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opencc-by-4.0Dec 2019View details →

Fig. 1 in Complete mitochondrial genome of Nyctalus aviator and phylogenetic analysis of the family Vespertilionidae

Fig. 1. Neighbor Joining (NJ) phylogeny of Vespertilionidae was inferred from concatenated nucleotide sequences of 13 mitogenomic protein-coding genes. Node labels indicate the bootstrap values. GenBank accession numbers for the sequences are indicated next to species designations.

opencc-by-4.0Mar 2018View details →

Repeat-masked Strix occidentalis caurina nuclear genome version 1.0 and complete mitochondrial genome

StrOccCau_1.0_nuc_finalMito_RepeatMasked.fa.bz2 : This file is homology-based and de novo model-based repeat-masking of the reference Strix occidentalis caurina genome StrOccCau_1.0_nuc.fa from Hanna et al., 2017a,b) with the mitochondrial genome from Hanna et al. (2017c). StrOccCau_1.0_nuc_finalMito_RepeatMasked.bed.bgz : This is a file in Browser Extensible Data (BED) format that provides the genomic intervals of the N-regions in the above masked assembly. The N-regions include hard-masked low complexity and repeat regions as well as N-regions that were gaps in the original assembly. I compressed the file using the bgzip tool from HTSlib version 1.7 (Davies et al. 2018). See full details of the creation of these files in section 2.1 of the materials and methods at protocols.io (http://dx.doi.org/10.17504/protocols.io.rmrd456). If you use these data, please cite the following: Hanna ZR. 2018. Repeat-masked Strix occidentalis caurina nuclear genome version 1.0 and complete mitochondrial genome. Version 1.0.0. Zenodo.   References Davies R, Randall JC, McCarthy SA, Bonfield J, Pollard MO, Marshall J, et al. 2018. HTSlib. Version 1.7. [Accessed 2018 Mar 19]. Available from: https://github.com/samtools/htslib Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017a. Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes. Genome Biology and Evolution. 9: 2522–2545. DOI: 10.1093/gbe/evx158 Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, et al. 2017b. Supplemental dataset for Northern Spotted Owl (Strix occidentalis caurina) genome assembly version 1.0. Zenodo. DOI: 10.5281/zenodo.822859 Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. 2017c. Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ. 5: e3901. DOI: 10.7717/peerj.3901

opencc-by-4.0Mar 2021View details →

Figure 3 in Complete mitochondrial genome of an Arctic Collared Lemming subspecies endemic to the Novaya Zemlya Archipelago, Russia

Figure 3. Bayesian Inference phylogenetic tree of the concatenated protein coding and rRNA genes based on available mitogenomes of Arctic Collared Lemming Dicrostonyx torquatus. The red font indicates the Novaya Zemlya subspecies D. torquatus ungulatus. The numbers near nodes represent Bayesian Posterior Probabilities (BPP) of MrBayes / Bootstrap Support (BS) values of IQ-Tree. The values above 95% for both BPP/BS are replaced with an asterisk. Outgroup taxa (Dicrostonyx hudsonius and D. groenlandicus) are not shown.

opencc-by-4.0Mar 2021View details →

Figure 1 in Complete mitochondrial genome of an Arctic Collared Lemming subspecies endemic to the Novaya Zemlya Archipelago, Russia

Figure 1. Morphology of Novaya Zemlya Collared Lemming Dicrostonyx torquatus ungulatus (von Baer, 1841) from Novaya Zemlya Archipelago, Arctic Russia [topotype No. RMBH Lem16]: (A, B) specimen: (A) dorsal view, (B) ventral view; (C, D, E) crania: (C) dorsal view, (D) ventral view, (E) lateral view; (F, G) lower jaw: (F) outer lateral view, (G) inner lateral view; (H, I) molar rows: (H) maxillary, and (I) mandibular. Scale bars = 10 mm. (Photos: Elizaveta A. Spitsyna).

Fig. 1. Diplodiscus japonicus and Diplodiscus mehari mitochondrial genomes arrangement. All 22 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 1. Diplodiscus japonicus and Diplodiscus mehari mitochondrial genomes arrangement. All 22 tRNA genes are designated by the one-letter code with numbers differentiating each of the two tRNAs leucine and serine. All genes are coded by the same DNA strand and are transcribed clockwise. NCR refers to the non-coding region.

Fig. 5 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 5. Proportions between rates of non-synonymous (dN) and synonymous (dS) nucleotide substitutions (dN/dS). Bar chart for pairwise proportions of dN/dS for each of the mitochondrial subunits of the Diplodiscus spp.

Fig. 4 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 4. Sliding window analysis of the complete mt genome sequences of 11 Paramphistomoidea trematodes. A sliding window of 300 bp (in 10 bp overlapping steps) was used to estimate nucleotide diversity Pi (π) across the alignments. Nucleotide diversity was plotted against the mid-point positions of each window. Each gene boundary is identified.

Fig. 5 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 5. Phylogenetic tree Note: (A): Maximum likelihood (ML) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset; (B): Bayesian inference (BI) phylogenetic tree inferred from the mitochondrial genome based on the 13 PCGs dataset.

Fig. 4 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 4. Mitochondrial genome organization of Platygaster robiniae and 11 species of Platygastroidea, compared with the ancestral pancrustacean mt genome organization. Note: tRNA genes are indicated by single letter amino acid codes, L1, L2, S1 and S2 denote tRNALeu(CUN), tRNALeu(UUR), tRNASer(AGN) and tRNASer(UCN), respectively. Genes are transcribed from left to right except those indicated by underlining. Gene movements, relative to the ancestral organization, are indicated with arrows.

Fig. 3 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 3. Relative synonymous codon usage (RSCU) of 12 protein coding genes of Diplodiscus japonicus and Diplodiscus mehari. The termination codon is not given.

Fig. 2 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 2. Amino acids (A) and relative synonymous codons (B) of protein-coding genes of the mitochondrial genome of Platygaster robiniae.

Fig. 2. A in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 2. A + T content and nucleotide skew of genes, individual elements, and the complete mitogenome of 11 Paramphistomoidea trematodes.

Fig. 1 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Fig. 1. Genetic map of the complete mitochondrial genome of Platygaster robiniae. Notes: the blue arrow represents the direction of gene transcription; the black peak represents the deviation of GC%; the purple and green peaks represent the deviation in GC skew; green refers to positive skew, and purple indicates negative skew. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Characterization of the complete mitochondrial genomes of Diplodiscus japonicus and Diplodiscus mehari (Trematoda: Diplodiscidae): Comparison with the members of the superfamily Paramphistomoidea and phylogenetic implication

Fig. 6. Phylogenetic relationships of Diplodiscus japonicus and Diplodiscus mehari with other 30 representative Digenea trematodes based on concatenated amino acid sequences of 12 protein coding genes analyzed by maximum likelihood (ML) and Bayesian inference (BI) using Gyrodactylus salaris as the outgroup. Statistical support values (Bootstrap/posterior probability) of ML/BI analysis are shown above the nodes. Circles indicate ML/BI = 100/1.0, other values are given above the nodes. Suborders and families are highlighted by individual colors. Accession numbers are given for each species at the end of each sequence. The scale bar corresponds to the estimated number of substitutions per site. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Comparative analyses of the fragmented mitochondrial genomes of wild pig louse Haematopinus apri from China and Japan

Fig. 2. The complete mitochondrial genome of wild pig louse Haematopinus apri form China. Each minichromosome has a coding region and a non-coding region (NCR, in black). The names and transcript orientation of genes are indicated in the coding region and the minichromosomes are placed in alphabetical order of protein-coding genes and rRNA genes. Abbreviations: atp6 and atp8, ATP synthase F0 subunits 6 and 8; cytb, cytochrome b; cox1-3, cytochrome c oxidase subunits 1–3; nad1-6 and nad4L, NADH dehydrogenase subunits 1–6 and 4L; rrnS and rrnL, small and large subunits of ribosomal RNA. tRNA genes are indicated with their single-letter abbreviations of the corresponding amino acids.

Fig. 7 in Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

Fig. 7. Maximum likelihood (ML) phylogenetic tree from entire mt genomes (15,254 bp alignment). Tip-labels indicate NCBI accession numbers. Numbers above branches show Maximum Likelihood bootstrap support whereas numbers below branches show the Bayesian Posterior Probability support. Ixodes pavlovskyi Pomerantzev, 1946, one of the species of "other Ixodes" clade (sensu Barker et al., 2021), for which an entire mitochondrial (mt) genome was available in GenBank, was set as the outgroup. The scale bar indicates 0.07 nucleotide substitutions per nucleotide site for the 15,254 nucleotide sites in our alignment of theses entire mt genomes. So, for example, there were about 1067 nucleotide substitutions along the branch that leads to I. (Ceratixodes) uriae plus I. (Sternalixodes) holocyclus plus I. (Exopalpiger) fecialis, which is marked with an asterisk (i.e. 0.07 nucleotide substitutions per nucleotide site x 15,254 nucleotide sites (bps) = 1067 nucleotide substitutions). Ticks in bold were sequenced in the present study.

Fig. 6 in Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

Fig. 6. The mitochondrial genomes of Ixodes (Sternalixodes) confusus, I. (St.) myrmecobii, I. (St.) cornuatus, I. (St.) hirsti and I. (St.) trichosuri. Protein-coding genes are shown in green, tRNAs are in yellow, rRNAs are in red whereas the two control regions are in blue. Protein-coding genes are labelled by their fourcharacter abbreviations, tRNAs are labelled by their one-letter amino acid abbreviations whereas the two control regions are labelled as CR1 and CR2. Variation in the size of mitochondrial genome is indicated in parenthesis. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

Fig. 5. Ixodes confusus Roberts (1960), scanning electron micrographs of female. A, Idiosoma, dorsal view; B, Idiosoma showing posterior portion of scutum and alloscutum; C, Idiosoma, ventral view; D, Spiracular plate; E, Gnathosoma, dorsal view; F, Porose areas; G, Gnathosoma, ventral view; H, Coxae. Specimens: A-H, B5510 Etty Bay, Qld. Scale-bars: A, C, 1 mm; B, E, G, H, 0.5 mm; D, F, 0.2 mm.

Fig. 3 in Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

Fig. 3. Holotype (male) of Ixodes confusus Roberts (1960) from Sogeri, Papua New Guinea (QM QM-G2456), horizontal scale bar 1 mm, vertical scale bar 2.7 mm.

Fig. 4 in Rediscovery of Ixodes confusus in Australia with the first description of the male from Australia, a redescription of the female and the mitochondrial (mt) genomes of five species of Ixodes

Fig. 4. Ixodes confusus Roberts (1960), scanning electron micrographs of male. A, Idiosoma, dorsal view; B, Idiosoma, ventral view; C, Anal plate; D, Spiracular plate; E, Gnathosoma, dorsal view; F, Gnathosoma, anteroventral view; G, Coxae. Specimens: A, B6697 Mt Molloy, Qld; B, C, D, F, G B5511 Etty Bay; E, B5537 Cardwell. Scale-bars: A, B, 1 mm; C, D, 0.4 mm; E, F, 0.2 mm; G, 0.5 mm.