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Supplementary material 5 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S2. Relative Synonymous Codon Usage (RSCU) of Parabreviscolexniepini : Explanation note: Codon families are labelled on the x-axis. Values on the top of the bars denote amino acid usage.
Supplementary material 4 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Figure S1. Sequence alignment of trnS1 for Parabreviscolexniepini and other cestodes : Explanation note: The position of the anticodon sequences was indicated.
Supplementary material 2 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S2. The list of cestodes species and outgroups used for comparative mitogenomic and phylogenetic analyses :
Supplementary material 1 from: Xi B-W, Zhang D, Li W-X, Yang B-J, Xie J (2018) Characterization of the complete mitochondrial genome of Parabreviscolex niepini Xi et al., 2018 (Cestoda, Caryophyllidea). ZooKeys 783: 97-112. https://doi.org/10.3897/zookeys.783.24674
Table S1. Primers used to amplify and sequence the mitochondrial genomes of Parabreviscolexniepini :
Complete set of data and script for the Kallisto/Sleuth & CLC analysis comparison
<p>Complete set of files that underlies the final report for the Kallisto/Sleuth and CLC analysis comparison.</p>
FGMP: assessing fungal genome completeness
<p>Datasets for FGMP tool (7,773 protein markers)</p> <p>7773_markers.fa.gz (A single representative sequence per orthologous group)</p> <p>7773_profiles_cutOff.tbl (FGMP significance thresholds)</p> <p>AllOneR.hmm.gz (FGMP hidden Markov models)</p> <p> </p> <p> </p>
FIGURE 3. Inferred phylogenetic relationship among 23 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 3. Inferred phylogenetic relationship among 23 taxa based on nucleotide sequences of mitochondrial 13 PCGs using Bayesian Inference (BI) (a) and maximum likelihood (ML) (b).
FIGURE 2. Predicted secondary structures for 22 in The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae
FIGURE 2. Predicted secondary structures for 22 tRNA genes of the S. pieli mitogenome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. The minus sign (-) indicates Watson-Crick base pairing and plus sign (.) indicates G-U base pairing.
FIGURE 4 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 4. Genetic distance of individual genes within Oedipodinae. Each boxplot represents P distance for 13 PCGs, rrnL and rrnS in sixteen Oedipodinae species. Lower horizontal bar, non-outlier smallest observation; lower edge of rectangle, 25 percentile; central bar within rectangle, median; upper edge of rectangle, 75 percentile; upper horizontal non-outlier largest observation; open circle, outlier.
FIGURE 1 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 1. Hilethera xinjiangensis sp. nov. male: A. body dorsal view; B. head frontal view; C. head and pronotum lateral view; D. body lateral view; E. head and pronotum dorsal view; F. end of abdomen dorsal view; G. epiphallus.
FIGURE 6 in A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome
FIGURE 6. Phylogenetic reconstruction of Oedipodinae using mitochondrial PCGs and rRNAs concatenated dataset inferred from Bayesian inference (BI, on the left of figure) and Maximum likelihood (ML, on the right of figure). Values on nodes indicate branch support, BI posterior probabilities (PP) / Maximum likelihood Bootstrap support values (BV). Asterisks are used to indicate maximum support (1.0 for PP and 100% for BV). Accession number of each species recorded in GenBank was indicated in brackets.
States of genome assembly supporting data for complete genome assembly of clinical multidrug resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial resistance genes and plasmids.
<p>Assemblies for each isolate and assembly stage is in .gfa and .fasta format.</p> <p>the best SPAdes assembly is also included in the .zip files.</p> <p>1) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong.<br> 2) Unicycler with illumina data and Nanopore data from the first sequencing run, filtered with FiltLong and error corrected with Canu<br> 3) Unicycler with illumina data and Nanopore data from the first and second sequencing run, filtered with FiltLong.<br> 4) manual finshing of assembly 3. <br> Methods are described in the paper and at the github repository (https://github.com/thsyd/bfassembly)</p> <p> </p>
Figs 17–20 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 17–20. Male terminalia of P. salpinflexus sec. Franz & Cardona-Duque (2013); (17) sternum VIII; (18) sternum IX; (19) tegmen; (20) aedeagus, dorsal and ventral view.
Figs 21–24 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 21–24. Female terminalia of P. salpinflexus sec. Franz & Cardona-Duque (2013); (21) sternum VIII; (22) coxites; (23) spermatheca, lateral view; (24) spermatheca, frontal view.
Figs 37–40 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 37–40. Comparative morphology of the male sternum VIII in Perelleschus sec. Franz & Cardona-Duque (2013); (37) P. evelynae sec. Franz & Cardona-Duque (2013); (38) P. sulcatae sec. Franz & Cardona-Duque (2013); (39) P. splendidus sec. Franz & Cardona- Duque (2013); (40) P. variabilis sec. Franz & Cardona-Duque (2013).
Fig. 35 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Fig. 35. Larvae and pupae of Perelleschus sec. Franz & Cardona- Duque (2013) inside the red pulp of a Carludovica palmata [nonfocal] infructescence.
Figs 7–11 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 7–11. Habitus and mouthparts of P. salpinflexus sec. Franz & Cardona-Duque (2013); (7) female, dorsal view; (8) female, lateral view; (9) labium, ventral view; (10) maxilla, dorsal view; (11) mandible, ventral view.
Figs 29–32 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 29–32. Male terminalia of P. spinothylax sec. Franz & Cardona-Duque (2013); (29) sternum VIII; (30) sternum IX; (31) tegmen; (32) aedeagus, dorsal and ventral view.
Figs 25–28 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 25–28. (25) and (26): habitus of P. spinothylax sec. Franz & Cardona-Duque (2013); (25) male, dorsal view; (26) male, lateral view. (27) and (28) comparison of labial shape, ventral view: (27) P. salpinflexus sec. Franz & Cardona-Duque (2013); (28) P. spinothylax sec. Franz & Cardona-Duque (2013).
Figs 1–6 in Description of two new species and phylogenetic reassessment of Perelleschus O'Brien & Wibmer, 1986 (Coleoptera: Curculionidae), with a complete taxonomic concept history of Perelleschus sec. Franz & Cardona-Duque, 2013
Figs 1–6. Graphic summary of six succeeding classifications and phylogenies for the species of Perelleschus sec. Franz & Cardona-Duque (2013), representing a nearly complete taxonomic concept history for this genus-level concept. (1) Günther (1936); (2) Voss (1954); (3) Wibmer & O'Brien (1986); (4) Franz & O'Brien (2001); (5) Franz (2006); (6) Franz & Cardona-Duque (2013). See also Tables 2–4 and Table 5 in Appendix, supplementary material online.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.