Large mitochondrial genome and mitochondrial DNA size polymorphism in the mosquito parasite, Romanomermis culicivorax

Metagenomic Analysis of Bacteria, Fungi, Bacteriophages, and Helminths in the Gut of Giant Pandas

To obtain full details of gut microbiota, including bacteria, fungi, bacteriophages, and helminths, in giant pandas (GPs), we created a comprehensive microbial genome database and used metagenomic sequences to align against the database. We delineated a detailed and different gut microbiota structures of GPs. A total of 680 species of bacteria, 198 fungi, 185 bacteriophages, and 45 helminths were found. Compared with 16S rRNA sequencing, the dominant bacterium phyla not only included Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria but also Cyanobacteria and other eight phyla. Aside from Ascomycota, Basidiomycota, and Glomeromycota, Mucoromycota, and Microsporidia were the dominant fungi phyla. The bacteriophages were predominantly dsDNA Myoviridae, Siphoviridae, Podoviridae, ssDNA Inoviridae, and Microviridae. For helminths, phylum Nematoda was the dominant. In addition to previously described parasites, another 44 species of helminths were found in GPs. Also, differences in abundance of microbiota were found between the captive, semiwild, and wild GPs. A total of 1,739 genes encoding cellulase, β-glucosidase, and cellulose β-1,4-cellobiosidase were responsible for the metabolism of cellulose, and 128,707 putative glycoside hydrolase genes were found in bacteria/fungi. Taken together, the results indicated not only bacteria but also fungi, bacteriophages, and helminths were diverse in gut of giant pandas, which provided basis for the further identification of role of gut microbiota. Besides, metagenomics revealed that the bacteria/fungi in gut of GPs harbor the ability of cellulose and hemicellulose degradation.

The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species

To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).

Structure and variation of the Anseriformes mitochondrial DNA control region

The control region is the major non-coding segment of animal mitochondrial DNA. To infer the structure and variation of Anseriformes mitochondrial DNA control region, the control region sequences of 52 species were analyzed. The length of the control region sequences ranged from 968 bp (Chenonetta jubata) to 1335 bp (Anseranas semipalmata) and can be separated into three domains. There is a deletion of 100-130 bp in Anatinae, compared to other groups of Anserinae. The average genetic distances among the species within the genera varied from 4.14% (Anser) to 10.58% (Cygnus). The average genetic distances showed insignificantly negative correlation with ts/tv. Domain I is the most variable among the three domains among all the genera. Five conserved sequence boxes in the domain II of Anseriformes sequences were identified. The alignment of the Anseriformes five boxes sequences showed considerable sequence variation. CSB-1, -2 and 3 were not found in the Anseriformes. Maximum-likelihood method was used to construct a phylogenetic tree, which grouped all of the genera into four divergent clades. Anseranas + Chauna and Dendrocygna were identified as early offshoots of the Anatidae. All the remaining taxa fell into two clades that correspond to the two subfamilies Anserinae and Anatiane.

Biological evidence for the world's smallest tRNAs

Due to their function as adapters in translation, tRNA molecules share a common structural organization in all kingdoms and organelles with ribosomal protein biosynthesis. A typical tRNA has a cloverleaf-like secondary structure, consisting of acceptor stem, D-arm, anticodon arm, a variable region, and T-arm, with an average length of 73 nucleotides. In several mitochondrial genomes, however, tRNA genes encode transcripts that show a considerable deviation of this standard, having reduced D- or T-arms or even completely lack one of these elements, resulting in tRNAs as small as 66 nts. An extreme case of such truncations is found in the mitochondria of Enoplea. Here, several tRNA genes are annotated that lack both the D- and the T-arm, suggesting even shorter transcripts with a length of only 42 nts. However, direct evidence for these exceptional tRNAs, which were predicted by purely computational means, has been lacking so far. Here, we demonstrate that several of these miniaturized armless tRNAs consisting only of acceptor- and anticodon-arms are indeed transcribed and correctly processed by non-encoded CCA addition in the mermithid Romanomermis culicivorax. This is the first direct evidence for the existence and functionality of the smallest tRNAs ever identified so far. It opens new possibilities towards exploration/assessment of minimal structural motifs defining a functional tRNA and their evolution.

Rampant gene rearrangement and haplotype hypervariation among nematode mitochondrial genomes

Rare syntenic conservation, sequence duplication, and the use of both DNA strands to encode genes are signature architectural features defining mitochondrial genomes of enoplean nematodes. These characteristics stand in contrast to the more conserved mitochondrial genome sizes and transcriptional organizations of mitochondrial DNAs (mtDNAs) derived from chromadorean nematodes. To address the frequency of gene rearrangement within nematode mitochondrial DNA (mtDNA), mitochondrial genome variation has been characterized within a more confined enoplean taxonomic unit, the family Mermithidae. The complete nucleotide sequences of the mosquito parasitic nematodes Romanomermis culicivorax, R. nielseni, and R. iyengari mtDNA have been determined. Duplicated expanses encompassing different regions of the mitochondrial genomes were found in each of these congeners. These mtDNA shared few rRNA and protein gene junctions, indicating extensive gene rearrangement within the Romanomermis lineage. Rapid structural changes are also observed at the conspecific level where no two individual nematodes carry the same haplotype. Rolling circle amplification was used to isolate complete mitochondrial genomes from individuals in local populations of Thaumamermis cosgrovei, a parasite of terrestrial isopods. Mitochondrial DNA length variants ranging from 19 to 34 kb are observed, but haplotypes are not shared between any two individuals. The complete nucleotide sequences of three haplotypes have been determined, revealing a constant region encoding most mitochondrial genes and a hypervariable segment that contains intact and pseudogene copies of several mitochondrial genes, duplicated to different copy numbers, resulting in mtDNA size variation. Constant rearrangement generates new T. cosgrovei mtDNA forms.

Atypical mitochondrial DNA from the deep-sea scallop Placopecten magellanicus

The mitochondrial DNA of most metazoan animals is highly conserved in size, averaging about 17 kilobase paris (kbp). The mitochondrial DNA from the deep-sea scallop Placopecten magellanicus, in contrast, has been found to be approximately 34 kbp long. It is also highly variable in size from individual to individual and is unusual in the extent of its size variation. Mitochondrial DNAs from individuals collected at the same site differ by as much as 7 kbp. The size variation is due largely to differences in the number of copies of a tandemly repeated 1.2-kbp element.

Allomermis solenopsi n. sp. (Nematoda: Mermithidae) parasitising the fire ant Solenopsis invicta Buren (Hymenoptera: Formicidae) in Argentina

Allomermis solenopsi n. sp. (Mermithidae: Nematoda) is described from the fire ant Solenopsis invicta Buren (Hymenoptera: Formicidae) in Argentina. Diagnostic characters of the new species include stiff and erect processes on the surface of the mature egg, small female amphids, extension of the latero-medial rows of male genital papillae beyond the middle rows, an obliquely truncate spicule tip and a ventrally swollen male terminus. This is the first record of Allomermis Steiner, 1924 from South America and the first host record for members of this genus. Previous records of mermithids from Solenopsis spp. are summarised. The placement in Allomermis was confirmed by molecular analyses based on nuclear 18S ribosomal DNA sequences, the first such molecular framework for the Mermithidae. The possible life-cycle of the parasite is discussed, with the aim of using A. solenopsi as a biological control agent for fire ants in the United States.

Mitochondrial genome haplotype hypervariation within the isopod parasitic nematode Thaumamermis cosgrovei

Characterization of mitochondrial genomes from individual Thaumamermis cosgrovei nematodes, obligate parasites of the isopod Armadillidium vulgare, revealed that numerous mtDNA haplotypes, ranging in size from 19 to 34 kb, are maintained in several spatially separated isopod populations. The magnitude and frequency of conspecific mtDNA size variation is unprecedented among all studied size-polymorphic metazoan mitochondrial genomes. To understand the molecular basis of this hypervariation, complete nucleotide sequences of two T. cosgrovei mtDNA haplotypes were determined. A hypervariable segment, residing between the atp6 and rrnL genes, contributes exclusively to T. cosgrovei mtDNA size variation. Within this region, mtDNA coding genes and putative nonfunctional sequences have accumulated substitutions and are duplicated and rearranged to varying extents. Hypervariation at this level has enabled a first insight into the life history of T. cosgrovei. In five A. vulgare hosts infected with multiple nematodes, four carried nematodes with identical mtDNA haplotypes, suggesting that hosts may become infected by ingesting a recently hatched egg clutch or become parasitized by individuals from the same brood prior to dispersal of siblings within the soil.

Novel Repetitive Structures, Deviant Protein-Encoding Sequences andUnidentified ORFs in the Mitochondrial Genome of the BrachiopodLingula anatina

Complete sequence determination of the brachiopod Lingula anatina mtDNA (28,818 bp) revealed an organization that is remarkably atypical for an animal mt-genome. In addition to the usual set of 37 animal mitochondrial genes, which make up only 57% (16,555 bp) of the entire sequence, the genome contains lengthy unassigned sequences. All the genes are encoded in the same DNA strand, generally in a compact way, whereas the overall gene order is highly divergent in comparison with known animal mtDNA. Individual genes are generally longer and deviate considerably in sequence from their homologues in other animals. The genome contains two major repeat regions, in which 11 units of unassigned sequences and six genes (atp8, trnM, trnQ, trnV, and part of cox2 and nad2) are found in repetition, in the form of nested direct repeats of unparalleled complexity. One of the repeat regions contains unassigned repeat units dispersed among several unique sequences, novel repetitive structure for animal mtDNAs. Each of those unique sequences contains an open reading frame for a polypeptide between 80 and 357 amino acids long, potentially encoding a functional molecule, but none of them has been identified with known proteins. In both repeat regions, tRNA genes or tRNA gene-like sequences flank major repeated units, supporting the view that those structures play a role in the mitochondrial gene rearrangements. Although the intricate repeated organization of this genome can be explained by recurrent tandem duplications and subsequent deletions mediated by replication errors, other mechanisms, such as nonhomologous recombinations, appear to explain certain structures more easily.

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.

Organization of the large mitochondrial genome in the isopod Armadillidium vulgare

The mitochondrial DNA (mtDNA) in animals is generally a circular molecule of approximately 15 kb, but there are many exceptions such as linear molecules and larger ones. RFLP studies indicated that the mtDNA in the terrestrial isopod Armadillidium vulgare varied from 20 to 42 kb. This variation depended on the restriction enzyme used, and on the restriction profile generated by a given enzyme. The DNA fragments had characteristic electrophoretic behaviors. Digestions with two endonucleases always generated fewer fragments than expected; denaturation of restriction profiles reduced the size of two bands by half; densitometry indicated that a number of small fragments were present in stoichiometry, which has approximately twice the expected concentration. Finally, hybridization to a 550-bp 16S rDNA probe often revealed two copies of this gene. These results cannot be due to the genetic rearrangements generally invoked to explain large mtDNA. We propose that the large A. vulgare mtDNA is produced by the tripling of a 14-kb monomer with a singular rearrangement: one monomer is linear and the other two form a circular dimer. Densitometry suggested that these two molecular structures were present in different proportions within a single individual. The absence of mutations within the dimers also suggests that replication occurs during the monomer phase.

Disorders of nuclear-mitochondrial intergenomic signalling

In addition to sporadic or maternally-inherited mutations of the mitochondrial genome, abnormalities of mtDNA can be transmitted as mendelian traits. The latter are believed to be caused by mutations in still unknown nuclear genes, which deleteriously interact with the mitochondrial genome. Two groups of mtDNA-related mendelian disorders are known: those associated with mtDNA large-scale rearrangements and those characterized by severe reduction of the mtDNA copy number. The most frequent presentation of the first group of disorders is an adult-onset encephalomyopathy, defined clinically by the syndrome of progressive external ophthalmoplegia "plus", genetically by autosomal dominant transmission of the trait, and molecularly by the presence of multiple deletions of mtDNA. The second group of disorders comprises early-onset, organ-specific syndromes, associated with mtDNA depletion, that are presumably transmitted as autosomal recessive traits. Linkage analysis and search for candidate genes are two complementary strategies to clarify the molecular basis of these disorders of the nuclear-mitochondrial intergenomic signalling.

Searching for genes affecting the structural integrity of the mitochondrial genome

Mendelian traits associated with qualitative or quantitative abnormalities of mtDNA are presumably caused by mutations in nucleus-encoded genes that deleteriously interact with the mitochondrial genome. Qualitative abnormalities of mtDNA are typically represented by pleioplasmic multiple mtDNA deletions, that are detected in stable tissues, including skeletal muscle, of patients affected by Autosomal Dominant Chronic Progressive External Ophthalmoplegia. Quantitative abnormalities are represented by tissue-specific depletion of mtDNA, associated with different clinical presentation in infancy or childhood. Linkage analysis and search for candidate genes are two complementary strategies aimed at identifying the genes responsible for these disorders.

Characterization of the length polymorphism in the A + T-rich region of the Drosophila obscura group species

In the twelve Drosophila obscura group species studied, belonging to the affinis, obscura, and pseudoobscura subgroups, the mitochondrial DNA length ranges from 15.8 to 17.2 kb. This length polymorphism is mainly due to insertions/deletions in the variable region of the A + T-rich region. In addition, one species (D. tristis) possess a tandem duplication of a 470-bp fragment that contains the replication origin. The same duplication has occurred at least twice in the Drosophila evolutionary history due to the fact that the repetition is analogous to repetitions found in the four species of the D. melanogaster complex. By comparing the nucleotide sequence of the conserved region in D. ambigua, D. obscura, D. yakuba, D. teissieri, and D. virilis, we show the presence of a secondary structure, likely implied in the replication origin, which could favor the generation of this kind of duplications. Finally, we propose that the high A and T content in the variable region of the A + T-rich region favors the formation of less-stable secondary structures, which could explain the generation of minor insertion/deletions found in this region.

Nucleus-driven mutations of human mitochondrial DNA

Neuromuscular disorders due to abnormalities of mitochondrial energy supply have become an important area of human pathology. In particular, lesions of the mitochondrial genome (mtDNA), a small extra-nuclear chromosome which encodes 13 subunits of the respiratory chain complexes, are responsible for a steadily increasing number of neuromuscular syndromes. In addition to sporadic or maternally-inherited mutations, either qualitative or quantitative abnormalities of mtDNA can be transmitted as Mendelian traits, leading to well-defined mitochondrial encephalomyopathies. The latter are presumably caused by mutations in still unknown nucleus-encoded genes which deleteriously interact with the mitochondrial genome. These observations are of importance from both clinical and theoretical points of view, because they are the first examples of diseases produced by abnormalities of the nuclear control over mitochondrial biogenesis.

Recent appearance and molecular characterization of mitochondrial DNA deletions within a defined nematode pedigree

The mitochondrial genome of Romanomermis culicivorax, a parasitic nematode of mosquitoes, contains an amplified 3.0-kilobase (kb) locus organized as direct repeats and as noncontiguous, inverted copies. These amplified sequences are actively undergoing rearrangement. One recent event has resulted in a 1133-base pair (bp) deletion located entirely within a single amplified segment. The deletion junction occurs between two imperfect 58-bp repeats, implicating strand pairing in this alteration. A second event has generated mitochondrial DNA (mtDNA) forms differing by a single, intact 3.0-kb repeating unit. By analyzing molecules derived from independently reared subcultures, it appears these new mtDNA forms arose within the last 170 nematode generations. Our results indicate that the occurrence and selection of novel animal mitochondrial genomes can now be studied in this experimentally manipulable nematode system.

Role of sequence amplification in the generation of nematode mitochondrial DNA polymorphism

Romanomermis culicivorax, an obligate parasitic nematode of mosquitos, possesses an unusually large mitochondrial genome. Individuals are monomorphic for one of several mitochondrial DNA (mtDNA) size variants ranging from 26-32 kb. In this report, we demonstrate that the mitochondrial genome size differential in three isofemale lineages is due to the presence of mtDNA sequences amplified to different copy numbers within each mtDNA molecule. Restriction enzyme analysis and DNA sequencing studies reveal that each mitochondrial genome contains one of two 3.0 kb repeat types that differ by approximately 30 bp. This difference is primarily due to a short (23 bp) imperfect tandem duplication present within the larger of two polymorphic repeating units. The 3.0 kb reiterated DNA sequences are present as direct, tandem repeats and as inverted portions of the same sequence located elsewhere in the genome. Based on mtDNA analysis of an independently reared R. culicivorax culture, we conclude that events resulting in mitochondrial genome rearrangement occurred in natural field populations prior to propagation within the laboratory.

Tandem duplications in animal mitochondrial DNAs: variation in incidence and gene content among lizards

Size, location, gene content, and incidence were determined for 10 lizard mitochondrial DNA duplications. These range from 0.8 to 8.0 kilobases (kb) and account for essentially all of the observed size variation (17-25 kb). Cleavage-site mapping and transfer-hybridization experiments indicate that each duplication is tandem and direct, includes at least one protein or rRNA gene, and is adjacent to or includes the D loop-containing control region. Duplication boundaries are nonrandomly distributed, and most appear to align with tRNA genes, suggesting that these may play a role in the duplication process. Duplications are infrequent and usually restricted to particular individuals or populations. They appear to be ephemeral; in no case is the same duplication shared by mitochondrial DNAs from closely related species. Mitochondrial DNA duplications occur significantly more often in triploid than diploid lizards and at similar frequencies in hybrids and nonhybrids.