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PubMed2006

Molecular phylogeny of silkmoths reveals the origin of domesticated silkmoth, Bombyx mori from Chinese Bombyx mandarina and paternal inheritance of Antheraea proylei mitochondrial DNA.

Molecular phylogeny of some of the economically important silkmoths was derived using three mitochondrial genes, 12S rRNA, 16S rRNA, and COI, and the control region (CR). Maximum likelihood (ML) analyses showed two distinct clades, one consisting of moths from Bombycidae family and the other from Saturniidae family. The mitochondrial CR showed length polymorphisms with indels. The ML analyses for complete mitochondrial genome sequences of Bombyx mori (strains Aojuku, C108, Backokjam, and Xiafang), Japanese and Chinese strains of B. mandarina (Japanese mandarina and Chinese mandarina) and, Antheraea pernyi revealed two distinct clades, one comprising of B. mori strains and the other with B. mandarina, and A. pernyi forming an outgroup. Pairwise distances revealed that all of the strains of B. mori studied are closer to Chinese than to Japanese mandarina. Phylogenetic analyses based on whole mitochondrial genome sequences, the finding of a tandem triplication of a 126bp repeat element only in Japanese mandarina, and chromosome number variation in B. mandarina suggest that B. mori must have shared its recent common ancestor with Chinese mandarina. Another wild species of the Bombycidae family, Theophila religiosa, whose phylogenetic status was not clear, clustered together with the other bombycid moths in the study. Analysis of the interspecific hybrid, A. proylei gave evidence for paternal inheritance of mitochondrial DNA.

Animals↗

PubMed2003

Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features.

We report complete mitochondrial (mt) genomes for a penguin (little blue, Eudyptula minor) and a goose (greater white-fronted, Anser albifrons). A revised annotation of avian and reptile mt genomes has been carried out, which improves consistency of labeling gene start and stop positions. In conjunction with this, a summary of mt gene features is presented and a number of conserved patterns and interesting differences identified. The protein-coding genes from the two new genomes were analysed together with those from 17 other birds plus outgroup (reptile) taxa. The unrooted amino acid tree from 19 avian genomes was locally stable with many high bootstrap values using several maximum likelihood methods. In particular, Anseriformes (goose and duck) grouped strongly with Galliformes (chicken) to form Gallianseres, while the penguin paired firmly with the stork. The position where the outgroup joined the avian tree varied with the combination of outgroup taxa used. The three best supported positions of the root were passerine, but the traditional rooting position between paleognaths and neognaths could not be excluded.

Animals↗

PubMed2005

Mitochondrial DNA sequence and gene organization in the [corrected] Australian blacklip [corrected] abalone Haliotis rubra (leach).

The complete mitochondrial DNA of the blacklip abalone Haliotis rubra (Gastropoda: Mollusca) was cloned and 16,907 base pairs were sequenced. The sequence represents an estimated 99.85% of the mitochondrial genome, and contains 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes found in other metazoan mtDNA. An AT tandem repeat and a possible C-rich domain within the putative control region could not be fully sequenced. The H. rubra mtDNA gene order is novel for mollusks, separated from the black chiton Katharina tunicata by the individual translocations of 3 tRNAs. Compared with other mtDNA regions, sequences from the ATP8, NAD2, NAD4L, NAD6, and 12S rRNA genes, as well as the control region, are the most variable among representatives from Mollusca, Arthropoda, and Rhynchonelliformea, with similar mtDNA arrangements to H. rubra. These sequences are being evaluated as genetic markers within commercially important Haliotis species, and some applications and considerations for their use are discussed.

Animals↗

PubMed2005

Mitochondrial genome of Pogona vitticepes (Reptilia; Agamidae): control region duplication and the origin of Australasian agamids.

The complete mitochondrial DNA sequence for an Australian agamid Pogona vitticepes was determined. Twenty-two tRNA genes, two rRNA genes, thirteen protein-coding genes, and two control regions were identified in this mitochondrial genome. The second control region was inserted between NADH dehydrogenase subunits 5 and 6 genes. The duplication of the control region was found in all Australasian agamids examined and was not found in other Asian or African taxa. The two control regions had nearly identical sequences within species but they were divergent among species, suggesting their concerted sequence evolution. Phylogenetic analyses including divergence time estimation without assuming the molecular clock suggested that the duplication of the control region occurred on a lineage leading to the Australasian agamids 25-45 million years ago after their divergence from a Southeast Asian Physignathus cocincinus. Our finding thus supports the recent dispersal origin of Australasian agamids in connection with plate tectonic movement of Australia to the proximity of Southeast Asia.

Animals↗

PubMed2004

Evolution of the mitochondrial genome: protist connections to animals, fungi and plants.

The past decade has seen the determination of complete mitochondrial genome sequences from a taxonomically diverse set of organisms. These data have allowed an unprecedented understanding of the evolution of the mitochondrial genome in terms of gene content and order, as well as genome size and structure. In addition, phylogenetic reconstructions based on mitochondrial DNA (mtDNA)-encoded protein sequences have firmly established the identities of protistan relatives of the animal, fungal and plant lineages. Analysis of the mtDNAs of these protists has provided insight into the structure of the mitochondrial genome at the origin of these three, mainly multicellular, eukaryotic groups. Further research into mtDNAs of taxa ancestral and intermediate to currently characterized organisms will help to refine pathways and modes of mtDNA evolution, as well as provide valuable phylogenetic characters to assist in unraveling the deep branching order of all eukaryotes.

Animals↗

PubMed2026

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships among Syndiclis species.

The complete mitochondrial genome (mitogenome) of Syndiclis anlungensis, a critically endangered tropical tree, was determined in this study. The mitogenome spans 2,368,454 bp across four contigs and harbors 41 protein-coding genes, 22 tRNA genes, and three rRNA genes. Potential mutation regions, including 1317 repeat sequences and 698 simple sequence repeats (SSRs), were accurately located in the S. anlungensis mitogenome. Sixty-five transferred fragments of the repeats were found between its mitochondrial and chloroplast genomes. When compared to three other Laurales mitogenomes, extensive gene order shuffling is evident, leaving only five conserved gene clusters intact. Codon usage analysis reveals a pronounced A/T bias in both mitochondrial and chloroplast genes, and three mitochondrial genes (atp9, rps19, and sdh3) stand out for their high divergence across eleven Syndiclis taxa. Selection analyses indicate strong purifying pressure on rpl2, rpl16, and sdh3 (Ka/Ks < 1), with no positive selection detected. Using 41 mitochondrial protein-coding gene sequences from sixteen and three individuals of Syndiclis and Beilschmiedia species, respectively, our phylogenetic tree recovers Syndiclis as monophyletic, with two well-supported clades: one includes S. anlungensis, S. chinensis, S. lotungensis, S. marlipoensis, and a putative new Syndiclis species from Yunnan; the other contains S. furfuracea, S. hongkongensis, S. kwangsiensis, and three putative new Syndiclis species from Guangdong and Vietnam.

Genome, Mitochondrial↗

PubMed2004

Phylogenetic relationships and biogeography of the genus Chondrostoma inferred from mitochondrial DNA sequences.

A phylogeny of the species of the nase genus Chondrostoma was constructed from a complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise the current systematics of this group, and to infer a biogeographical model of the Mediterranean area during the Cenozoic period. We confirmed the monophyly of the genus Chondrostoma, and defined seven different lineages within it: Polylepis, Arcasii, Lemmingii, Toxostoma, Nasus, C. genei, and C. soetta. The separation of main lineages within Chondrostoma occurred in the Middle-Upper Miocene, approximately 11 million years ago, while the greatest species radiation took place in the Pliocene close to the time the current drainages system were created. It is unlikely that this genus experienced an extensive dispersal during the Messinian, in the Lago-Mare Phase. Given the level of current knowledge, a biogeographical model constructed on the basis of vicariant events seems more realistic than does a dispersalist model.

Animals↗

PubMed2000

Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences.

We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.

Animals↗

PubMed2001

The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny.

The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups). The analyses corroborated the view that turtles are at the base of the bird-crocodile branch. This position of the turtles makes Diapsida paraphyletic. The origin of the squamates was estimated at 294 million years (Myr) ago and that of the turtles at 278 Myr ago. Phylogenetic analysis of mammalian relationships using the additional outgroups corroborated the Marsupionta hypothesis, which joins the monotremes and the marsupials to the exclusion of the eutherians.

Alligators and Crocodiles↗

PubMed2005

Partial mitochondrial genome sequences of Ostrinia nubilalis and Ostrinia furnicalis.

Contiguous 14,535 and 14,536 nt near complete mitochondrial genome sequences respectively were obtained for Ostrinia nubilalis and Ostrinia furnicalis. Mitochondrial gene order was identical to that observed from Bombyx. Sequences comparatively showed 186 substitutions (1.3% sequence divergence), 170 CDS substitutions (131 at 3(rd) codon positions), and an excess of transition mutation likely resulting by purifying selection (d(N)/d(S) = omega congruent with 0.15). Overall substitution rates were significantly higher at 4-fold (5.2%) compared to 2-fold degenerate codons (2.6%). These are the 3(rd) and 4(th) lepidopteran mitochondrial genome reference sequences in GenBank and useful for comparative mitochondrial studies.

Animals↗

PubMed2004

[Sequence and organization of Muntiacus reevesi mitochondrial genome].

A shot-gun DNA sequence strategy was employed,in which the mitochondrial genome library of Muntiacus reevesi has been constructed to obtain the complete mitochondrial genome sequence. The Chinese Muntjac's mitochondrial genome, consisting of 16354 base pairs which encode genes for 13 proteins, 2 rRNAs, and 22 tRNAs, is similar to those mammals in both order and orientation. The sequence of rRNA gene, some of the protein-coding regions and tRNAs are highly homologous in mammals. Differences existing in the length and sequence of the D-loop regions account for the variations in mammals mitochondrial genomes.

Animals↗

PubMed2006

The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon.

Complete mitochondrial genome sequences are presented from two dipluran hexapods (i.e., a group of "primarily wingless insects") of the genus Campodea and compared to those of other arthropods. Their gene order is the same as in most other hexapods and crustaceans. Structural changes have occurred in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2 as well as in both ribosomal RNAs. These mtDNAs have striking biases in nucleotide and amino acid composition. Although the two Campodea species are morphologically highly similar, their genetic divergence is larger than expected, suggesting a long evolutionary history, perhaps under stable ecological conditions.

Animals↗

PubMed2004

Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences.

To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.

Animals↗

PubMed1997

Mitochondrial gene arrangement of the horseshoe crab Limulus polyphemus L.: conservation of major features among arthropod classes.

Numerous complete mitochondrial DNA sequences have been determined for species within two arthropod groups, insects and crustaceans, but there are none for a third, the chelicerates. Most mitochondrial gene arrangements reported for crustaceans and insect species are identical or nearly identical to that of Drosophila yakuba. Sequences across 36 of the gene boundaries in the mitochondrial DNA (mtDNA) of a representative chelicerate. Limulus polyphemus L., also reveal an arrangement like that of Drosophila yakuba. Only the position of the tRNA(LEU)(UUR) gene differs; in Limulus it is between the genes for tRNA(LEU)(CUN) and ND1. This positioning is also found in onychophorans, mollusks, and annelids, but not in insects and crustaceans, and indicates that tRNA(LEU)(CUN)-tRNA(LEU)(UUR)-ND1 was the ancestral gene arrangement for these groups, as suggested earlier. There are no differences in the relative arrangements of protein-coding and ribosomal RNA genes between Limulus and Drosophila, and none have been observed within arthropods. The high degree of similarity of mitochondrial gene arrangements within arthropods is striking, since some taxa last shared a common ancestor before the Cambrian, and contrasts with the extensive mtDNA rearrangements occasionally observed within some other metazoan phyla (e.g., mollusks and nematodes).

Amino Acid Sequence↗

PubMed1994

Phylogenetic analysis of the Coscoroba coscoroba using mitochondrial srRNA gene sequences.

In order to study the phylogenetic relationships among Coscoroba, goose, and swan lineages, sequences for the complete mitochondrial small ribosomal RNA (srRNA) gene were determined from five waterfowl species. Parsimony and distance analyses support the branching of Coscoroba prior to the divergence of geese and swans, and maximum likelihood analyses give almost equal support to that pattern and to the sister group relationship between Coscoroba and swans. The monophyly of the geese was confirmed at a statistically significant level. In sequence comparisons among waterfowl, transitions increase linearly with transversions, and so we conclude that the lack of complete resolution of Coscoroba's position is not due to sequence saturation alone, but also reflects relatively close branching times.

Animals↗

PubMed2000

Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion.

We explored the phylogenetic utility and limits of the individual and concatenated mitochondrial genes for reconstructing the higher-level relationships of teleosts, using the complete (or nearly complete) mitochondrial DNA sequences of eight teleosts (including three newly determined sequences), whose relative phylogenetic positions were noncontroversial. Maximum-parsimony analyses of the nucleotide and amino acid sequences of 13 protein-coding genes from the above eight teleosts, plus two outgroups (bichir and shark), indicated that all of the individual protein-coding genes, with the exception of ND5, failed to recover the expected phylogeny, although unambiguously aligned sequences from 22 concatenated transfer RNA (tRNA) genes (stem regions only) recovered the expected phylogeny successfully with moderate statistical support. The phylogenetic performance of the 13 protein-coding genes in recovering the expected phylogeny was roughly classified into five groups, viz. very good (ND5, ND4, COIII, COI), good (COII, cyt b), medium (ND3, ND2), poor (ND1, ATPase 6), and very poor (ND4L, ND6, ATPase 8). Although the universality of this observation was unclear, analysis of successive concatenation of the 13 protein-coding genes in the same ranking order revealed that the combined data sets comprising nucleotide sequences from the several top-ranked protein-coding genes (no 3rd codon positions) plus the 22 concatenated tRNA genes (stem regions only) best recovered the expected phylogeny, with all internal branches being supported by bootstrap values >90%. We conclude that judicious choice of mitochondrial genes and appropriate data weighting, in conjunction with purposeful taxonomic sampling, are prerequisites for resolving higher-level relationships in teleosts under the maximum-parsimony optimality criterion.

Animals↗

PubMed1998

Deleterious mutations at the mitochondrial ND3 gene in South American marsh rats (Holochilus).

Statistical analyses of DNA sequences have revealed patterns of nonneutral evolution in mitochondrial DNA of mice, humans, and Drosophila. Here we report patterns of mitochondrial sequence evolution in South American marsh rats (genus Holochilus). We sequenced the complete mitochondrial ND3 gene in 82 Holochilus brasiliensis and 21 H. vulpinus to test the neutral prediction that the ratio of nonsynonymous to synonymous nucleotide changes is the same within and between species. Within H. brasiliensis we observed a greater number of amino acid polymorphisms than expected based on interspecific comparisons. This contingency table analysis suggests that many amino acid polymorphisms are mildly deleterious. Several tests of the frequency distribution also revealed departures from a neutral, equilibrium model, and these departures were observed for both nonsynonymous and synonymous sites. In general, an excess of rare sites was observed, consistent with either a recent selective sweep or with populations not at mutation-drift equilibrium.

Amino Acid Sequence↗

PubMed2006

[Screening of differentially expressed genes in rats with cardiomyopathy after bone marrow mesenchymal stem cell transplantation].

OBJECTIVE: Earlier studies have confirmed that mesenchymal stem cells (MSCs) can transdifferentiate into myocytes and improve heart function in 2 weeks. But the mechanism is not clear. In this study, the mechanism of improvement of heart function after transplantation of MSCs was examined with suppression subtractive hybridization (SSH). METHODS: MSCs were isolated from thighone and tibia of Wistar rats, purified by adhesion-screening method, and expanded in vitro. Intraperitoneal injection of doxorubicin (at 2.5 mg/kg/time and total doses of 15 mg/kg) established cardiomyopathy models. MSCs were transplanted into cardiomyocytes. The differential genes between tester (rats with cardiomyopathy that were injected with MSCs) and driver (rats with cardiomyopathy that were injected with equivalent volume of culture medium) were screened with suppression subtractive hybridization. RESULTS: After 4 weeks of intraperitoneal injection of doxorubicin, left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) decreased by 26.48% and 40.61%, respectively (P < 0.01), as compared with those of normal group. Cardiomyopathy model was established successfully. And the heart function of the rats with cardiomyopathy was significantly improved after transplantation. Sixteen gene fragments were detected, and 12 of them were up-regulated in testers. They were rattus norvegicus mitochondrial BN/SsNHsdMCW, rattus norvegicus strain mitochondrial F344 X BN F1, rattus norvegicus mitochondrion H(+)-ATP synthase alphase subunit (Atp5al) mRNA, rattus norvegicus BHE/Cdb tRNA-Lys gene, rat mitochondrial H(+)-ATP synthase alpha subunit mRNA, rattus norvegic (wild-caught animal) complete mitochondrial genome, rattus norvegic clone BB.1.4.1 unknown Glu-Pro dipeptide repeat protein mRNA, Arabidopsis thaliana transgenic line C DNA, rat mitochondrial ATP synthase beta subunit mRNA, rattus norvegic mitochondrial genome, rat cardiac troponin T mRNA and rat mRNA for beta-globin. Four gene fragments were down-regulated in testers. They were rat mRNA for sarcomeric mitochondrial creatine kinase, rat mRNA for ribosomal phosphoprotein P2, rat alpha-crystallin B chain mRNA and rattus norvegicus NADH-ubiquinone oxidoreductase Fe-S protein 7 mRNA. CONCLUSION: The expression of the genes relating to mitochondrial synthesizing and contracting proteins synthesizing increased after MSC transplantation. The genes might enhance energy synthesis and promote MSC transdifferentiate into myocytes, and then improve heart function of rats with cardiomyopathy.

Animals↗