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Supplementary dataset to publication: Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes.
<p>This is the modified supplemented material to the publication “Complete genome sequence of ovine Mycobacterium avium subsp. paratuberculosis strain JIII-386 (MAP-S/type III) and its comparison to MAP-S/type I, MAP-C, and M. avium complex genomes”.</p> <p>The complete circular genome of Mycobacterium avium subsp. paratuberculosis (MAP) strain JIII-386 from Germany, closed by Nanopore technology in this study, was presented and compared with the draft genome of JIII-386, previously published in [doi:10.1093/gbe/ew154], the closed genome of the MAP-S/type I strain Telford, the MAP-S/type III draft genome of strain S397, twelve closed MAP-C (type II) strains and eight closed Mycobacterium avium (M. a.) strains of subsp. hominissuis (MAH) and subsp. avium (MAA). Structural comparisons clearly revealed the mosaic nature of MAP genomes, the differences between MAP subtypes I, II and III, and the higher diversity of MAP-S compared to MAP-C genomes. </p> <p>The material provides a wealth of detailed results from these analyses and comparisons. These include a list of identified ncRNA and Riboswitches, as well as additional genes in finished JIII-386, the gene content of identified prophage regions, copy number of identified transposable elements and a list of selected virulence-associated genes in the different MAP-type (I - III) strains. The genomic islands identified and included genes along with their predicted functions were presented for six MAP genomes (belonging to MAP-S/type I and III, and MAP-C), one MAH genome and one MAA genome. One table shows the corresponding genomic islands in the genomes of JIII-386, Telford and three MAP-C genomes. Furthermore, homologous genes of known MAP-S specific Large Sequence Polymorphisms regions (LSP<sup>S</sup> = LSP-S) were recorded in different MAP-S type strains, one MAH and one MAA strain, as well as genes of deletions #1 (LSP<sup>A</sup>-20), #2, and s-delta-1, previously described as MAP-S-specific deletions, their presence or absence in 3 MAP-S, 12 MAP-C, 4 MAH, and 4 MAA strains were listed. Different presence or absence of genes, but also identified frameshifts or disruptions of various virulence-associated genes could lead to the different MAP-type specific phenotypic characteristics. Comprehensive core and pan genome analyses (results listed in six tables) revealed unique genes and genes likely to have been acquired by horizontal gene transfer in different MAP types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M. a. strains.</p> <p> </p>
Marker files for assessing Prochlorococcus genome completness
<p>Use these files with CheckM to assess Prochlorococcus genome completeness:</p> <p><em>pro-marker-checkm-refined.txt</em></p> <p>List of custom PFAM and TIGRFAM identifiers used to assess genome completeness in <em>Prochlorococcus</em> using checkM</p> <p><em>pro-marker-checkm-refined.ms</em></p> <p>CheckM marker file of custom PFAM and TIGRFAM identifiers used to assess genome completeness in <em>Prochlorococcus</em>.</p> <p><em>pro-marker-checkm-refined.hmm</em></p> <p>HMM file of custom Prochlorococcus markers for use with CheckM and hmmer3</p>
The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding
<div>PN40024, a highly homozygous inbred line originating from ‘Helfensteiner’, was used for T2T genome assembly. In total, 21 Gb (21 024 461 524 bp, ∼42× coverage) HiFi reads were generated by the PacBio platform. For the preliminary assembly, hifiasm was used to assemble the HiFi reads. We then used MUMmer and the 12X.v0 genome version (V. vinifera genome assembly 12X.v0 to order the 38 contigs into 19 chromosomes.</div> <p> The PN_T2T genome size was finally generated (494.87 Mb), being 69 Mb longer than 12X.v0 using the same statistical method. The k-mer metric was used to evaluate genomic homozygosity, estimated at 99.8%. The BUSCO for this genome is up to 98.5%.</p> <p>The PN40024.T2T genome assembly: PN.fa</p> <p>The PN40024.T2T gene annotation: PN_T2T.v5.1.gff3</p> <p>The PN40024.T2T TE annotation: PN_T2T_TE.gff</p> <p>The PN40024.T2T centromere annotation: PN.trf.gff3</p> <p>The PN40024.T2T protein sequence: PN_protein.fa</p> <p>The PN40024.T2T cds sequence: PN40024.cds.fa</p> <p>Comparison of gene annotation among PN_T2T and PN_T2T.v5.1, 12X.v0, 12X.v2, PN40024.v4, PN40024.v4.1: correlation.list.txt</p> <p>Mitochondrial assembly sequence of PN40024: PN_T2T_mit.fa</p> <p>Annotation of mitochondrial assembly for PN40024:PN_T2T_mit.gff3</p> <p>Chloroplast assembly sequence of PN40024: PN_T2T_chl.fa</p> <p>Annotation of chloroplast assembly for PN40024: PN_T2T_chl.gff3</p> <p>Citation: </p> <p>Please cite this paper when using the data of PN_T2T for your publications.</p> <p>Xiaoya Shi, Shuo Cao, Xu Wang, Siyang Huang, Yue Wang, Zhongjie Liu, Wenwen Liu, Xiangpeng Leng, Yanling Peng, Nan Wang, Yiwen Wang, Zhiyao Ma, Xiaodong Xu, Fan Zhang, Hui Xue, Haixia Zhong, Yi Wang, Kekun Zhang, Amandine Velt, Komlan Avia, Daniela Holtgräwe, Jérôme Grimplet, José Tomás Matus, Doreen Ware, Xinyu Wu, Haibo Wang, Chonghuai Liu, Yuling Fang, Camille Rustenholz, Zongming Cheng, Hua Xiao, Yongfeng Zhou, The complete reference genome for grapevine (<em>Vitis vinifera</em> L.) genetics and breeding, <em>Horticulture Research</em>, Volume 10, Issue 5, May 2023, uhad061, <a href="https://doi.org/10.1093/hr/uhad061">https://doi.org/10.1093/hr/uhad061</a></p>
Supplementary Materials associated with paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships'
<p>This is a repository for coverage depth graphs and ML-phylogenetic trees that are associated with the paper 'Complete linear mitochondrial genomes for Cephea cephea and Mastigias albipunctata (Scyphozoa: Rhizostomeae), with an analysis of phylogenetic relationships' by Tan KC, Collins AG and Ames CL.</p>
Complete genome analysis of a novel narnavirus in sweet viburnum (Viburnum odoratissimum)
<p>genome.fasta is Vo narna-like virus complete genomo file.</p><p>JPSH_1.fq.gz and JPSH_1.fq.gz are transcriptome sequencing raw data.</p><p>JPSH.fq.gz is siRNA sequencing raw data.</p><p>trinity.JPSH.Trinity.fasta is Trinity assembly result.</p><p>trinity.nr.JPSH is DIAMOND-BLASTX result</p><p> </p>
Figure 3. The phylogenetic relationship between G in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 3. The phylogenetic relationship between G. bucephalus and the other Pipistrellini species is inferred by maximum likelihood analysis based on cytb sequences. The numbers in the branches show the bootstrap values. Vespertilio species are used as outgroups.
Figure 1 in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 1. Map of the G. bucephalus mitogenome. Gray color indicates the PCG regions; red color— tRNAs; yellow color—rRNAs. The heavy strand in the outer circle encodes 28 genes, whereas 9 genes are encoded in the light strand in the inner circle.
Figure 2. The phylogenetic relationship between G in The Complete Mitochondrial Genome of Glischropus bucephalus (Vespertilionidae; Chiroptera) Provides New Evidence for Pipistrellus Paraphyly
Figure 2. The phylogenetic relationship between G. bucephalus and the other Vespertilioninae species is inferred by the maximum likelihood analysis based on the concatenated protein-coding gene sequences. The bootstrap values (indicated by the slashes on the branches) correspond to the trees constructed on full sequences (three codon positions), the first two codon positions (third positions omitted), and two positions with the exclusion of the Nd6 gene. The asterisks mark branches that in the second or third case have a different topology than shown. Myotis species are used as outgroups.
Figure 13. A in Erratum: JING LIU, HAIYU LUO, XIANGYI LU & XUN BIAN (2021) New additions to the Chinese Agraeciini Redtenbacher, 1891 (Orthoptera, Tettigoniidae: Conocephalinae) with report the complete mitochondrial genome of Palaeoagraecia brunnea Ingrisch, 1998. Zootaxa, 5072: 238–254.
Figure 13. A phylogenetic tree obtained from bayesian inference analysis based on 13 protein-coding genes.
Fig. 3 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 3. Predicted secondary structure of the rrnl in the Acanthacorydalis orientalis mt genome. Roman numerals denote the conserved Watson-Crick base pairing and dot (•) indicates G-U base pairing.
Fig. 4 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 4. Predicted secondary structure of the rrns in the A. orientalis mt genome. Roman numerals denote the conserved domain structure. Dash (-) indicates Watson-Crick base pairing and dot (•) indicates G-U base pairing.
Fig. 1 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 1. Mitochondrial genome map of Acanthacorydalis orientalis. The tRNAs are denoted by the color blocks and are labeled according to the IUPACIUB single-letter amino acid codes. Gene name without underline indicates the direction of transcription
Fig. 2 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 2. Inferred secondary structure of 22 tRNAs of the Acanthacorydalis orientalis mt genome. The tRNAs are labeled with the abbreviations of their corresponding amino acids. Dash (-) indicates Watson-Crick bonds and dot (·) indicates GU bonds.
Fig. 5 in Sequencing and analysis of the complete mitochondrial genome of the giant dobsonfly Acanthacorydalis orientalis (McLachlan) (Insecta: Megaloptera: Corydalidae)
Fig. 5. Phylogenetic relationships among the sequenced Megaloptera insects. Numbers at the nodes are Bayesian posterior probabilities (left) and ML bootstrap values (right).
Fig. 6 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 6. The phylogenetic relationship of Bonasa among Galliformes based on the complete mitogenome. Branch lengths and topologies were obtained from Maximum Likelihood analyses. The numbers were the bootstrap values of MP/ML/BI trees in turn. * indicates that MP or BI tree was inconsistent with ML tree.
Fig. 4 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 4. The structure of CR in Bonasa sewerzowi mitochondrial genome and comparasion with B. bonasia.
Fig. 5 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 5. Nucleotide composition of different partitions from two Bonasa mitogenomes. AT-skew, (A-T)/(A+T); GC-skew, (G-C)/(G+C); PCG-1st, the first codon positions of PCGs; PCG-2nd, the second codon positions of PCGs; PCG-3rd, the third codon positions of PCGs.
Fig. 3 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 3. The srRNA secondary structure of Bonasa sewerzowi mitogenome and comparasion with B. bonasia. The different nucleotides in B. bonasia was pointed out.
Fig. 1 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 1. Gene map of the B. sewerzowi mitochondrial genome. Transfer RNA genes are designated by single-letter amino acid codes. L1, L2, S1, and S2 denote trnL (uur), trnL (cun), trnS (ucn) and trnS (agy), respectively.
Fig. 2 in Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis
Fig. 2. The lrRNA secondary structure of Bonasa sewerzowi mitogenome and comparasion with B. bonasia. The different nucleotides in B.
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.