Editing of the grapevine mitochondrial cytochrome b mRNA and molecular modeling of the protein

Cytochrome b (COB), the central catalytic subunit of ubiquinol cytochrome c reductase, is a component of the transmembrane electron transfer chain that generates proton motive force. Some plant COB mRNAs are processed by RNA editing, which changes the gene coding sequence. This report presents the sequences of the grapevine (Vitis vinifera L.) mitochondrial gene for apocytochrome b (cob), the edited mRNA and the deduced protein. Grapevine COB is 393 amino acids long and is 98% identical to homologs in rapeseed, Arabidopsis thaliana and Oenothera sp. Twenty-one C-U editing sites were identified in the grapevine cob mRNA, resulting in 20 amino acid changes. These changes increase the overall hydrophobicity of the protein and result in a more conserved protein. Molecular modeling of grapevine COB shows that residues changed by RNA editing fit the secondary structure characteristic of an integral membrane protein. This is the first complete mitochondrial gene reported for grapevine. Novel RNA editing sites were identified in grapevine cob, which have not been previously reported for other plants.     

Taenia asiatica and Taenia saginata: genetic divergence estimated from their mitochondrial genomes

We conducted a differential identification of Taenia asiatica and Taenia saginata, through the mapping of mitochondrial genomes and the sequencing of the cox1 and cob genes. The entire mitochondrial genomes of T. asiatica and T. saginata were amplified by long-extension PCR and cloned; each was approximately 14 kb in size. Restriction maps of T. asiatica and T. saginata mitochondrial genomes were then constructed using 13 restriction enzymes. The resulting restriction patterns enable us to estimate their genetic divergence at 4.8%. The actual sequence divergence was computed 4.5% from the cox1 gene, and 4.1% from the cob gene. These results support the designation of T. asiatica as a separate species from T. saginata.     

Mitochondrial Cytochrome b mRNA Editing in Dinoflagellates: Possible Ecological and Evolutionary Associations?

To verify the hypothesis that mt mRNA editing is widespread in dinoflagellates, we analyzed cytochrome b (cob) mRNA editing for six species representing distinct ecotypes and taxonomic classes of Dinophyceae. Editing is detected in all, which is similar to the three other species studied previously in that edited sites appear to aggregate in four clusters and occur predominantly at first and second positions of codons (93%), overwhelmingly involving A --> G, U --> C, or C --> U substitutions with a smaller number of G --> C, G --> A changes. Comparative analyses on editing characteristics reveal interesting trends related to phylogenetic relatedness and ecological features. Editing density (percentage of nucleotide that is affected by editing) increases from early to derived lineages. Higher editing densities also map to red tide-forming lineages. Furthermore, similarity of location of edited codons (LOE) and the type of nucleotide changes (TOE) in different lineages mirror the taxonomic affinity of the lineages. Phylogenetic trees constructed from LOE and TOE resemble those inferred from cob sequences. The results bolster our earlier hypothesis that cob editing is widespread in dinoflagellates and suggest that density, location, and type of editing may bear yet-to-be-defined evolutionary and ecological significance.     

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.     

Exploitation of mitochondrial nad6 as a complementary marker for studying population variability in Lepidoptera

The applicability of mitochondrial nad6 sequences to studies of DNA and population variability in Lepidoptera was tested in four species of economically important moths and one of wild butterflies. The genetic information so obtained was compared to that of cox1 sequences for two species of Lepidoptera. nad6 primers appropriately amplified all the tested DNA targets, the generated data proving to be as informative and suitable in recovering population structures as that of cox1. The proposal is that, to obtain more robust results, this mitochondrial region can be complementarily used with other molecular sequences in studies of low level phylogeny and population genetics in Lepidoptera.     

Molecular Characterization of Taenia multiceps Isolates from Gansu Province,China by Sequencing of Mitochondrial Cytochrome C Oxidase Subunit 1

A total of 16 Taenia multiceps isolates collected from naturally infected sheep or goats in Gansu Province, China were characterized by sequences of mitochondrial cytochrome c oxidase subunit 1 (cox1) gene. The complete cox1 gene was amplified for individual T. multiceps isolates by PCR, ligated to pMD18T vector, and sequenced. Sequence analysis indicated that out of 16 T. multiceps isolates 10 unique cox1 gene sequences of 1,623 bp were obtained with sequence variation of 0.12-0.68%. The results showed that the cox1 gene sequences were highly conserved among the examined T. multiceps isolates. However, they were quite different from those of the other Taenia species. Phylogenetic analysis based on complete cox1 gene sequences revealed that T. multiceps isolates were composed of 3 genotypes and distinguished from the other Taenia species.     

mRNA EDITING AND SPLICED‐LEADER RNA TRANS‐SPLICING GROUPS OXYRRHIS,NOCTILUCA, HETEROCAPSA,AND AMPHIDINIUM AS BASAL LINEAGES OF DINOFLAGELLATES1

Identification of novel dinoflagellate taxa through molecular analysis is hindered by lack of well‐defined basal lineages. To address this issue, we attempted to reassess the phylogenetic status of Oxyrrhis marina Dujard. as well as other potentially basal taxa. The analysis was based on two newly established premises: (1) editing density of mitochondrial cob and cox1 mRNA increases from basal to later diverging lineages; (2) nuclear‐encoded mRNA in dinoflagellates is trans‐spliced to receive a 22 bp spliced leader (SL) at the 5′‐end. We analyzed these two genetic traits in O. marina, Noctiluca scintillans (Macartney) Kof. et Swezy, Heterocapsa triquetra (Ehrenb.) F. Stein, H. rotundata (Lohmann) Ge. Hansen, Amphidinium carterae Hulburt, and A. operculatum Clap. et J. Lachm. Surprisingly, no editing was detected in cob and cox1 mRNAs in these lineages, except for a small number of editing events in Amphidinium. However, nuclear‐encoded mRNAs in these species contained the SL sequence at the 5′‐end, indicative of SL RNA trans‐splicing. These findings, together with the recent cob‐cox1‐18S rRNA three‐gene phylogeny, suggest the following: (1) O. marina is a basal dinoflagellate; (2) Heterocapsa, Amphidinium, and Noctiluca likely are also early diverging lineages of dinoflagellates, and the position of Heterocapsa is inconsistent with literature and needs further investigation; and (3) the presence of the 22 bp SL and mitochondrial (mt) mRNA editing can be considered a landmark of dinoflagellate splits.     

Characterization of the complete mitochondrial genome of Tryporyza incertulas, in comparison with seven other Pyraloidea moths

The complete 15,223-bp mitochondrial genome (mitogenome) of Tryporyza incertulas (Walker) (Lepidoptera: Pyraloidea: Crambidae) was determined, characterized and compared with seven other species of superfamily Pyraloidea. The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. Compared with other moths of Pyraloidea, the A + T biased (77.0%) of T. incertulas was the lowest. Eleven protein-coding genes (PCGs) utilized the standard ATN, but cox1 used CGA and nad4 used AAT as the initiation codons. Ten protein-coding genes had the common stop codon TAA, except nad3 having TAG as the stop codon, and cox2, nad4 using T, TA as the incomplete stop codons, respectively. All of the tRNA genes had typical cloverleaf secondary structures except trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. There was a spacer between trnQ and nad2, which was common in Lepidoptera moths. A 6-bp motif ‘ATACTA’ between trnS2(UCN) and nad1, a 7-bp motif “AGC(T)CTTA” between trnW and trnC and a 6-bp motif “ATGATA” of overlapping region between atp8 and atp6 were found in Pyraloidea moths. The A + T-rich region contained an ‘ATAGT(A)’-like motif followed by a poly-T stretch. In addition, two potential stem-loop structures, a duplicated 19-bp repeat element, and two microsatellites ‘(TA)₁₂’ and ‘(TA)₉’ were observed in the A + T-rich region of T. incertulas mitogenome. Finally, the phylogenetic relationships of Pyraloidea species were constructed based on amino acid sequences of 13 PCGs of mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These molecular-based phylogenies supported the morphological classification on relationships within Pyraloidea species.