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865 results for “Mitochondrial genomes”
Supplementary material 8 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S4. Control region of the M. elongatus mitochondrial genome
Supplementary material 5 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S1. Relative synonymous codon usage (RSCU) in the M. elongatus mitogenome
Supplementary material 6 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure S2. Codon distribution in the M. elongatus mitogenome
Supplementary material 1 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Table S1. Primers used for PCR
Figure 2 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Figure 2 Phylogenetic relationships of Gobioninae based on complete mitochondrial genomes using maximum likelihood (ML) analyses. ML bootstrap values are shown at the nodes.
Supplementary material 3 from: Zhang R, Tang Q, Deng L (2021) The complete mitochondrial genome of Microphysogobio elongatus (Teleostei, Cyprinidae) and its phylogenetic implications. ZooKeys 1061: 57-73. https://doi.org/10.3897/zookeys.1061.70176
Table S3. Codon usage in the PCGs of the Microphysogobio elongatus mitogenome
Figure 5 from: Wang P, Yang H, Zhou W, Hwang C, Zhang W, Qian Z (2014) The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae. ZooKeys 451: 33-48. https://doi.org/10.3897/zookeys.451.8537
Figure 5 - Phylogenetic tree inferred by maximum likelihood (ML) and maximum parsimony (MP) methods based on 13 protein genes. The tree is rooted with Aplysia californica. Numbers on or under the nodes represent bootstrap values of MP and ML respectively.
Figure 4 from: Wang P, Yang H, Zhou W, Hwang C, Zhang W, Qian Z (2014) The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae. ZooKeys 451: 33-48. https://doi.org/10.3897/zookeys.451.8537
Figure 4 - Relative synonymous codon usage (RSCU) in the Camaena cicatricosa mt genome. Codon families are provided on the x axis.
Figure 3 from: Wang P, Yang H, Zhou W, Hwang C, Zhang W, Qian Z (2014) The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae. ZooKeys 451: 33-48. https://doi.org/10.3897/zookeys.451.8537
Figure 3 - Inferred secondary structures of 22 tRNA genes in Camaena cicatricosa. Dashed (-) indicates Watson-Crick base pairing and (•) indicates G-U base pairing.
Figure 1 from: Wang P, Yang H, Zhou W, Hwang C, Zhang W, Qian Z (2014) The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae. ZooKeys 451: 33-48. https://doi.org/10.3897/zookeys.451.8537
Figure 1 - The mt genome of Camaena cicatricosa. The tRNA genes are labeled based on the IUPACIUB single letter amino acid codes. Genes with underline illuminate the direction of transcription from 3' to 5', and without underline illuminating from 5' to 3'. Numbers and overlapping lines within the circle indicate PCR fragments amplified for sequencing (see Table 1).
Figure 2 from: Lin J-H, Zhou W-C, Ding H-L, Wang P, Ai H-M (2016) The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys 589: 55-69. https://doi.org/10.3897/zookeys.589.7637
Figure 2 - Relative synonymous codon usage (RSCU) in the Cernuella virgata mt genome. Codon families are provided on the x axis.
Figure 1 from: Lin J-H, Zhou W-C, Ding H-L, Wang P, Ai H-M (2016) The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys 589: 55-69. https://doi.org/10.3897/zookeys.589.7637
Figure 1 - The mt genome of Cernuella virgata. The tRNA genes are labeled based on the IUPACIUB single letter amino acid codes. Genes with underline illustrate the direction of transcription from 3' to 5', and without underline revealing from 5' to 3'. Numbers and overlapping lines within the circle indicate PCR fragments amplified for sequencing (see Table 1).
Figure 4 from: Lin J-H, Zhou W-C, Ding H-L, Wang P, Ai H-M (2016) The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys 589: 55-69. https://doi.org/10.3897/zookeys.589.7637
Figure 4 - Phylogenetic tree inferred by maximum likelihood (ML) method based on 13 protein genes. The tree is rooted with Aplysis californica and Galba pervia. Numbers on the nodes represent bootstrap values.
Figure 3 from: Lin J-H, Zhou W-C, Ding H-L, Wang P, Ai H-M (2016) The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys 589: 55-69. https://doi.org/10.3897/zookeys.589.7637
Figure 3 - Inferred secondary structures of 22 tRNA genes in Cernuella virgata. Dashes (-) indicate Watson-Crick base pairing and bullets (•) indicate G-U base pairing.
Figure 1 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 1 - Mitochondrial genome of Praticolella mexicana UTRGV and McAllen illustrated with an image of the species holotype (ANSP 426031). Gene order and sizes are shown relative to one another, not including non-coding regions. Genes are color coded by H (black) or L (red) strand. IUPAC single letter codes are used to identify tRNA genes.
Figure 3 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 3 - Maximum likelihood phylogeny of gene order. Analysis in MLGO yielded a single tree. Branch support >50% is shown based on 100 bootstrap replicates. Bradybaenidae and Helicidae were recovered as monophyletic, but Helicoidea was not.
Figure 4 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 4 - Ancestral gene order reconstructions for Helicoidea. Columns (A–E) correspond to labeled nodes in Figure 2. IUPAC single letter codes are used to identify tRNA genes. Rearrangements in red and blue are unique to Helicidae. The convergent rearrangement seen in Bradybaenidae, Camaena, and Praticolella is shown in yellow. The green rearrangement is unique to Aegista.
Figure 2 from: Minton RL, Martinez Cruz MA, Farman ML, Perez KE (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154. https://doi.org/10.3897/zookeys.626.9633
Figure 2 - Maximum likelihood phylogeny of Stylommatophora protein coding genes. Analysis in IQTREE yielded a single tree (log likelihood = -89104.188) under the mtZOA+F+I+G4 model. Branch support >50% is shown based on 10,000 ultra-fast bootstrap replicates. Helicoidea, Bradybaenidae, and Helicidae were recovered as monophyletic. Nodes A-E refer to rearrangements shown in Figure 4.
Figure 4 from: Geng X, Cheng R, Xiang T, Deng B, Wanga Y, Deng D, Zhang H (2016) The complete mitochondrial genome of the Chinese Daphnia pulex (Cladocera, Daphniidae). ZooKeys 615: 47-60. https://doi.org/10.3897/zookeys.615.8581
Figure 4 - Phylogenetic tree obtained by the maximum-likelihood (ML) method and bootstrap values (1000 repetitions) of the branches were indicated. Daphnia magna and Daphnia carinata were used as outgroups.
Figure 2 from: Geng X, Cheng R, Xiang T, Deng B, Wanga Y, Deng D, Zhang H (2016) The complete mitochondrial genome of the Chinese Daphnia pulex (Cladocera, Daphniidae). ZooKeys 615: 47-60. https://doi.org/10.3897/zookeys.615.8581
Figure 2 - Nucleotide compositions of the two Daphnia pulex from Chinese Chaohu (Ch) and North America (Na). CDS: protein-coding genes; 1st: first codon position; 2nd: second codon position; 3rd: third codon position; tRNA: tRNA genes; rRNA: rRNA genes; D-loop: A+T-rich region. In addition, stop codons were excluded.
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