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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.
Figure 1 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 1 - Structure of Chinese Daphnia pulex mitochondrial genome. COI, COII, COIII refer to the cytochrome oxidase subunits, Cytb refers to cytochrome b, ND1 - ND6 refer to NADH dehydrogenase components, and rrL and rrnS refer to rRNAs. tRNA genes are denoted by one letter symbol according to the IPUC-IUB single-letter amino acid codes. L1, L2, S1 and S2 denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN) and tRNASer(UCN), respectively. D-loop indicates A+T-rich region. Gene names outside the ring are coded on the majority strand while those inside are on the minority strand.
Supplementary material 1 from: Shan S, Wang Y (2022) Complete mitochondrial genomes of Boiga kraepelini and Hebius craspedogaster (Reptilia, Squamata, Colubridae) and their phylogenetic implications. ZooKeys 1124: 191-206. https://doi.org/10.3897/zookeys.1124.87861
Table S1, S2
Test datasets for GenoVi: draft and complete genomes
<p>Test dataset for GenoVi (Genome Visualizer).<br> All the genomes available in this repository were used to create all the analysis done by Cumsille et al., 2022 for the publication of GenoVi.</p>
Supplementary material 1 from: Wu J, Xu D, Wei X, Liao W, Li X, Zhuo Z (2023) Characterization of the complete mitochondrial genome of the longhorn beetle, Batocera horsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles. ZooKeys 1168: 387-402. https://doi.org/10.3897/zookeys.1168.105328
Batocera horsfieldi and 22 species
Supplementary material 2 from: Zhao T, Song N, Lin X, Zhang Y (2023) Complete mitochondrial genomes of the slugs Deroceras laeve (Agriolimacidae) and Ambigolimax valentianus (Limacidae) provide insights into the phylogeny of Stylommatophora (Mollusca, Gastropoda). ZooKeys 1173: 43-59. https://doi.org/10.3897/zookeys.1173.102786
Relative synonymous codon usage (RSCU) for 13 protein-coding genes of Ambigolimax valentianus
Supplementary material 1 from: Zhao T, Song N, Lin X, Zhang Y (2023) Complete mitochondrial genomes of the slugs Deroceras laeve (Agriolimacidae) and Ambigolimax valentianus (Limacidae) provide insights into the phylogeny of Stylommatophora (Mollusca, Gastropoda). ZooKeys 1173: 43-59. https://doi.org/10.3897/zookeys.1173.102786
Taxa included in this study, including GenBank Accession numbers and literature references
Supplementary material 3 from: Zhao T, Song N, Lin X, Zhang Y (2023) Complete mitochondrial genomes of the slugs Deroceras laeve (Agriolimacidae) and Ambigolimax valentianus (Limacidae) provide insights into the phylogeny of Stylommatophora (Mollusca, Gastropoda). ZooKeys 1173: 43-59. https://doi.org/10.3897/zookeys.1173.102786
The secondary structures of tRNA genes inferred for the mitogenome of Ambigolimax valentianus
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.