complete mitochondrial (mt) genome of the snail Camaena cicatricosa (Müller, 1774) has been sequenced and annotated in this study. The entire circular genome is 13,843 bp in size and represents the first camaenid mt genome, with content of 31.9%A, 37.9%T, 13.5%C and 16.7%G. Gene content, codon usage and base organization show similarity to a great extent to the sequenced mt genome from Stylommatophora, whereas, gene order is different from them, especially the positions of tRNA^Cys, tRNA^Phe, COII, tRNA^Asp, tRNA^Gly, tRNA^His and tRNA^Trp. All protein coding genes use standard initiation codons ATN except for COII with GTG as start signal. Conventional stop codons TAA and TAG have been assigned to all protein coding genes. All tRNA genes possess the typical clover leaf structure, but the TψC arm of tRNA^Asp and dihydrouridine arm of tRNA^Ser(AGN) only form a simple loop. Shorter intergenic spacers have been found in this mt genome. Phylogenetic study based on protein coding genes shows close relationship of Camaenidae and Bradybaenidae. The presented phylogeny is consistent with the monophyly of Stylommatophora.