Mitochondrial genome of the American shad Alosa sapidissima

The complete mitochondrial genome of Alosa sapidissima has been determined. The total length of the mitogenome was 16,697 bp and had a gene content (13 protein-coding, 22 tRNAs and 2 rRNAs. Except for the seven tRNA and Nd6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 28.3% A, 24.8% T, 28.9% C, 17.9% G, with an AT content of 53.1%. The DNA sequence of Alosa. sapidissima shared 97.1, 93.9, 88.8 and 82.3% sequence identity with that of Alosa alosa, Alosa pseudoharengus. Molecular data here presented provide a useful toll for evolutionary as well as population genetic studied.     

Evidence of mitochondrial DNA clones of Siberian sturgeon, Acipenser baerii, within Russian sturgeon, Acipenser gueldenstaedtii, caught in the River Volga

Eleven of 34 sturgeons caught in the River Volga classified morphologically as Acipenser gueldenstaedtii were identified as Acipenser baerii from sequence analysis of the mitochondrial cytochrome- b gene. The Caspian Sea and its tributaries including the Volga are not native habitats of A. baerii . No A. baerii haplotype was observed in A. gueldenstaedtii from the Sea of Azov or the South Caspian Sea. Genetic contamination of A. gueldenstaedtii with A. baerii or A. baerii hybrids has occurred in the Volga. Crosses and backcrosses of these specimens with native A. gueldenstaedtii resulted in the loss of the morphological diagnostic A. baerii features. These findings are of special concern for conservation and management programmes, as well as for specimen identification for caviar trading control.     

Mitochondrial tRNAs as light strand replication origins: Similarity between anticodon loops and the loop of the light strand replication origin predicts initiation of DNA replication

Stem-loop hairpins formed by mitochondrial light strand replication origins (OL) and by heavy strand DNA coding for tRNAs that form OL-like structures initiate mitochondrial replication. The loops are recognized by one of the two active sites of the vertebrate mitochondrial gamma polymerase, which are homologuous to the active sites of class II amino-acyl tRNA synthetases. Therefore, the polymerase site recognizing the OL loop could recognize tRNA anticodon loops and sequence similarity between anticodon and OL loops should predict initiation of DNA replication at tRNAs. Strengths of genome-wide deamination gradients starting at tRNA genes estimate extents by which replication starts at that tRNA. Deaminations (A→G and C→T) occur proportionally to time spent single stranded by heavy strand DNA during mitochondrial light strand replication. Results show that deamination gradients starting at tRNAs are proportional to sequence similarity between OL and tRNA loops: most for anticodon-, least D-, intermediate for TψC-loops, paralleling tRNA synthetase recognition interactions with these tRNA loops. Structural and sequence similarities with regular OLs predict OL function, loop similarity is dominant in most tRNAs. Analyses of sequence similarity and structure independently substantiate that DNA sequences coding for mitochondrial tRNAs sometimes function as alternative OLs. Pathogenic mutations in anticodon loops increase similarity with the human OL loop, non-pathogenic polymorphisms do not. Similarity/homology alignment hypotheses are experimentally testable in this system.     

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.     

Nucleotide sequence of the mitochondrial genes coding for tRNAglyGGR and tRNAvalGUR.

Yeast mitochondrial DNA-pBR322 recombinant DNA molecules known to contain tRNA genes from a tRNA rich region of the yeast genome were used as a source of DNA for restriction mapping and tRNA gene sequence analysis. We report here restriction maps of two segments of yeast mitochondrial DNA and the sequence of mitochondrial genes coding for tRNAglyGGR and tRNAvalGUR. Both genes are flanked by A + T rich DNA and neither has an intervening sequence nor codes for a 3' CCA end. The tRNA structures deduced from the genes have the usual cloverleaf structures and invariant nucleotides. This combination of DNA sequencing and restriction mapping has enabled us to determine that the tRNAvalGUR and a previously sequenced tRNA, the tRNApheUUY are transcribed from the same strand of DNA.     

Mitochondrial replication origin stability and propensity of adjacent tRNA genes to form putative replication origins increase developmental stability in lizards

Secondary structure stability of mitochondrial origins of light-strand replication (OL) presumably reduces delayed formation of light-strand initiating replication forks on the heavy strand. Delayed replication initiation prolongs single strandedness of the heavy strand. More mutations accumulate during the prolonged time spent single stranded. Presumably, delayed replication initiation and excess mutations affect mitochondrial biochemical processes and ultimately morphological outcomes of development at the whole-organism level. This predicts that developmental stability increases with OL secondary structure stability and with formation of OL-like structures by the five tRNA genes flanking recognized OLs. Stable OLs and high percentages of OL-resembling secondary structures of adjacent tRNA genes (predicted by Mfold) correlate positively with developmental stability in three lizard families (Anguidae, Amphisbaenidae, and Polychrotidae). Accounting for effects of the regular OL, Sfold-predicted OL-like propensity of the entire tRNA gene cluster (not of individual genes) correlates with increased developmental stability in Anguidae, also across the entire free-energy range of Boltzmann's distribution of secondary structures. In the fossorial Amphisbaenidae, the OL-like structure-forming propensity of tRNA genes correlates positively with developmental stability for the distribution's sub-optimally stable regions, and negatively for its optimally stable regions, suggesting the thermoregulated functioning of OL vs. flanking tRNA genes as replication origins. Results for polychrotid tRNA genes are intermediate. Anguid tRNA genes possibly function in addition to the regular OL. Mitochondrial tRNA genes may thus frequently acquire and lose the alternative OL function, without sequence (gene) duplication and loss of their primary function.     

Phylogenetic relationships of the North American sturgeons (order Acipenseriformes) based on mitochondrial DNA sequences

The evolutionary relationships of the extant species within the order Acipenseriformes are not well understood. Nucleotide sequences of four mitochondrial genes (12S rRNA, COII, tRNA(Phe), and tRNA(Asp) genes) in North American sturgeon and paddlefish were examined to reconstruct a phylogeny. Analysis of the combined gene sequences suggests a basal placement of the paddlefish with regard to the sturgeons. Nucleotide sequences of all four genes for the three Scaphirhynchus species were identical. The position of Scaphirhynchus based on our data was uncertain. Within the genus Acipenser, the two Acipenser oxyrinchus subspecies were very similar in sequence and found to be basal to the remaining Acipenser species examined. Based on our data, Acipenser transmontanus and Acipenser medirostris were sister taxa, as were Acipenser fulvescens and Acipenser brevirostrum. Comparison of our results with hypotheses of sturgeon relationships proposed by previous authors is presented. The sequence data presented here are phylogenetically useful and provide a solid foundation of genetic information for the North American Acipenseriformes that can be expanded to include Eurasian species to provide a global picture of sturgeon evolution.     

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 Plateau zokor Myospalax baileyi

Plateau zokors Myospalax baileyi are subterranean rodents and endemic to the cold and hypoxic (2800-4300 m above sea level) climate of the farm, prairie, alpine prairie, and meadow habitats across the Tibetan plateau. The complete mitochondrial (mt) genome of M. baileyi has been determined. Our results showed that the total length of the mitogenome was 16,351 bp, and had a gene content of 13 protein coding, 22 tRNAs and 2 rRNAs. Except for the seven tRNA and Nd6 genes, all other mt genes are encoded on the heavy strand. The overall base composition of the heavy strand is 33.65% A, 29.65% T, 24.42% C, and 12.28% G, with an AT content of 63.3%.     

Characterization of mitochondrial genome of sea cucumber <Emphasis Type="Italic">Stichopus horrens</Emphasis>: A novel gene arrangement in Holothuroidea

The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens (Holothuroidea: Stichopodidae: Stichopus) is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene (nad6) and five tRNA genes (tRNA ^Ser(UCN) , tRNA ^Gln , tRNA ^Ala , tRNA ^Val , tRNA ^Asp ) which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases (AT skew=0.025; GC skew=−0.188). A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes except nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu (16.29%), Ser (10.34%) and Phe (8.37%). All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.     

Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes)

The complete mitogenome sequence of a vulnerable species Onychostoma lini was determined using polymerase chain reaction and directly sequenced with primer walking method. The complete mitogenome was 16,595?bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene order and composition of O. lini was similar to most other fishes. The descending order of the base composition on heavy strand was 31.6% A, 27.9% C, 24.6% T, and 15.9% G, with a relatively lower level of G and a slight AT bias of 56.2%. The codon usage followed the typical vertebrate mitochondrial pattern (ATG or GTG for start codon and TAA or TAG for stop codon). The complete mitogenome sequence of O. lini provides fundamental data for further conversation genetics and captive breeding studies on this species.     

Transfer RNA genes in the cap-oxil region of yeast mitochondrial DNA.

A cytoplasmic "petite" (rho-) clone of Saccharomyces cerevisiae has been isolated and found through DNA sequencing to contain the genes for cysteine, histidine, leucine, glutamine, lysine, arginine, and glycine tRNAs. This clone, designated DS502, has a tandemly repeated 3.5 kb segment of the wild type genome from 0.7 to 5.6 units. All the tRNA genes are transcribed from the same strand of DNA in the direction cap to oxil. The mitochondrial DNA segment of DS502 fills a sequence gap that existed between the histidine and lysine tRNAs. The new sequence data has made it possible to assign accurate map positions to all the tRNA genes in the cap-oxil span of the yeast mitochondrial genome. A detailed restriction map of the region from 0 to 17 map units along with the locations of 16 tRNA genes have been determined. The secondary structures of the leucine and glutamine tRNAs have been deduced from their gene sequences. The leucine tRNA exhibits 64% sequence homology to an E. coli leucine tRNA.     

Molecular phylogeny of Acipenserinae and black caviar species identification.

The first phylogenetic tree for the Acipenserinae based on the combined sequence data for fragments of three mitochondrial genes, the cytochrome b (650 bp) gene, 12S (150 bp) and 16S (350 bp) rRNA genes is described. Three general conclusions are inferred from the tree: 1) Scaphirhynchus albus is the sister-species of all Acipenser and Huso species; 2) The two species of Huso are embedded within the genus Acipenser. Therefore, the genus Huso is not a separate taxonomic unit; and 3) There are three main clades within Acipenser: (a) A. sturio-A. oxyrinchus, (b) A. schrenckii-A. transmontanus, and (c) all Ponto-Caspian species plus A. dabryanus and A. brevirostrum. A method based on the identification of diagnostic nucleotide positions in the cytochrome b gene was developed and used to survey the United States and European caviar markets. The survey of 95 lots of caviar obtained at the American market suggests that in December 1995 and April 1996 17% of the designations made by caviar suppliers were mislabeled with respect to species identification. In December of 1996, this figure jumped to 32%. The main commercially harvested species (Huso huso, A. stellatus, A. gueldenstaedtii, A. schrenckii, and H. dauricus), as well as A. nudiventris, A. persicus, and A. baerii are threatened due to the increased demand of the international caviar market.     

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.     

The complete mitochondrial genome of Chinese rare minnow, Gobiocypris rarus (Teleostei: Cypriniformes)

The Chinese rare minnow, Gobiocypris rarus, which is endemic to China, is an attractive aquatic laboratory animal in China. In the present study, the complete mitogenome sequence of G. rarus has been determined using long polymerase chain reaction (PCR) method. It was 16,601 bp in length and contained 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region, the gene composition and order of which are similar to most other vertebrates. Except for eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The overall base composition of the heavy strand is 29.5% A, 27.6% T, 25.7% C, and 17.2% G, with a slight AT bias of 57.1%. There are 10 regions of gene overlap totaling 27 bp and 13 intergenic spacer regions totaling 63 bp. The mitogenome sequence of G. rarus could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the whole mitogenomic data.     

Two ancient bacterial endosymbionts have coevolved with the planthoppers (Insecta: Hemiptera: Fulgoroidea)

Background

Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.

Results

We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.

Conclusion

The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.     

草鱼(Ctenopharyngodon idellus)线粒体DNA控制区及其两侧tRNA基因的克隆与结构分析

动物线粒体ＤＮＡ控制区是线粒体基因组复制与基因表达的最主要的调控区．采用杂交和测序的方法对草鱼线粒体ＤＮＡ控制区进行定位、克隆并测定了控制区及其旁侧的ｔＲＮＡＰｈｅ、ｒＲＮＡＰｒｏ和ｒＲＮＡＴｈｒ三个基因的序列,与多种脊椎动物的相应序列进行了比较,并进行了结构分析．草鱼线粒体控制区全长９２７ｂｐ,含有与酵母和爪蟾线粒体启动子相似的序列,其ＣＳＢⅠ、ＣＳＢⅡ和ＣＳＢⅢ序列与其他几种动物的ＣＳＢ比较相当保守,ＴＡＳ与其回文基序可形成稳定的茎环结构,成为Ｈ－链复制的终止信号．草鱼线粒体ｔＲＮＡＰｈｅ、ｔＲＮＡＰｒｏ和ｔＲＮＡＴｈｒ可折叠成三叶草形二级结构,其基因具有许多不同于细胞质ｔＲＮＡ基因的结构特点,可能反映了线粒体ｔＲＮＡ与线粒体核糖体具有不寻常的作用方式     

Organization of tRNA and rRNA genes in N. crassa mitochondria: intervening sequence in the large rRNA gene and strand distribution of the RNA genes.

Through analysis of cloned fragments of N. crassa mitochondrial DNA, we have derived a physical map for the region of the mitochondrial genome which encodes the ribosomal RNAs and most of the tRNAs. We have located RNA genes on this map by hybridization of purified 32P end-labeled RNA probes, and our findings are as follows. First, the gene for the large ribosomal RNA contains an intervening sequence of approximately 2000 bp. Second, the genes for the small and large ribosomal RNAs are not adjacent, as previously reported, and the region between them contains a number of tRNA genes, including that for the mitochondrial tRNATyr, which is located close to the small rRNA gene on the same strand of the mitochondrial DNA. Third, there is a second cluster of tRNA genes on the mitochondrial DNA following the large ribosomal RNA gene, but there is no evidence for the presence of tRNA genes in the intervening sequence of the large ribosomal RNA. Fourth, hybridization of labeled ribosomal and transfer RNAs to the separated strands of a cloned 16 kbp DNA fragment covering this region indicates that the two ribosomal RNAs and most, if not all, of the mitochondrial tRNAs are encoded on one strand of the mitochondrial DNA.