The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts

We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.     

Numerous gene rearrangements in the mitochondrial genome of the wallaby louse, Heterodoxus macropus (Phthiraptera)

The complete arrangement of genes in the mitochondrial (mt) genome is known for 12 species of insects, and part of the gene arrangement in the mt genome is known for over 300 other species of insects. The arrangement of genes in the mt genome is very conserved in insects studied, since all of the protein-coding and rRNA genes and most of the tRNA genes are arranged in the same way. We sequenced the entire mt genome of the wallaby louse, Heterodoxus macropus, which is 14,670 bp long and has the 37 genes typical of animals and some noncoding regions. The largest noncoding region is 73 bp long (93% A+T), and the second largest is 47 bp long (92% A+T). Both of these noncoding regions seem to be able to form stem-loop structures. The arrangement of genes in the mt genome of this louse is unlike that of any other animal studied. All tRNA genes have moved and/or inverted relative to the ancestral gene arrangement of insects, which is present in the fruit fly Drosophila yakuba. At least nine protein-coding genes (atp6, atp8, cox2, cob, nad1-nad3, nad5, and nad6) have moved; moreover, four of these genes (atp6, atp8, nad1, and nad3) have inverted. The large number of gene rearrangements in the mt genome of H. macropus is unprecedented for an arthropod.     

The Mitochondrial Genome of a Deep-Sea Bamboo Coral (Cnidaria,Anthozoa, Octocorallia,Isididae): Genome Structure and Putative Origins of Replication Are Not Conserved Among Octocorals

Octocoral mitochondrial (mt) DNA is subject to an exceptionally low rate of substitution, and it has been suggested that mt genome content and structure are conserved across the subclass, an observation that has been supported for most octocorallian families by phylogenetic analyses using PCR products spanning gene boundaries. However, failure to recover amplification products spanning the nad4L-msh1 gene junction in species from the family Isididae (bamboo corals) prompted us to sequence the complete mt genome of a deep-sea bamboo coral (undescribed species). Compared to the "typical" octocoral mt genome, which has 12 genes transcribed on one strand and 5 genes on the opposite (cox2, atp8, atp6, cox3, trnM), in the bamboo coral genome a contiguous string of 5 genes (msh1, rnl, nad2, nad5, nad4) has undergone an inversion, likely in a single event. Analyses of strand-specific compositional asymmetry suggest that (i) the light-strand origin of replication was also inverted and is adjacent to nad4, and (ii) the orientation of the heavy-strand origin of replication (OriH) has reversed relative to that of previously known octocoral mt genomes. Comparative analyses suggest that intramitochondrial recombination and errors in replication at OriH may be responsible for changes in gene order in octocorals and hexacorals, respectively. Using primers flanking the regions at either end of the inverted set of five genes, we examined closely related taxa and determined that the novel gene order is restricted to the deep-sea subfamily Keratoisidinae; however, we found no evidence for strand-specific mutational biases that may influence phylogenetic analyses that include this subfamily of bamboo corals.     

The mitochondrial genome of Priapulus caudatus Lamarck (Priapulida: Priapulidae)

We sequenced and annotated the complete mitochondrial (mt) genome of the priapulid Priapulus caudatus in order to provide a source of phylogenetic characters including an assessment of gene order arrangement. The genome was 14,919 bp in its entirety with few, short non-coding regions. A number of protein-coding and tRNA genes overlapped, making the genome relatively compact. The gene order was: cox1, cox2, trnK, trnD, atp8, atp6, cox3, trnG, nad3, trnA, trnR, trnN, rrnS, trnV, rrnL, trnL(yaa), trnL(nag), nad1, -trnS(nga), -cob, -nad6, trnP, -trnT, nad4L, nad4, trnH, nad5, trnF, -trnE, -trnS(nct), trnI, -trnQ, trnM, nad2, trnW, -trnC, -trnY; where '-' indicates genes transcribed on the opposite strand. The gene order, although unique amongst Metazoa, shared the greatest number of gene boundaries and the longest contiguous fragments with the chelicerate Limulus polyphemus. The mt genomes of these taxa differed only by a single inversion of 18 contiguous genes bounded by rrnS and trnS(nct). Other arthropods and nematodes shared fewer gene boundaries but considerably more than the most similar non-ecdysozoan.     

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.     

Mitochondrial gene order change in Schistosoma (Platyhelminthes: Digenea: Schistosomatidae)

In the flatworm genus Schistosoma, species of which include parasites of biomedical and veterinary importance, mitochondrial gene order is radically different in some species. A PCR-based survey of 19 schistosomatid spp. established which of 14 Schistosoma spp. have the ancestral (plesiomorphic) or derived gene order condition. A phylogeny for Schistosoma was estimated and used to infer the origin of the gene order change which is present in all members of a clade containing Schistosoma incognitum and members of the traditionally recognised Schistosoma indicum, Schistosoma mansoni and Schistosoma haematobium spp. groups. Schistosoma turkestanicum, with the plesiomorphic gene order state, is sister to this clade. Common interval analysis suggests change in gene order, from ancestral to derived, consisted of two sequential transposition events: (a) nad1_nad3 to nad3_nad1 and (b) [atp6,nad2]_[nad3,nad1,cox1,rrnL,rrnS,cox2,nad6] to [nad3,nad1,cox1,rrnL,rrnS,cox2,nad6]_[atp6,nad2], where gene order of fragments within square brackets remain unchanged. Gene order change is rare in parasitic flatworms and is a robust synapomorphy for schistosome spp. that exhibit it. The schistosomatid phylogeny casts some doubt on the origin of Schistosoma (Asian or African), highlights the propensity for species to host switch amongst mammalian (definitive) hosts, and indicates the likely importance of snail (intermediate) hosts in determining and defining patterns of schistosome radiation and continental invasion. Mitogenomic sampling of Schistosoma dattai and Schistosoma harinasutai to determine gene order, and within key species, especially S. turkestanicum and S. incognitum, to determine ancestral ranges, may help discover the geographic origins of gene order change in the genus. Samples of S. incognitum from India and Thailand suggest this taxon may include cryptic species.     

Cis- and trans-splicing and RNA editing are required for the expression of nad2 in wheat mitochondria

In wheat mitochondria, the gene coding for subunit 2 of the NADH-ubiquinone oxidoreductase (nad2) is divided into five exons located in two distant genomic regions. The first two exons of the gene, a and b, lie 22?kb downstream of exons c, d, and e, on the same DNA strand. All introns of nad2 are group II introns. A trans-splicing event is required to join exons b and c. It involves base pairing of the two precursor RNAs in the stem of domain IV of the intron. A gene coding for tRNA^Tyr is located upstream of exon c. In addition to splicing processes, mRNA editing is also required for the correct expression of nad2. The mature mRNA is edited at 36 positions, distributed over its five exons, resulting in 28 codon modifications. Editing increases protein hydrophobicity and conservation.     

Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations

We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.     

Cis- and trans-splicing and RNA editing are required for the expression of nad2 in wheat mitochondria

In wheat mitochondria, the gene coding for subunit 2 of the NADH-ubiquinone oxidoreductase (nad2) is divided into five exons located in two distant genomic regions. The first two exons of the gene, a and b, lie 22 kb downstream of exons c, d, and e, on the same DNA strand. All introns of nad2 are group II introns. A trans-splicing event is required to join exons b and c. It involves base pairing of the two precursor RNAs in the stem of domain IV of the intron. A gene coding for tRNA^Tyr is located upstream of exon c. In addition to splicing processes, mRNA editing is also required for the correct expression of nad2. The mature mRNA is edited at 36 positions, distributed over its five exons, resulting in 28 codon modifications. Editing increases protein hydrophobicity and conservation. Received: 11 August 1997 / Accepted: 2 February 1998     

The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to other Metazoa. The genome has an overall AT richness of 59.4%. We found seven regions of overlaps between tRNAs and protein-coding genes ranging from 2 to 11 nt, and seven regions of overlap between tRNAs, ranging from 1 to 8 nt, resulting in a total number of 46 overlapping nucleotides. Genes nad4, cox2, atp8, and nad3 are terminated by the abbreviated stop codon T and cytb is suggested to terminate on (ACT)AA; we postulate that mRNA editing is required to remove AC for TAA to be functional in terminating translation. Phylogenetic analysis of nucleotide and amino acid data place Flustrellidra in the Lophotrochozoa. DNA for this study originated from two populations resulting in a contig consisting of multiple haplotypes. Twenty-seven SNP sites were detected, the majority occurring in cox1 and nad5. With cox1 already established as a marker in bryozoan studies, we advocate the further testing of nad5.     

The complete mitochondrial genome of Tuta absoluta (Lepidoptera: Gelechiidae) and genetic variation in two newly invaded populations in China

Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is a devastating invasive pest worldwide, causing severe damage to tomatoes. Recently, it has been recorded in the northwestern and southwestern parts of China. Here, the mitogenomes and genetic variation of two newly invaded T. absoluta populations in Xinjiang and Yunnan, were determined. The results showed that the complete mitogenome size of T. absoluta is 15298 bp for the individual from Xinjiang and 15296 bp for the individual from Yunnan, which were both longer than the reported mitogenome from Spain (15290 bp). The mitogenome sequences of individuals collected from three locations showed high levels of sequence similarity, except for 8 polymorphic sites, which were in genes cox2 (1 site), cox3 (2 sites), cob (1 site), atp6 (1 site), nad1 (2 sites) and nad5 (1 site). Tuta absoluta mitogenomes share many features with other 6 Gelechiidae mitogenomes, except for several differences in the start and stop codons of protein-coding genes and the length of intergenic spacers. Seven partial mitochondrial genes (cox1, cox2, cox3, atp6, cob, nad1, and nad5) were used for genetic variation analysis, and significant population differentiation was found between the two populations based on cox2, atp6, nad1, and nad5. The complete mitogenomes and sensitive mitochondrial gene markers reported here provide useful data for further population genetics study of this pest.