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19 results for “complete mitochondrial DNA”
Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish
We used nuclear and mitochondrial DNA sequences from specimens collected throughout Lake Tanganyika to clarify the evolutionary relationship between Lamprologus callipterus and Neolamprologus fasciatus. The nuclear data supports the reciprocal monophyly of these two shell breeding lamprologine cichlids. However, mitochondrial DNA (mtDNA) sequences show that 1) L. callipterus includes two divergent and geographically disjunct (North-South) mtDNA lineages; and that 2) N. fasciatus individuals cluster in a lineage sister group to the northern lineage of L. callipterus. The two mtDNA lineages of L. callipterus diverged c. 684 Kya to 1.2 Mya, coinciding with a major water level low stand in Lake Tanganyika, which divided the lake into isolated sub-lakes. This suggests that the two mtDNA lineages originated as the result of the separation of L. callipterus populations in different sub-basins. The incongruent phylogenetic position of N. fasciatus can best be explained by an ancient unidirectional introgression from L. callipterus into N. fasciatus. Remarkably, our data indicate that this event resulted in the complete mtDNA replacement in N. fasciatus. Our data suggest that hybridization occurred soon after the divergence of the two L. callipterus mtDNA lineages, probably still during the water level low stand, and that subsequently the invading mtDNA lineage spread throughout the lake.
Supplementary material 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Inferred secondary structure of 22 tRNA genes in the mitochondrial DNA of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata). :
Supplementary material 1 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Phylogenetic analysis : Explanation note: ML tree constructed based on the cox1 barcodes of genus Theretra using B. mori as outgroups. The asterisk represents the species researched presently.
Figure 2 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region
Figure 2. Median-joining network of all the control region haplotypes found in Tetraophasis szechenyii. Notes: Missing haplotypes in the network are represented by black dots; circle sizes are proportional to the number of individuals sharing the same haplotypes (n); each mutation step is shown as a short line connecting neighbouring haplotypes; numbers of mutations between haplotypes are indicated near branches if greater than 1.
Figure 1 in Complete mitochondrial genome of Tetraophasis szechenyii Madarász, 1885 (Aves: Galliformes: Phasianidae), and its genetic variation as inferred from the mitochondrial DNA Control Region
Figure 1. Molecular phylogenetic tree derived from the complete DNA sequences of 12 mitochondrial protein-coding genes using Bayesian inference and maximum likelihood analyses. Notes:The numbers beside the nodes are Bayesian posterior probabilities (≥ 0.9 retained) and bootstrap proportions of maximum likelihood analyses calculated with 100 replicates (≥ 50% retained); Anas platyrhynchos and Alectura lathami were set as outgroups; *clades not supported by Bayesian inference.
Data from: Complete mitochondrial DNA replacement in a Lake Tanganyika cichlid fish
Open the record for dataset details and reuse information.
Figure 1 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Figure 1 - The mitochondrial genome of Pontoscolex corethrurus (Müller, 1857). Gene order and positions are shown, including the putative control region. IUPAC single letter codes are used to identify transfer RNA. The L1, L2, S1, and S2 transfer RNAs are differentiated on the basis of their anti-codons TAG, TAA, TCT, and TGA, respectively.
Figure 2 from: Conrado AC, Arruda H, Stanton DWG, James SW, Kille P, Brown G, Silva E, Dupont L, Taheri S, Morgan AJ, Simões N, Rodrigues A, Montiel R, Cunha L (2017) The complete mitochondrial DNA sequence of the pantropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Clitellata): Mitogenome characterization and phylogenetic positioning. ZooKeys 688: 1-13. https://doi.org/10.3897/zookeys.688.13721
Figure 2 - Phylogenetic relationships among phylum Annelida based on the combined 13,416 bp nucleotide positions. Total alignment length is greater than the combined P. corethrurus protein coding and rRNA sequence lengths due to overlapping protein coding sequences that are subsequently concatenated, and indel regions in the alignment. The posterior probability value of BI analyses and bootstrap support values of ML analyses (in the order: BI, ML) are indicated near the branches.
Figure 7 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 7 Phylogenetic analysis. Phylogenetic tree constructed using NJ and ML methods based on the amino acid sequences of 13 PCGs of 7 species with Bombyx mori (Lepidoptera: Bombycidae) and Antheraea pernyi (Lepidoptera: Saturniidae) as outgroups. The support values at the nodes represent bootstrap values for NJ and ML respectively.
Figure 1 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 1 The schematic illustration for mitogenome of T. japonica. Gene order and positions are shown. cox1, cox2, and cox3 refer to the cytochrome c oxidase subunits; cob refers to cytochrome b; nad1-nad6 refers to NADH dehydrogenase components; rrnL and rrnS refer to ribosomal RNAs. The bold lines on outer or inner ring represent that the genes lie in the majority-coding strand (J-strand) or the minority-coding strand (N-strand).
Figure 3 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 3 The relative synonymous codon usage (RSCU) in the mitogenome of T. japonica. The codons listed up the columns are absent in T. japonica.
Figure 5 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 5 Features of the A+T-rich region of T. japonica. The ATATG motif is shaded. The polyT stretch is underlined while the poly-A stretch is double underlined. The TA and GC repeats sequence are indicated by dotted underlining. The 28 bp repeats 'ATTAAATTAATAAATTAATATATTAATA' are labeled with wave underlining.
Supplementary material 2 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
List of annotated mitochondrial genes of T. japonica :
Figure 3 from: Zhao L, Gao T, Lu W (2015) Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications. ZooKeys 546: 181-195. https://doi.org/10.3897/zookeys.546.5964
Figure 3 - Phylogenetic relationships among Sciaenidae species based on the combined 9988 bp nucleotide positions. The posterior probability value of BI analyses and bootstrap support values of ML analyses (in the order: BI, ML) are indicated near the branches.
Figure 2 from: Zhao L, Gao T, Lu W (2015) Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications. ZooKeys 546: 181-195. https://doi.org/10.3897/zookeys.546.5964
Figure 2 - Potential secondary structure of the origin of L-strand replication (OL) of Bahaba taipingensis mtDNA.
Figure 6 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 6 Barcoding analysis of T. japonica.
Figure 2 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 2 The amino acids usage in the mitogenome of T. japonica. CDpT = codons per thousand codons.
Figure 4 from: Li J, Lin R-R, Zhang Y-Y, Hu K-J, Zhao Y-Q, Li Y, Huang Z-R, Zhang X, Geng X-X, Ding J-H (2018) Characterization of the complete mitochondrial DNA of Theretra japonica and its phylogenetic position within the Sphingidae (Lepidoptera, Sphingidae). ZooKeys 754: 127-139. https://doi.org/10.3897/zookeys.754.23404
Figure 4 The cloverleaf secondary structure of transfer RNA of T. japonica.
Figure 1 from: Zhao L, Gao T, Lu W (2015) Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications. ZooKeys 546: 181-195. https://doi.org/10.3897/zookeys.546.5964
Figure 1 - The structure of control region about Bahaba taipingensis.
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