The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii

Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of Meretrix lamarckii, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in M. lamarckii M-cox2 gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of M. lamarckii. Even if no direct involvement in DUI process has been demonstrated so far, the finding of cox2 insertions and supernumerary ORFs in M. lamarckii both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.     

Comprehensive analysis of the complete mitochondrial genome of Melanoplus differentialis (Acrididae: Melanoplinae) captured in Korea

In this study, we determined the complete mitochondrial genome of the invasive insect species Melanoplus differentialis captured in Korea. The complete mitochondrial genome of M. differentialis is 15,625 bp long and comprises 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs, with a GC ratio of 25.2%. In total, 353 SNPs and 11 INDEL regions (total length 67 bp) were found against the previously sequenced M. differentialis mitochondrial genome recorded as public genome data. The number of interspecific variations was greater than the number of intraspecific variations in this insect. Phylogenetic tree analysis showed that the mitochondrial genome clustered the Melanoplus clade with two previously reported Melanoplus sequences. However, the sequences were not divided at the species-level clade possibly as a consequence of misidentification caused by an error in the public database. Our results extend the molecular database status of Melanoplus by providing a novel complete mitochondrial genome sequence for M. differentialis that could serve as reference for further molecular studies.     

The Mitochondrial Genomes of Two Scallops, Argopecten irradians and Chlamys farreri (Mollusca: Bivalvia): The Most Highly Rearranged Gene Order in the Family Pectinidae

Molluscs in general and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Here, we determined the mitochondrial genomes of two scallops Argopecten irradians and Chlamys farreri. The complete mitochondrial genome of A. irradians is 16,211 nts in length and the nearly complete mitochondrial genome of C. farreri is 20,789 nts in length. Both of the genomes contain 35 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 21 transfer RNAs. In contrast to the typical animal mitochondrial genome, both of them lack one protein-coding gene atp8 and two trnSs, but show an additional copy of trnF in A. irradians and of trnM in C. farreri, respectively. Gene order and genome content were compared among the four sequenced scallops. Gene arrangement of C. farreri closely resembles that of Mizuhopecten yessoensis. However, two genomes of C. farreri and A. irradians show only three small identical gene blocks and two genomes of A. irradians and Placopecten magellanicus share only one gene block. Comparison of the gene arrangement demonstrated that the four scallops share few identical gene blocks although they belong to the same family. This feature is seldom observed in Metazoa, even in other molluscan classes. The dramatic gene rearrangement often occurs in bivalves, especially in marine bivalves. In addition, comparisons of genomic character among bivalves are also presented.     

Rate of change of the phytoplankton community in Itapeva Lake (North Coast of Rio Grande do Sul,Brazil), based on the wind driven hydrodynamic regime

The mussel Mytilus trossulus is an important component of the Baltic brackish water ecosystem. The genetic structure of mussel (M. trossulus) populations was studied in sites along the Polish coast, Southern Baltic for two segments of mitochondrial DNA (mtDNA). The mode of inheritance of Mytilus mtDNA is termed doubly uniparental; two genomes are passed independently down the female (the F genome) and male (the M genome) lines of descent. The M genome has not been detected at high frequency in M. trossulus, thus the present study focuses on the F genome. PCR and RFLP analysis was used to characterise haplotypes in the coding region ND2-COIII; PCR was used to detect length variants in a major noncoding region. Significant differentiation between populations was observed in the frequency of 24 coding region haplotypes and 14 different length variants. For the three most frequent coding region haplotypes, two (I and III) are associated with the length variants, whereas the third (II) is monomorphic for a single variant of short length. It is suggested that variant II is derived by introgression from a related species, M. edulis, and may be resistant to expansion in the noncoding region. In both regions studied, the Ewens–Watterson test reveals significant deviations from neutrality with an excess of rare variants. This might be due to selection against slightly deleterious variants and is consistent with previously published results for Mytilus taxa. The present study also points towards the potential utility of mtDNA length variation in studies of population differentiation of Mytilus.     

The complete mitochondrial genome of the hard clam <Emphasis Type="Italic">Meretrix meretrix</Emphasis>

Veneridae is a diverse, commercially important, and cosmopolitan family. Here we present the complete mitochondrial genome of the hard clam Meretrix meretrix (Bivalvia: Veneridae). The entire mitochondrial genome (mitogenome) sequence of M. meretrix is 19,826 bp in length, and contains 37 genes including 12 protein-coding genes, 2 ribosomal RNAs, and 23 tRNAs. All genes are encoded on the heavy strand. In contrast to the typical animal mitochondrial genome, it lacks the protein-coding gene ATP8, and has only one copy of the tRNA^Ser gene, but three duplications of the tRNA^Gln, which is the first report among the present molluscan mtDNAs. We observed that the gene arrangement between M. meretrix and M. petechialis is same except one more tRNAGln gene in M. meretrix., and the sequence similarity is as high as 99%, indicating that M. petechialis and M. meretrix could be treated as a junior synonym of M. meretrix. Maximum Likelihood and Bayeslan analysis of 12 concatenated protein-coding amino acid sequences place the Unionidae as a sister group to other bivalves, which reflects the general opinion that the Unionidae deverged very early in Bivalvia evolution.     

Complete mitochondrial genome of Tubulipora flabellaris (Bryozoa: Stenolaemata): the first representative from the class Stenolaemata with unique gene order

Mitochondrial genomes play a significant role in the reconstruction of phylogenetic relationships within metazoans. There are still many controversies concerning the phylogenetic position of the phylum Bryozoa. In this research, we have finished the complete mitochondrial genome of one bryozoan (Tubulipora flabellaris), which is the first representative from the class Stenolaemata. The complete mitochondrial genome of T. flabellaris is 13,763 bp in length and contains 36 genes, which lacks the atp8 gene in contrast to the typical metazoan mitochondrial genomes. Gene arrangement comparisons indicate that the mitochondrial genome of T. flabellaris has unique gene order when compared with other metazoans. The four known bryozoans complete mitochondrial genomes also have very different gene arrangements, indicates that bryozoan mitochondrial genomes have experienced drastic rearrangements. To investigate the phylogenetic relationship of Bryozoa, phylogenetic analyses based on amino acid sequences of 11 protein coding genes (excluding atp6 and atp8) from 26 metazoan complete mitochondrial genomes were made utilizing Maximum Likelihood (ML) and Bayesian methods, respectively. The results indicate the monopoly of Lophotrochozoa and a close relationship between Chaetognatha and Bryozoa. However, more evidences are needed to clarify the relationship between two groups. Lophophorate appeared to be polyphyletic according to our analyses. Meanwhile, neither analysis supports close relationship between Branchiopod and Phoronida. Four bryozoans form a clade and the relationship among them is T. flabellaris + (F. hispida + (B. neritina + W. subtorquata)), which is in coincidence with traditional classification system.     

The Complete Mitochondrial Genome Sequence and Characterization of Single-Nucleotide Polymorphisms in the Control Region of the Asian Seabass (Lates calcarifer)

We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.     

Variation within and among the chloroplast genomes ofMelaleuca alternifolia andM. linariifolia (Myrtaceae)

Melaleuca alternifolia andM. linariifolia are commercially important Australian species harvested for their essential oils. Both species have relatively narrow and disjunct distributions on the central coast of eastern Australia. Variation in the chloroplast genome was assessed for eight individuals from each of twelve populations, representing the species' geographic range. Low nucleotide diversity withinM. alternifolia contrasted with high nucleotide diversity inM. linariifolia. CpDNA data are consistent with the southern population ofM. alternifolia being a hybrid population withM. linariifolia. The two species are sympatric in this region. Variation inM. linariifolia was geographically structured, with northern populations differing from southern populations by seven restriction site mutations, five length mutations and an inversion. There was no evidence of hybridisation of the cp genome of northernM. linariifolia with the partially sympatric speciesM. trichostachya. Intra- and interspecific variation in the chloroplast genomes ofM. alternifolia, M. linariifolia, andM. trichostachya indicate considerable potential for the use of intraspecific cpDNA studies in examining phylogenetic relationships in melaleucas.     

The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)₁₂ element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes.     

The complete mitogenome of the Formosan termite, Coptotermes formosanus Shiraki

The Formosan termite Coptotermes formosanus Shiraki is a well-known invasive pest that causes severe damage to wooden structures in many parts of the world. Although several studies examined its phylogeographic patterns using a few mitochondrial genes, the phylogenetic relationships among C. formosanus are poorly understood because of the small number of mutations known among its mitochondrial genes. To provide a useful genetic tool for further analyses, we analyzed the complete mitochondrial genome sequence of C. formosanus using specimens collected from three isolated islands in the Ryukyu Archipelago of Japan. The circular mitogenome of these termites consisted of genes encoding 22 transfer RNAs, two ribosomal RNAs, and 13 mitochondrial proteins, as is the case for most animal mitochondrial genomes. The G + C content was 34.1%, and the total length varied slightly between 16,234 and 16,236 base pairs. The complete mitochondrial genomes of the three populations were more than 99.9% identical to each other and showed differences at six nucleotide positions. The COII, 12S rRNA, and 16S rRNA genes that are commonly used for phylogenetic analyses revealed only one substitution or no substitutions. The mitogenome sequences determined here should contribute to the design of new molecular markers for the clarification of the historical distribution process of C. formosanus and for further phylogenetic analyses with this and related termite species.     

Complete mitochondrial DNA sequence of the important honey bee pest,Varroa destructor (Acari: Varroidae)

Mites in the genus Varroa are the primary parasites of honey bees on several continents. Genetic analyses based on Varroa mitochondrial DNA have played a central role in establishing Varroa taxonomy and dispersal. Here we present the complete mitochondrial sequence of the important honey bee pest Varroa destructor. This species has a relatively compact mitochondrial genome (15,218 bp). The order of genes encoding proteins is identical to that of most arthropods. Ten of 22 transfer RNAs are in different locations relative to hard ticks, and the 12S ribosomal RNA subunit is inverted and separated from the 16S rRNA by a novel non-coding region, a trait not yet seen in other arthropods. We describe a dispersed set of 45 oligonucleotide primers that can be used to address genetic questions in Varroa. A subset of these primers should be useful for taxonomic and phylogenetic studies in other mites and ticks. This revised version was published online in July 2006 with corrections to the Cover Date.     

Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants

We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.     

Elucidation of Schistosoma japonicum population dynamics in pigs using PCR-based identification of individuals representing distinct cohorts

The study reported here investigated the interactions of successive infections and acquired resistance of pigs to challenge infections of Schistosoma japonicum. Two morphologically indistinguishable geographical isolates from China (from Anhui and Zhejiang provinces) were used for the infections. The worms of the two isolates were distinguishable by PCR-linked restriction fragment length polymorphism analysis of the nicotinamide adenine dinucleotide phosphate dehydrogenase I gene of the mitochondrial genome. Thirty-two pigs divided into seven groups were used in the experiment. Two groups received a single infection by either the Anhui or the Zhejiang isolate. In Challenge Groups 1, 4, 6, 8 and 12, a primary infection of the Zhejiang isolate was followed by a challenge infection with the Anhui isolate at week 1, 4, 6, 8 or 12 after the primary infection. In this way it was possible to determine whether worms recovered by perfusion originated from the primary or the challenge infection. Only the challenge infection at week 1 resulted in a higher worm burden when compared with a single primary infection with the Zhejiang isolate. The results showed that challenge worms were able to establish, and that the proportion of worms originating from challenge infection increased at the later challenge infections, however without an increase in the total number of worms. In addition, mixed pairs of the two isolates were found in all challenge-infected groups. The results indicate that pigs are able to mount a partial resistance against re-infection with S. japonicum by 4 weeks after a primary infection, but that worms of the challenge infections eventually replace the primary infection. The finding of mixed pairs of the two isolates indicates that worms of S. japonicum are either polygamous or able to wait in solitude for up to 12 weeks for a partner.     

The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus <Emphasis Type="Italic">Fomitopsis palustris</Emphasis>

The complete mitochondrial genome sequence of the wood-decaying fungus Fomitopsis palustris (Basidiomycete, Agaricomycotina) was determined by next-generation sequencing technology. The complete sequence of the circular mitochondrial DNA of F. palustris was 63,479 bp in length with a 75.98% AT content. The mitochondrial genome encoded 14 conserved proteins, 2 ribosomal RNAs, 26 transfer RNAs, and 19 additional open reading frames. The coxI and cob genes contained six and one group I introns, respectively, and encoded eight open reading frames, including seven intron-encoded endonucleases. The complete mitochondrial genome of F. palustris presented herein represents the first such report for brown rot basidiomycetes. In addition, the BLAST score ratio and phylogenetic analysis may open new avenues to understanding the evolutionary status of this fungus .     

Analysis of the mitochondrial genome of Schistocerca gregaria gregaria (Orthoptera: Acrididae)

In the present study, we present the full sequence of the mitochondrial genome of the African desert locust Schistocerca gregaria gregaria. The size of 15625 bp reported matches very well with mitochondrial genomes of other Orthopteriodea. The mitochondrial genome comprises 13 protein‐coding genes, two ribosomal RNAs and 22 t‐RNAs with two t‐RNA (trnD and trnK) rearrangements that are typical for the taxon Caelifera. We compared the sequence with 12 mitochondrial genes of Schistocerca gregaria flaviventris and Schistocerca americana and used some of these data to construct phylogenetic trees, which confirm the close relationship between the two subspecies S. g. flaviventris and S. g. gregaria. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 296–305.     

Genome organization and variation in the 3′-partial sequence of garlic latent virus in China

Ten different isolates of a carlavirus were detected by degenerate PCR from 12 garlic samples collected from 6 provinces in China, and the complete genome sequence of the Zhejiang isolate ZJ1 and 3’-terminal sequences of 9 other isolates were determined. The RNA genome of isolate ZJ1 consisted of 8363nts excluding the 3’-poly (A) tail, and the genome organization was similar to other carlaviruses with 6 open reading frames encoding a replicase, TGB1, TGB2, TGB3, CP and NABP respectively. Sequence comparisons showed that all 10 isolates were Garlic latent virus (GarLV). The variations in the TGB2, TGB3 and NABP were more significant than those in the CP. High homology was also detected between those isolates and Shallot latent virus (ShLV). Phylogenetic analysis suggested that GarLV isolates from garlic can be divided into 4 main groups and Chinese isolates belonged to each group. This is the first reported molecular analysis of members of the genus Carlavirus in China.     

The Mitochondrial Genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerable Economization in the Length and Structural Features of Encoded Genes

The complete sequence of the mitochondrial genome of the plant parasitic nematode Xiphinema americanum sensu stricto has been determined. At 12626bp it is the smallest metazoan mitochondrial genome reported to date. Genes are transcribed from both strands. Genes coding for 12 proteins, 2 rRNAs and 17 putative tRNAs (with the tRNA-C, I, N, S1, S2 missing) are predicted from the sequence. The arrangement of genes within the X. americanum mitochondrial genome is unique and includes gene overlaps. Comparisons with the mtDNA of other nematodes show that the small size of the X. americanum mtDNA is due to a combination of factors. The two mitochondrial rRNA genes are considerably smaller than those of other nematodes, with most of the protein encoding and tRNA genes also slightly smaller. In addition, five tRNAs genes are absent, lengthy noncoding regions are not present in the mtDNA, and several gene overlaps are present. [Reviewing Editor: Dr. Yues van de Peer] F. Lamberti: Deceased, 2004     

Organization of the Mitochondrial Genome of Mantis Shrimp Pseudosquilla ciliata (Crustacea: Stomatopoda)

We determined the nearly complete mitochondrial genome of Pseudosquilla ciliata (Crustacea, Stomatopoda), including all protein-coding genes and all but one of the transfer RNAs. There were no gene rearrangements relative to the pattern shared by crustaceans and hexapods. Phylogenetic analysis using concatenated amino acid sequences of the mitochondrial protein-coding genes confirmed a basal position of Stomatopoda among Eumalacostraca. Pancrustacean relationships based on mitogenomic data were analyzed and are discussed in relation to crustacean and hexapod monophyly and hexapod affinities to crustacean subtaxa.     

Pre-Pleistocene Refugia and Differentiation between Populations of the Caucasian Salamander (Mertensiella caucasica)

A 350-bp fragment of the mitochondrial cytochrome-b gene was sequenced in the Caucasian salamander, Mertensiella caucasica, representing 10 populations from across its range along the Black Sea coast. Five haplotypes were discovered among 65 fragments analyzed, differing at 2–50 positions. The highest differentiation between haplotypes was observed in animals from the eastern part of the species' range (Borjomi) compared to those from the remainder of the species' range. Randomly amplified nuclear DNA revealed a pattern of spatial genetic variation similar to that of the mitochondrial genome. M. caucasica, as currently known, represents two evolutionary lineages that evolved independently, perhaps since the lower Pliocene. These lineages represent taxa, possibly to be described as species, distributed in the Borjomi area in central Georgia and in southwestern Georgia and northeastern Turkey. The multivariate analysis of morphological data did not reveal significant differences between the taxa. However, substantial morphological differentiation was observed within both lineages, showing parallel patterns in body proportions and coloration patterns. This variation is possibly associated with extant ecological conditions. Salamanders with reduced pigmentation from southwestern Georgia were not genetically distinguishable from neighboring populations.