Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans

The terrestrial flatworm Microplana scharffi (Geoplanidae, Microplaninae): mitochondrial genome, phylogenetic proximity to the Bipaliinae and genes related to regeneration

A genome skimming approach of sequencing was undertaken on a subfamily of terrestrial flatworms that had been neglected in genomic studies until now, namely the Microplaninae as represented here by Microplana scharffi. A single run of short-read sequencing enabled retrieval of the complete mitogenome, the two paralogous versions of the 18S gene, the elongation factor gene EF1α, plus two genes involved in the regeneration process, namely those coding for ß-CATENIN-1 and adenomatous polyposis coli (APC). The 15,297 bp mitogenome lacks a functional tRNA-Ala and has a mandatory alternative TTG start codon in its cox1 gene. The multiprotein phylogeny, inferred from mitogenome proteins, positions M. scharffi as sister-group to the Bipaliinae with maximum support, although the organisation of the mitogenomes shows features previously never observed among Bipaliinae, such as the conserved 32 bp overlap between ND4 and ND4L. Similarly to what has been observed in recent publications on other species of Geoplanidae, the two types of 18S genes display strongly different coverages and are only 90.57% identical. Additionally, alien DNA was identified in the pool of contigs in the form of the complete mitochondrial genome of Lumbricus rubellus, confirming previous observations on the feeding habits of M. scharffi.

The complete mitochondrial genome of the pirate butterfly Catacroptera cloanthe (Stoll, 1781) (Insecta: Lepidoptera: Nymphalidae: Kallimini)

The pirate butterfly Catacroptera cloanthe (Stoll, 1781) (Nymphalidae: Kallimini) is a monotypic genus of butterfly that occupies grassland and savanna habitats in Sub-Saharan Africa, and exhibits seasonal variation. Genome skimming by Illumina sequencing allowed the assembly of a 78.8% AT-rich complete circular mitogenome of 15,204 bp from C. cloanthe. The mitogenome has a typical butterfly gene order consisting of 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Catacroptera cloanthe COX1 begins with an atypical CGA start codon, while COX2, ND3, ND4, and ND5 end with incomplete T or TA stop codons, completed by the addition of the poly-A tail during mRNA processing. Bayesian phylogenetic reconstruction placed Catacroptera cloanthe as sister to Mallika jacksoni in the monophyletic tribe Kallimini, which was consistent with previous phylogenetic hypotheses.

Phylogenetic analysis of the complete mitochondrial genome of the Japanese peacock butterfly Aglais io geisha (Stichel 1907) (Insecta: Lepidoptera: Nymphalidae)

The peacock butterfly Aglais io (Linnaeus, 1758) (Nymphalidae: Nymphalinae: Nymphalini) is a colorful and charismatic flagship butterfly species whose range spans from the British Isles and Europe through temperate Asia and the Far East. In Europe, it has been used as a model species for studying the effects of GMO maize pollen on caterpillar growth and survivorship. The Japanese subspecies, Aglais io geisha (Stichel 1907), is not as well studied as its European counterpart. Genome skimming by Illumina sequencing allowed the assembly of a complete circular mitochondrial genome (mitogenome) of 15,252 bp from A. io geisha consisting of 80.6% AT nucleotides, 13 protein-coding genes, 22 tRNAs, two rRNAs, and a control region in the gene order typical of butterfly species. Aglais io geisha COX1 gene features an atypical start codon (CGA) while COX1, COX2, CYTB, ND1, ND3, ND4, and ND5 display incomplete stop codons finished by the addition of 3' A residues to the mRNA. Bayesian phylogenetic reconstruction places A. io geisha within a clade with European A. io mitogenomes in the tribe Nymphalini, which is consistent with previous phylogenetic hypotheses.

Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms

The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.

Genetic Evolution and Implications of the Mitochondrial Genomes of Two Newly Identified Taenia spp. in Rodents From Qinghai-Tibet Plateau

The larva of Taeniidae species can infect a wide range of mammals, causing major public health and food safety hazards worldwide. The Qinghai-Tibet Plateau (QTP), a biodiversity hotspot, is home to many species of rodents, which act as the critical intermediate hosts of many Taeniidae species. In this study, we identified two new larvae of Taenia spp., named T. caixuepengi and T. tianguangfui, collected from the plateau pika (Ochotona curzoniae) and the Qinghai vole (Neodon fuscus), respectively, in QTP, and their mitochondrial genomes were sequenced and annotated. Phylogenetic trees based on the mitochondrial genome showed that T. caixuepengi has the closest genetic relationship with T. pisiformis, while T. tianguangfui was contained in a monophyletic group with T. crassiceps, T. twitchelli, and T. martis. Biogeographic scenarios analysis based on split time speculated that the speciation of T. caixuepengi (∼5.49 Mya) is due to host switching caused by the evolution of its intermediate host. Although the reason for T. tianguangfui (∼13.11 Mya) speciation is not clear, the analysis suggests that it should be infective to a variety of other rodents following the evolutionary divergence time of its intermediate host and the range of intermediate hosts of its genetically close species. This study confirms the species diversity of Taeniidae in the QTP, and speculates that the uplift of the QTP has not only a profound impact on the biodiversity of plants and animals, but also that of parasites.

Extensive gene rearrangements in the mitogenomes of congeneric annelid species and insights on the evolutionary history of the genus Ophryotrocha

BACKGROUND

Annelids are one the most speciose and ecologically diverse groups of metazoans. Although a significant effort has been recently invested in sequencing genomes of a wide array of metazoans, many orders and families within the phylum Annelida are still represented by a single specimen of a single species. The genus of interstitial annelids Ophryotrocha (Dorvilleidae, Errantia, Annelida) is among these neglected groups, despite its extensive use as model organism in numerous studies on the evolution of life history, physiological and ecological traits. To compensate for the paucity of genomic information in this genus, we here obtained novel complete mitochondrial genomes of six Ophryotrocha species using next generation sequencing. In addition, we investigated the evolution of the reproductive mode in the Ophryotrocha genus using a phylogeny based on two mitochondrial markers (COXI and 16S rDNA) and one nuclear fragment (Histone H3).

RESULTS

Surprisingly, gene order was not conserved among the six Ophryotrocha species investigated, and varied greatly as compared to those found in other annelid species within the class Errantia. The mitogenome phylogeny for the six Ophryotrocha species displayed a separation of gonochoric and hermaphroditic species. However, this separation was not observed in the phylogeny based on the COX1, 16S rDNA, and H3 genes. Parsimony and Bayesian ancestral trait reconstruction indicated that gonochorism was the most parsimonious ancestral reproductive mode in Ophryotrocha spp.

CONCLUSIONS

Our results highlight the remarkably high level of gene order variation among congeneric species, even in annelids. This encourages the need for additional mitogenome sequencing of annelid taxa in order to properly understand its mtDNA evolution, high biodiversity and phylogenetic relationships.

The complete mitochondrial genome and phylogenetic analysis of the European map butterfly Araschnia levana (Insecta: Lepidoptera: Nymphalidae)

The European map butterfly Araschnia levana (Linnaeus, 1758) is a species showing extreme seasonal polyphenism. The complete 15,207 bp circular A. levana mitogenome consisting of 81.6% AT nucleotides, was assembled by Illumina genome skimming. It includes 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and a control region in the typical butterfly gene order. Araschnia levana COX1 features an atypical CGA start codon and ATP6, COX1, COX2, ND1, ND3, and ND4 have incomplete stop codons completed by 3′A residues added to the mRNA. Phylogenetic reconstruction places A. levana as a basal lineage within tribe Nymphalini, consistent with previous phylogenetic hypotheses.

Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis)

Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

The mitochondrial genome of Dipetalonema gracile from a squirrel monkey in China

Dipetalonema gracile is a common parasite in squirrel monkeys (Saimiri sciureus), which can cause malnutrition and progressive wasting of the host, and lead to death in the case of massive infection. This study aimed to identify a suspected D. gracile worm from a dead squirrel monkey by means of molecular biology, and to amplify its complete mitochondrial genome by polymerase chain reaction (PCR) and sequence analysis. The results identified the worm as D. gracile, and the full length of its complete mitochondrial genome was 13,584 bp, which contained 22 tRNA genes, 12 protein-coding genes, two rRNA genes, one AT-rich region and one small non-coding region. The nucleotide composition included A (16.89%), G (20.19%), T (56.22%) and C (6.70%), among which A + T = 73.11%. The 12 protein-coding genes used TTG and ATT as start codons, and TAG and TAA as stop codons. Among the 22 tRNA genes, only trnS1AGN and trnS2UCN exhibited the TΨC-loop structure, while the other 20 tRNAs showed the TV-loop structure. The rrnL (986 bp) and rrnS (685 bp) genes were single-stranded and conserved in secondary structure. This study has enriched the mitochondrial gene database of Dipetalonema and laid a scientific basis for further study on classification, and genetic and evolutionary relationships of Dipetalonema nematodes.

Evolutionary progression of mitochondrial gene rearrangements and phylogenetic relationships in Strigidae (Strigiformes)

The bird mitogenome is generally considered to have a conservative genome size, consistent gene content, and similar gene order. As more mitogenomes are sequenced, mitochondrial (mt) gene rearrangements have been frequently identified among diverse birds. Within two genera (Bubo and Strix) of typical owls (Strigidae, Strigiformes), the rearrangement of the mt gene has been a subject of debate. In the current study, we first sequenced the whole mitogenomes of S. uralensis and B. scandiaca and resequenced the entire mitogenome of B. bubo. By combining our data with previously sequenced mitogenomes in Strigidae, we examined the mt gene rearrangements in the family and attempted to reconstruct the evolutionary progression of these rearrangements. The mitogenomes were then used to review the phylogenies of Strigidae. Most mitogenomes exhibited the ancestral gene order (A) in Strigidae. The ancestral gene order in the previously published mitogenome of B. bubo was found to be incorrect. We determined the mt gene order (the duplicate tRNA^Thr-CR, B) and discovered two additional mt gene orders (the duplicate tRNA^Glu-L-CR and CR, C and D) in the Bubo and Strix genera. Gene order B was likely derived from A by a tandem duplication of the region spanning from tRNA^Thr to CR. The other two modified gene orders, C and D, were likely derived from B by further degenerations or deletions of one copy of specific duplicated genes. We also preliminarily reconstructed the evolutionary progression of mt gene rearrangements and discussed maintenance of the duplicated CR in the genera. Additionally, the phylogenetic trees based on the mitogenomes supported the division of Strigidae into three subfamilies: Ninoxinae + (Surniinae + Striginae). Within the Striginae clade, the four genera formed a phylogenetic relationship: Otus + (Asio + (Bubo + Strix)). This suggests that Otus firstly diverges in their evolutionary history, and Bubo and Strix show a close relationship. B. bubo, B. blakistoni and B. scandiaca form a clade should be considered members of the same genus. The well-supported topology obtained in our Bayesian inference (BI) and maximum likelihood (ML) analyses of Strigid mitogenomes suggests that these genomes are informative for constructing phylogenetic relationships.

Comparative analysis of Ancylostoma ceylanicum mitochondrial genome with other Ancylostoma species

Ancylostoma ceylanicum may inhabit the small intestine of canids, felids and humans, can pose a potential risk to public health. This study is the first time to amplify complete mitochondrial genome sequence of A. ceylanicum from dog and to compare it with Ancylostoma tubaeforme, Ancylostoma duodenale and Ancylostoma caninum. The results showed that the complete mitochondrial genome of A. ceylanicum was 13,660 bp in length, including 12 protein-coding genes, 2 rRNA genes and 22 tRNA genes and 3 non-coding regions (AT-rich region, SNCR and LNCR). Its mtDNA was the shortest, biased toward A and T at base composition, and higher than other three Ancylostoma species at total AT content. Its nad5 and nad6 genes used TTG and ATT as initiation codons, while other three Ancylostoma species used ATT and GTG or ATG. The 22 tRNA genes were different in length among four Ancylostoma species, but their anticodons were the same. Among 12 protein-coding genes, the cox1 gene was the lowest at AT content and minimum at Ka/Ks while the nad2 gene was the opposite. The phylogenetic tree showed that in the lineage of Ancylostoma, A. ceylanicum occurred on a branch external to other three Ancylostoma species, and A. caninum and A. tubaeforme had closer phylogenetic relationship than A. duodenale. This study not only enhances the mitochondrial genome database of Ancylostomatidae nematodes, but also provides new data for further phylogenetic studies among Ancylostomatidae nematodes.

The complete mitochondrial genome of parasitic nematode Camallanus cotti: extreme discontinuity in the rate of mitogenomic architecture evolution within the Chromadorea class

BACKGROUND

Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallanina suborder (Dracunculoidea superfamily) exhibited a unique gene order, the other objective of this research was to study the evolution of mitochondrial architecture in the Spirurida order. Thus, we sequenced the complete mitogenome of the Camallanus cotti fish parasite and conducted structural and phylogenomic comparative analyses with all available Spirurida mitogenomes.

RESULTS

The mitogenome is exceptionally large (17,901 bp) among the Chromadorea and, with 46 (pseudo-) genes, exhibits a unique architecture among nematodes. Six protein-coding genes (PCGs) and six tRNAs are duplicated. An additional (seventh) tRNA (Trp) was probably duplicated by the remolding of tRNA-Ser2 (missing). Two pairs of these duplicated PCGs might be functional; three were incomplete and one contained stop codons. Apart from Ala and Asp, all other duplicated tRNAs are conserved and probably functional. Only 19 unique tRNAs were found. Phylogenomic analysis included Gnathostomatidae (Spirurina) in the Camallanina suborder.

CONCLUSIONS

Within the Nematoda, comparable PCG duplications were observed only in the enoplean Mermithidae family, but those result from mitochondrial recombination, whereas characteristics of the studied mitogenome suggest that likely rearrangement mechanisms are either a series of duplications, transpositions and random loss events, or duplication, fragmentation and subsequent reassembly of the mitogenome. We put forward a hypothesis that the evolution of mitogenomic architecture is extremely discontinuous, and that once a long period of stasis in gene order and content has been punctuated by a rearrangement event, such a destabilised mitogenome is much more likely to undergo subsequent rearrangement events, resulting in an exponentially accelerated evolutionary rate of mitogenomic rearrangements. Implications of this model are particularly important for the application of gene order similarity as an additive source of phylogenetic information. Chromadorean nematodes, and particularly Camallanina clade (with C. cotti as an example of extremely accelerated rate of rearrangements), might be a good model to further study this discontinuity in the dynamics of mitogenomic evolution.

The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment

The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep‐sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein‐coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon‐like noncanonical open reading frames (ORFs), and a control region‐like (CR‐like) element. All of the mitochondrial genes were coded by the same strand (the H‐strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep‐sea environment.

Systematic analysis of plant mitochondrial and chloroplast small RNAs suggests organelle-specific mRNA stabilization mechanisms

Land plant organellar genomes encode a small number of genes, many of which are essential for respiration and photosynthesis. Organellar gene expression is characterized by a multitude of RNA processing events that lead to stable, translatable transcripts. RNA binding proteins (RBPs), have been shown to generate and protect transcript termini and eventually induce the accumulation of short RNA footprints. We applied knowledge of such RBP-derived footprints to develop software (sRNA miner) that enables identification of RBP footprints, or other clusters of small RNAs, in organelles. We used this tool to determine mitochondrial and chloroplast cosRNAs (clustered organellar sRNAs) in Arabidopsis. We found that in mitochondria, cosRNAs coincide with transcript 3'-ends, but are largely absent from 5'-ends. In chloroplasts this bias is absent, suggesting a different mode of 5' processing, possibly owing to different sets of RNases. Furthermore, we identified a large number of cosRNAs that represent silenced insertions of mitochondrial DNA in the nuclear genome of Arabidopsis. Steady-state RNA analyses demonstrate that cosRNAs display differential accumulation during development. Finally, we demonstrate that the chloroplast RBP PPR10 associates in vivo with its cognate cosRNA. A hypothetical role of cosRNAs as competitors of mRNAs for PPR proteins is discussed.

The mitochondrial genome of Paragonimus westermani (Kerbert, 1878), the Indian isolate of the lung fluke representative of the family Paragonimidae (Trematoda)

Among helminth parasites, Paragonimus (zoonotic lung fluke) gains considerable importance from veterinary and medical points of view because of its diversified effect on its host. Nearly fifty species of Paragonimus have been described across the globe. It is estimated that more than 20 million people are infected worldwide and the best known species is Paragonimus westermani, whose type locality is probably India and which infects millions of people in Asia causing disease symptoms that mimic tuberculosis. Human infections occur through eating raw crustaceans containing metacercarie or ingestion of uncooked meat of paratenic hosts such as pigs. Though the fluke is known to parasitize a wide range of mammalian hosts representing as many as eleven families, the status of its prevalence, host range, pathogenic manifestations and its possible survivors in nature from where the human beings contract the infection is not well documented in India. We took advantage of the whole genome sequence data for P. westermani, generated by Next Generation Sequencing, and its comparison with the existing data for the P. westermani for comparative mt DNA phylogenomic analyses. Specific primers were designed for the 12 protein coding genes with the aid of existing P. westermani mtDNA as the reference. The Ion torrent next generation sequencing platform was harnessed to completely sequence the mitochondrial genome, and applied innovative approaches to bioinformatically assemble and annotate it. A strategic PCR primer design utilizing the whole genome sequence data from P. westermani enabled us to design specific primers capable of amplifying all regions of the mitochondrial genome from P. westermani. Assembly of NGS data from libraries enriched in mtDNA sequence by PCR gave rise to a total of 11 contigs spanning the entire 14.7 kb mt DNA sequence of P. westermani available at NCBI. We conducted gap-filling by traditional Sanger sequencing to fill in the gaps. Annotation of non-protein coding genes successfully identified tRNA regions for the 24 tRNAs coded in mtDNA and 12 protein coding genes. Bayesian phylogenetic analyses of the concatenated protein coding genes placed P. westermani within the family Opisthorchida. The complete mtDNA sequence of P. westermani is 15,004 base pairs long; the lung fluke is the major etiological agent of paragonimiasis and the first Indian representative for the family Paragonimidae to be fully sequenced that provides important genetic markers for ecological, population and biogeographical studies and molecular diagnostic of digeneans that cause trematodiases.

Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species

BACKGROUND

Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes.

RESULTS

The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia.

CONCLUSIONS

The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species.

Complete mitochondrial genome of Locusta migratoria migratoria (Orthoptera: Oedipodidae): three tRNA-like sequences on the N-strand

The complete 16053 bp mitochondrial genome (mitogenome) sequence of Locusta migratoria migratoria has been determined. This mitogenome contains the base compositional biases and codon usage typical of metazoans, and the RSCU values indicate a negative correlation with the C and G contents in codon. The orientation and gene order of the L. migratoria migratoria is identical to Locusta migratoria migratoiodes. An unusual feature of the L. migratoria migratoria mitogenome is the presence of three tRNA-like structures on the N-strand: one tRNA(Ile)-like and two tRNA(Leu(CUN))-like sequences. The tRNA-like sequences have proper folding structures and anticodons sequences. Two repeated DNA sequences, Rpt I and Rpt II, were found in the A+T-rich region of the L. migratoria migratoria mitogenome. Both repeated sequences have various features. In the 5' region of Rpt I, a 51 bp fragment is localized in the srRNA gene; and there are two tandemly sub-repeated DNA sequences (sub-Rpts), Rpt 1-4, within Rpt I and Rpt II. One stem-loop structure on the N-strand that may be involved in the N-strand replication initiation was found in the A+T-rich region.

Complete mitochondrial genomes of two cockroaches, Blattella germanica and Periplaneta americana, and the phylogenetic position of termites

The mitochondrial genomes are one of the most information-rich markers in phylogenetics. The relationships within superorder Dictyoptera have been debated in the literature. However, the closely related termites (Isoptera) are retained as unranked taxon within the order Blattaria (cockroaches). In this work, we sequenced the complete mitogenomes of two cockroaches, reconstructed the molecular phylogeny and attempted to infer the phylogenetic position of termites in Blattaria more reliably. The complete mtDNA nucleotide sequences of the peridomestic American cockroach (Periplaneta americana L.) and the domestic German cockroach (Blattella germanica L.) are 15,025 and 15,584 bp in size, respectively. The genome shares the gene order and orientation with previously known Blattaria mitogenomes. Most tRNAs could be folded into the typical cloverleaf secondary structure, but the tRNA-Ser (AGN) of P. americana appears to be missing the dihydrouridine arm. Using nucleotide and amino acid sequences as phylogenetic markers, we proposed that termites should be treated as a superfamily (Termitoidea) of cockroaches. We suggested that Polyphagoidea was the sister group of Termitoidea in Blattaria and supported that the suborder Caelifera is more closely related to the Phasmatodea than to the suborder Ensifera of Orthoptera.

The morphology and genetic characterization of Iheringascaris goai n. sp. (Nematoda: Raphidascarididae) from the intestine of the silver whiting and spotted catfish off the central west coast of India

In this study a new species of nematode, Iheringascaris goai n. sp., is reported from two fish hosts, including silver whiting, Sillago sihama, and spotted catfish, Arius maculatus, caught off the Central West Coast of India at Goa. The new species can be differentiated morphologically from I. inquies, the most closely related species collected from cohabiting marine fish. The distinguishing characteristics are distinct cuticular striations, a unilateral excretory system, the presence of dentigerous ridges on the inner margin of the lips and the ratio of oesophagus to body length. In males, the ratio of spicules to body length is higher and the number of pre-anal papillae is less in comparison to those in I. inquies. In addition, the tail curves ventrad in males, while in females, the vulva is post-equatorial. The sequence alignment of 18S rDNA and cytochrome c oxidase subunit I with sequences of known species selected from the same superfamily shows a significant difference. The morphological and molecular differences reported here can, therefore, be used to assign the specimen to a new species.

A comparative analysis of mitochondrial genomes in Orthoptera (Arthropoda: Insecta) and genome descriptions of three grasshopper species

The complete sequences of mitochondrial DNA (mtDNA) from the three new grasshopper species, Euchorthippus fusigeniculatus, Mekongiana xiangchengensis and Mekongiella xizangensis, consisting of 15772 bp, 15567 bp, and 15885 bp, respectively, were analyzed and compared to mtDNAs from other 19 Orthoptera species obtained from GenBank. The three mitochondrial genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes. and an A+T-rich region in the same order as those of the other analyzed caeliferan species, but different from those of the ensiferan species by the rearrangement of trnD and trnK. The putative initiation codon for the cox1 gene is ATC in E. fusigeniculatus, CTG in M. xiangchengensis and CCG in M. xizangensis. All secondary structures of tRNA-Ser((AGN)) in the three species lack a DHU arm. In this study, we stressed the comparative analysis of the stem-loop secondary structure in A+T-rich region of all Orthoptera species available to date, and report new findings which may facilitate further investigation and better understanding of this secondary structure. Finally, we undertook a phylogenetic study of all Orthoptera species available from GenBank to date based on three different datasets using parsimony, maximum likelihood, and Bayesian inference. Our result showed that protein-coding genes (PCG) and amino acid sequences (PCG_PROT) provided good resolution of higher-level relationships within the Orthoptera, whereas ribosomal RNA genes (RIBO) perform poorly under different optimality criteria.

Complete set of mitochondrial pan-edited mRNAs in Leishmania mexicana amazonensis LV78

Editing of mRNA transcribed from the mitochondrial cryptogenes ND8 (G1), ND9 (G2), G3, G4, ND3 (G5), RPS12 (G6) was investigated in Leishmania mexicana amazonensis, strain LV78, by amplification of the cDNA, cloning and sequencing. For each of these genes, extensively and partially edited transcripts were found to be relatively abundant compared to the respective pre-edited molecules. Moreover, the editing patterns observed in a majority of transcripts of each gene were consistent among themselves which allowed for inferring consensus editing sequences. The open reading frames contained in the consensus sequences were predicted to encode polypeptides that were highly similar to their counterparts in other species of Trypanosomatidae. Several kinetoplast DNA minicircles from this species available in the public domain were found to contain genes for guide RNAs which mediate editing of some of the mRNAs. The results indicate that the investigated strain of L. m. amazonensis has preserved its full editing capacity in spite of the long-term maintenance in culture. This property differs drastically from the other Leishmania species which lost some or all of the G1-G5 mRNA editing ability in culture.

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles

Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

The complete mitochondrial genome of Deracantha onos (Orthoptera: Bradyporidae)

The complete mitochondrial genome 15,650 bp in size of the Deracantha onos has been determined. The gene content, base composition and codon usage of D. onos are coincident to typical hexapods mitochondrial genomes. Genes arrangement of D. onos is identical to Gryllotalpa orientalis, Ruspolia dubia and Anabrus simplex, in that the relative locations of tRNA(Lys) and tRNA(Asp) was different to that of Locusta migratoria. All tRNAs could be folded into the typical cloverleaf secondary structure, excluding tRNA(Ser(AGN)) which forms another structure according to the Steinberg-Cedergren tertiary structure. Sequence analysis of the A + T-rich region with Dot-plot did not find any conspicuous repeat clusters. Two poly-thymine (poly-T) nucleotide stretches of 20 bp and 11 bp in size, which may involved in the recognition of replication origin, were found on the H-strand and L-strand in the A + T-rich region of the D. onos mitogenome, respectively. One open reading frame (ORF) 87 amino acids in size was found on the H-strand, but Protein Blast searches analysis indicated that it was a nonfunctional ORF.

The mitochondrial genome of Ruspolia dubia (Orthoptera: Conocephalidae) contains a short A+T-rich region of 70 bp in length

The complete sequence (14 971 bp) of the Ruspolia dubia mitochondrial genome was determined and annotated. The genome contains the gene content, base composition, and codon usage typical of metazoan mitochondrial genomes. All 37 genes are conserved in the positions observed most frequently in insect mitochondrial genome structures. The secondary structures of both small subunit and large subunit rRNA were predicted. The most unusual features found were the initiation codon (TTA) of COI and a short A+T-rich region of 70 bp in length. In addition, a short, highly conserved polythymidine stretch that was previously described in Orthoptera and Diptera was also present in the A+T-rich region.

Segregation and Recombination of a Multipartite Mitochondrial DNA in Populations of the Potato Cyst Nematode Globodera pallida

The discovery that the potato cyst nematode Globodera pallida has a multipartite mitochondrial DNA (mtDNA) composed, at least in part, of six small circular mtDNAs (scmtDNAs) raised a number of questions concerning the population-level processes that might act on such a complex genome. Here we report our observations on the distribution of some scmtDNAs among a sample of European and South American G. pallida populations. The occurrence of sequence variants of scmtDNA IV in population P4A from South America, and that particular sequence variants are common to the individuals within a single cyst, is described. Evidence for recombination of sequence variants of scmtDNA IV in P4A is also reported. The mosaic structure of P4A scmtDNA IV sequences was revealed using several detection methods and recombination breakpoints were independently detected by maximum likelihood and Bayesian MCMC methods.

The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward A and T, as is typical for insect mtDNAs. There is also a significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of nucleotides. The hypothetical secondary structure of the LSU rRNA has also been reconstructed, obtaining a structural model similar to that of other insects.

Proteome Analysis of an Aerobic Hyperthermophilic Crenarchaeon, Aeropyrum pernix K1

We analyzed the proteome of a crenararchaeon, Aeropyrum pernix K1, by using the following four methods: (i) two-dimensional PAGE followed by MALDI-TOF MS, (ii) one-dimensional SDS-PAGE in combination with two-dimensional LC-MS/MS, (iii) multidimensional LC-MS/MS, and (iv) two-dimensional PAGE followed by amino-terminal amino acid sequencing. These methods were found to be complementary to each other, and biases in the data obtained in one method could largely be compensated by the data obtained in the other methods. Consequently a total of 704 proteins were successfully identified, 134 of which were unique to A. pernix K1, and 19 were not described previously in the genomic annotation. We found that the original annotation of the genomic data of this archaeon was not adequate in particular with respect to proteins of 10-20 kDa in size, many of which were described as hypothetical. Furthermore the amino-terminal amino acid sequence analysis indicated that surprisingly the translation of 52% of their genes starts with TTG in contrast to ATG (28%) and GTG (20%). Thus, A. pernix K1 is the first example of an organism in which TTG is the most predominant translational initiation codon.

The DNA beta satellite component associated with ageratum yellow vein disease encodes an essential pathogenicity protein (betaC1)

Ageratum yellow vein disease (AYVD) is caused by the geminivirus ageratum yellow vein virus (AYVV) and an associated DNA beta satellite. We have mapped a DNA beta transcript to a highly conserved open reading frame (betaC1 ORF). The most abundant transcript 5'-terminus is located 8 bases upstream of the betaC1 ORF putative initiation codon while the transcript terminates at multiple sites downstream from the putative termination codon. Disruption of betaC1 protein expression by the introduction of an internal nonsense codon prevented infection of the AYVV-satellite complex in ageratum and altered the phenotype in Nicotiana benthamiana to that produced by AYVV alone although the mutant was maintained in systemically infected tissues. Modification of the putative initiation codon to a nonsense codon produced an intermediate phenotype in N. benthamiana and a mild yellow vein phenotype in ageratum, suggesting that betaC1 protein expression could be initiated from an alternative site. N. benthamiana plants containing a dimeric DNA beta transgene produced severe developmental abnormalities, vein-greening, and cell proliferation in the vascular bundles. Expression of betaC1 protein from a potato virus X (PVX) vector also induced abnormal plant growth. Our results demonstrate that the satellite encodes at least one protein that plays a major role in symptom development and is essential for disease progression in ageratum, the natural host of the AYVD complex.

A mutation at the start codon defines the differential requirement of dpy-11 in Caenorhabditis elegans body hypodermis and male tail

dpy-11 encodes a thioredoxin-like molecule that is important for both body and male sensory ray morphogenesis in Caenorhabditis elegans. A mutant allele, s287, has a point mutation with its start codon, AUG, converted into AUA, presumably leading to null function. Since only a weak loss-of-function phenotype was observed, we tested whether an alternative start codon or the converted AUA could be used for translation initiation with reduced efficiency. Based on a functional assay of mutant phenotype complementation and biochemical analysis examining the in vivo synthesis of wild-type and mutant proteins, we conclude that AUA can be used as a less-efficient start codon for initiating translation of DPY-11. Our results also provide direct evidence that the body hypodermis and male tail of C. elegans have differential requirements of dpy-11 activity for their respective normal morphogenesis.

The opdB locus encodes the trypsin-like peptidase activity of Treponema denticola

High levels of Treponema denticola in subgingival dental plaque are associated with severe periodontal disease. T. denticola, along with Porphyromonas gingivalis and Bacteroides forsythus, are the only cultivatable oral microorganisms that produce significant amounts of "trypsin-like" peptidase activity. The ability of subgingival plaque to hydrolyze N-alpha-benzoyl-DL-arginine-2-naphthylamide (BANA) is associated with high levels of one or more of these organisms. The purpose of this study was to identify the gene encoding trypsin-like activity in T. denticola and thus facilitate molecular-level studies of its potential role in disease. Using published peptide sequences of a T. denticola surface-associated oligopeptidase with BANA-hydrolyzing activity, we identified the gene, designated opdB, in an apparently noncoding region of the T. denticola genome unannotated contigs (11/2000; http://www.tigr.org). The opdB gene begins with a TTG start codon and encodes a 685-residue peptide with high homology to the oligopeptidase B family in prokaryotes and eukaryotes. An isogenic T. denticola opdB mutant was constructed by allelic replacement mutagenesis using an ermF/AM gene cassette. The mutant lacked BANA-hydrolyzing activity and had a slightly slower growth rate than the parent strain. This mutant will be used in future studies of interactions of T. denticola with host cells and tissue.

Trichinella spiralis mtDNA: a nematode mitochondrial genome that encodes a putative ATP8 and normally structured tRNAS and has a gene arrangement relatable to those of coelomate metazoans

The complete mitochondrial DNA (mtDNA) of the nematode Trichinella spiralis has been amplified in four overlapping fragments and 16,656 bp of its sequence has been determined. This sequence contains the 37 genes typical of metazoan mtDNAs, including a putative atp8, which is absent from all other nematode mtDNAs examined. The genes are transcribed from both mtDNA strands and have an arrangement relatable to those of coelomate metazoans, but not to those of secernentean nematodes. All protein genes appear to initiate with ATN codons, typical for metazoans. Neither TTG nor GTT start codons, inferred for several genes of other nematodes, were found. The 22 T. spiralis tRNA genes fall into three categories: (i) those with the potential to form conventional "cloverleaf" secondary structures, (ii) those with TPsiC arm + variable arm replacement loops, and (iii) those with DHU-arm replacement loops. Mt-tRNA(R) has a 5'-UCG-3' anticodon, as in most other metazoans, instead of the very unusual 5'-ACG-3' present in the secernentean nematodes. The sequence also contains a large repeat region that is polymorphic in size at the population and/or individual level.

Mitochondrial sequence evolution in spiders: intraspecific variation in tRNAs lacking the TPsiC Arm

Analyses of mitochondrial DNA sequences from three species of Habronattus jumping spiders (Chelicerata: Arachnida: Araneae) reveal unusual inferred tRNA secondary structures and gene arrangements, providing new information on tRNA evolution within chelicerate arthropods. Sequences from the protein-coding genes NADH dehydrogenase subunit 1 (ND1), cytochrome oxidase subunit I (COI), and subunit II (COII) were obtained, along with tRNA, tRNA, and large-subunit ribosomal RNA (16S) sequences; these revealed several peculiar features. First, inferred secondary structures of tRNA and, likely, tRNA, lack the TPsiC arm and the variable arm and therefore do not form standard cloverleaf structures. In place of these arms is a 5-6-nt T arm-variable loop (TV) replacement loop such as that originally described from nematode mitochondrial tRNAs. Intraspecific variation occurs in the acceptor stem sequences in both tRNAs. Second, while the proposed secondary structure of the 3' end of 16S is similar to that reported for insects, the sequence at the 5' end is extremely divergent, and the entire gene is truncated about 300 nt with respect to Drosophila yakuba. Third, initiation codons appear to consist of ATY (ATT and ATC) and TTG for ND1 and COII, respectively. Finally, Habronattus shares the same ND1-tRNA-16S gene arrangement as insects and crustaceans, thus illustrating variation in a tRNA gene arrangement previously proposed as a character distinguishing chelicerates from insects and crustaceans.

Distinct expression of splice variants of neuronal nitric oxide synthase in the human gastrointestinal tract

BACKGROUND & AIMS

Changes of neuronal nitric oxide synthase (nNOS) expression have been linked to several human gastrointestinal disorders such as achalasia, diabetic gastroparesis, and hypertrophic pyloric stenosis. They could be caused by differential transcriptional control or alternative splicing generating different nNOS proteins. The aims of this study were to characterize 5'-splice variants, promoter usage, and site-specific expression of nNOS in the human gastrointestinal tract.

METHODS

5'-Splice variants were characterized by immunoblotting, reverse-transcription polymerase chain reaction, 5'-rapid amplification of complementary DNA ends, and Southern blotting. Genomic analysis was performed by rapid amplification of genomic ends, followed by reporter gene assays.

RESULTS

Six different 5'-splice variants of nNOS-messenger RNA were identified showing specific expressions at various sites of the human gastrointestinal tract. Three variants encode for nNOSalpha, which has a specific N-terminal PDZ/GLGF domain and interaction sites for regulatory proteins. Two variants encode for nNOSbeta and 1 for nNOSgamma, which both lack the protein-binding domains of nNOSalpha. In addition to 2 known first exons, a novel first exon of human nNOS with a separate functionally active downstream promoter and multiple binding sites for transcription factors was identified and characterized.

CONCLUSIONS

Six 5'-mRNA splice variants of nNOS encoding 3 different nNOS proteins are expressed in the human gut. The differential expression of these proteins could be implicated in different biological functions.

Mitochondrial genome diversity in parasites

Mitochondrial genomes have been sequenced from a wide variety of organisms, including an increasing number of parasites. They maintain some characteristics in common across the spectrum of life-a common core of genes related to mitochondrial respiration being most prominent-but have also developed a great diversity of gene content, organisation, and expression machineries. The characteristics of mitochondrial genomes vary widely among the different groups of protozoan parasites, from the minute genomes of the apicomplexans to amoebae with 20 times as many genes. Kinetoplastid protozoa have a similar number of genes to metazoans, but the details of gene organisation and expression in kinetoplastids require extraordinary mechanisms. Mitochondrial genes in nematodes and trematodes appear quite sedate in comparison, but a closer look shows a strong tendency to unusual tRNA structure and alternative initiation codons among these groups. Mitochondrial genes are increasingly coming into play as aids to phylogenetic and epidemiologic analyses, and mitochondrial functions are being recognised as potential drug targets. In addition, examination of mitochondrial genomes is producing further insights into the diversity of the wide-ranging group of organisms comprising the general category of parasites.

The sequence and structure of the meadow grasshopper (Chorthippus parallelus) mitochondrial srRNA, ND2, COI, COII ATPase8 and 9 tRNA genes

The nucleotide sequence of the mitochondrial ND2, COI, COII, ATPase8, srRNA and nine tRNA genes have been sequenced from two individual of the meadow grasshopper Chorthippus parallelus. Comparisons are made to other insects for which the same regions are completely sequenced. Percentage A + T is found to be relatively low in C. parallelus though consistent with that of the other Orthopteran, Locusta migratoria. The relative number of substitutions observed in the different protein-coding genes was analysed between pairs of insect species sharing different levels of relatedness. A clear change in this rate was observed between the within-genus and between-genera comparisons. This change is interpreted in terms of the functional constraints acting on these four different genes. The patterns seem to result from an early saturation of COI and COII genes with synonymous substitutions, and a tolerance of ND2 and ATPase8 function to high levels of amino acid replacements. This analysis highlights a need for further sequence studies and comparisons between taxa of different levels of divergence in order to understand the patterns of mtDNA evolution on which many evolutionary investigations are based.

Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris

We have determined the complete nucleotide (nt) sequence of the mitochondrial genome of an oligochaete annelid, the earthworm Lumbricus terrestris. This genome contains the 37 genes typical of metazoan mitochondrial DNA (mtDNA), including ATPase8, which is missing from some invertebrate mtDNAs. ATPase8 is not immediately upstream of ATPase6, a condition found previously only in the mtDNA of snails. All genes are transcribed from the same DNA strand. The largest noncoding region is 384 nt and is characterized by several homopolymer runs, a tract of alternating TA pairs, and potential secondary structures. All protein-encoding genes either overlap the adjacent downstream gene or end at an abbreviated stop codon. In Lumbricus mitochondria, the variation of the genetic code that is typical of most invertebrate mitochondrial genomes is used. Only the codon ATG is used for translation initiation. Lumbricus mtDNA is A + T rich, which appears to affect the codon usage pattern. The DHU arm appears to be unpaired not only in tRNAser(AGN), as is typical for metazoans, but perhaps also in tRNAser(UCN), a condition found previously only in a chiton and among nematodes. Relating the Lumbricus gene organization to those of other major protostome groups requires numerous rearrangements.

Complete sequence and gene organization of the mitochondrial genome of the land snail Albinaria coerulea

The complete sequence (14,130 bp) of the mitochondrial DNA (mtDNA) of the land snail Albinaria coerulea was determined. It contains 13 protein, two rRNA and 22 tRNA genes. Twenty-four of these genes are encoded by one and 13 genes by the other strand. The gene arrangement shares almost no similarities with that of two other molluscs for which the complete gene content and arrangement are known, the bivalve Mytilus edulis and the chiton Katharina tunicata; the protein and rRNA gene order is similar to that of another terrestrial gastropod, Cepaea nemoralis. Unusual features include the following: (1) the absence of lengthy noncoding regions (there are only 141 intergenic nucleotides interspersed at different gene borders, the longest intergenic sequence being 42 nucleotides) (2) the presence of several overlapping genes (mostly tRNAs), (3) the presence of tRNA-like structures and other stem and loop structures within genes. An RNA editing system acting on tRNAs must necessarily be invoked for posttranscriptional extension of the overlapping tRNAs. Due to these features, and also because of the small size of its genes (e.g., it contains the smallest rRNA genes among the known coelomates), it is one of the most compact mitochondrial genomes known to date.

Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome

The 16,260-bp mitochondrial DNA (mtDNA) from the starfish Asterina pectinifera has been sequenced. The genes for 13 proteins, two rRNAs and 22 tRNAs are organized in an extremely economical fashion, similar to those of other animal mtDNAs, with some of the genes overlapping each other. The gene organization is the same as that for another echinoderm, sea urchin, except for the inversion of a 4.6-kb segment that contains genes for two proteins, 13 tRNAs and the 16S rRNA. Judging from the organization of the protein coding genes, mammalian mtDNAs resemble the sea urchin mtDNA more than that of the starfish. The region around the 3' end of the 12S rRNA gene of the starfish shows a high similarity with those for vertebrates. This region encodes a possible stem and loop structure; similar potential structures occur in this region of vertebrate mtDNAs and also in nonmitochondrial small subunit rRNA. A similar stem and loop structure is also found at the 3' end of the 16S rRNA genes in A. pectinifera, in another starfish Pisaster ochraceus, in vertebrates and in Drosophila, but not in sea urchins. The full sequence data confirm the presumption that AGA/AGG, AUA and AAA codons, respectively, code for serine, isoleucine, and asparagine in the starfish mitochondria, and that AGA/AGG codons are read by tRNA(GCUSer), which possesses a truncated dihydrouridine arm, that was previously suggested from a partial mtDNA sequence. The structural characteristics of tRNAs and possible mechanisms for the change in the mitochondrial genetic code are also discussed.

The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.

The complete mitochondrial DNA sequence of the horse, Equus caballus: extensive heteroplasmy of the control region

The sequence of the mitochondrial (mt) DNA of the horse (Equus caballus) was determined. The length of the sequence presented is 16,660 bp. This figure, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif GTGCACCT in the control region of different molecules. Boundaries of the 13 peptide-coding genes were determined by the presence of start and stop codons, and by analogy with other eutherian mtDNAs. Three genes (COIII, NADH3 and NADH4) were not terminated by a stop codon. Comparison among the peptide-coding genes of the horse and eight other mammals suggests that the boundaries of some mt genes should be redefined. The number of repeats in the control region was determined by sequencing 77 different clones (20 direct plus 57 PCR clones). The number of repeats ranged from 2 to 29. There was a pronounced overrepresentation of clones with many repeats (22-27). Very few clones had a repeat number that was close to the mean number of repeats.

Mitochondrial DNA of the sea anemone, Metridium senile (Cnidaria): prokaryote-like genes for tRNA(f-Met) and small-subunit ribosomal RNA, and standard genetic code specificities for AGR and ATA codons

The nucleotide sequence of a segment of the mitochondrial DNA (mtDNA) molecule of the sea anemone Metridium senile (phylum Cnidaria, class Anthozoa, order Actiniaria) has been determined, within which have been identified the genes for respiratory chain NADH dehydrogenase subunit 2 (ND2), the small-subunit rRNA (s-rRNA), cytochrome c oxidase subunit II (COII), ND4, ND6, cytochrome b (Cyt b), tRNA(f-Met), and the large-subunit rRNA (1-rRNA). The eight genes are arranged in the order given and are all transcribed from the same strand of the molecule. The overall order of the M. senile mt-genes differs from that of other metazoan mtDNAs. In M. senile mt-protein genes, AGA and AGG codons appear to have the standard genetic code specification of arginine, rather than serine as found for other invertebrate mt-genetic codes. Also, ATA has the standard genetic code specification of isoleucine. TGA occurs in three M. senile mt-protein genes and may specify tryptophan as in other metazoan, protozoan, and some fungal mt-genetic codes. The M. senile mt-rRNA(f-Met) gene has primary and secondary structure features closely resembling those of the Escherichia coli initiator tRNA, including standard dihydrouridine and T psi C loop sequences and a mismatch pair at the top of the aminoacyl stem. Determinations of the 5' and 3' end nucleotides of the M. senile mt-s-rRNAs indicated that these molecules have a homogenous size of 1,081 ntp, larger than any other known metazoan mt-s-rRNAs. Consistent with its larger size, the M. senile mt-s-rRNA can be folded into a secondary structure that more closely resembles that of the E. coli 16S rRNA than can any other metazoan mt-s-rRNA. These findings concerning M. senile mtDNA indicate that most of the unusual features regarding metazoan mt-genetic codes, rRNAs, and probably tRNAs developed after divergence of the Cnidarian line from the ancestral line common to other metazoa.

RNA editing of a conserved reading frame in plant mitochondria increases its similarity to two overlapping reading frames in Escherichia coli

An open reading frame (orfx) in mitochondria of the higher plants Oenothera berteriana and Arabidopsis thaliana is homologous to orf244 in the mitochondrial genome of Marchantia polymorpha. Homologous sequences are also present in carrot, potato and sugar beet. Profile analysis revealed similarity to two overlapping reading frames in the Escherichia coli genome. Potential translation initiation at conserved ATA (isoleucine) and TTG (leucine) codons is discussed. Transcripts of the open reading frame are altered by RNA editing in Arabidopsis and Oenothera downstream of these codons, suggesting this to be the functionally important region.