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Supplementary Tables of Whole Genome Sequencing and Assembly of the House Sparrow, Passer domesticus
<h2>Abstract</h2> <p>The common house sparrow, <em>Passer domesticus</em> is a small bird belonging to Passeridae. We provide here a high-quality whole genome sequencing and assembly for the house sparrow, The final genome assembly was made using a Shovill/SPAdes which consisted of contigs spanning 268193 bases. We employed rigorous statistical thresholds to check the coverage as the Passer genome showed considerable similarity with <em>Gallus gallus</em> (chicken) and <em>Taeniopygia guttata</em> (Zebra finch) genomes providing a functional annotation. This new annotated genome assembly will be a valuable resource as a reference for comparative and population genomic analyses of passerine, avian, and vertebrate evolution</p> <div> <p><strong>Significance</strong> Avian evolution has been of great interest in the context of extinction. Annotating the genomes such as Passerines would be a significant interest as we could understand the behavior/foraging traits and further explore their evolutionary landscape. In this work, we provide a full genome sequence of Indian house sparrow, <em>viz. Passer domesticus</em> which will serve as a useful resource in understanding the adaptability, evolution, geography, Allee effects and circadian rhythms.</p> </div>
Supplementary material 3 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
List of PCR primers and sequencing primers used in this study
Supplementary material 7 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Maximum Likelihood tree were inferred from the datasets COI + Cytb + 28S-D2 using IQ-tree
Supplementary material 4 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Summary of taxonomic groups used in Fig. 8
Supplementary material 6 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Predicted folding pattern for tRNAs of Synergus nanlingensis mitochondrial genome
Figure 8 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 8 Bayesian analysis of the MAFFT alignment data set inferred from the COI + Cytb + 28S-D2 data sets. Posterior probabilities are shown at each node.
Figure 6 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 6 Structures of control regions in the mitogenome of Synergus nanlingensis Wang & Zeng, 2023, sp. nov. Abbreviation: NTR, nontandem repeat. Yellow shows A + T-rich regions.
Figure 4 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 4 Mitochondrial genome of Synergus nanlingensis Wang & Zeng, 2023, sp. nov. sequenced in this study. Genes outside the circle are encoded by the majority strand, and genes inside are encoded by the minority strand. The tRNA genes are indicated by their one-letter corresponding amino acids. The GC content is plotted using a black sliding window. Abbreviations: atp6 and atp8, ATP-synthase subunits 6 and 8; cob, cytochrome b; cox1–3, cytochrome oxidase subunits 1–3; nad1–6 and nad4L, NADH dehydrogenase subunits 1–6 and 4 L; rrnL and rrnS, large and small rRNA subunits.
Figure 7 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 7 Mitochondrial genome organization and gene rearrangement in Synergus nanlingensis Wang & Zeng, 2023, sp. nov. compared with the ancestral type of the insect mitochondrial genome. All abbreviations are the same as in Table 1 in the main text. Arrow pointing to the right represents the J-strand and arrow pointing to the left represents the N-strand. Genes are drawn in their original order; intergenic distances are not included, and sizes of genes are not to scale. Yellow boxes indicate genes with different positions from two control regions reported in Cynipidae. and white boxes indicate genes that are different in terms of both position and strand associations from the putative ancestral pattern. Gray boxes show conserved gene blocks.
Figure 5 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 5 Relative synonymous codon usage (RSCU) of Synergus nanlingensis Wang & Zeng, 2023, sp. nov. mitochondrial genome. Codon families are labeled on the x-axis. Values on the top of the bars indicate the percentage of each amino acid used for the construction of 13 protein-coding genes (PCGs).
Supplementary material 5 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Pair-wise COI sequence distances in Synergus
Supplementary material 2 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
List of PCR primers used in this study
Figure 1 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 1 Synergus nanlingensis Wang & Zeng, 2023, sp. nov. a general habitus (♀) b general habitus (♂) c antenna (♀) d antenna (♂) e head in anterior view (♀) f head in anterior view (♂) g head in dorsal view (♀) h head in dorsal view (♂).
Figure 2 from: Duan Y-B, Wang Y-J, Zhu D-H, Zeng Y, Wang X-D (2024) Description and mitochondrial genome sequencing of a new species of inquiline gall wasp, Synergus nanlingensis (Hymenoptera, Cynipidae, Synergini), from China. Journal of Hymenoptera Research 97: 105-126. https://doi.org/10.3897/jhr.97.119433
Figure 2 Synergus nanlingensis Wang & Zeng, 2023, sp. nov. a head in lateral view (♀) b fore wing (♀) c head in posterior view (♀) d mesosoma, lateral view (♀) e mesosoma, dorsal view (♀) f propodeum, dorsal view (♀) g metasoma, lateral view (♀) h metasoma, lateral view (♂) i tarsal claw.
Genomic spectrograms of subsamplings from complete sequences of SARS-CoV-2
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Healthy woodchuck genome with viral sequences appended used for single-cell RNA-seq analysis
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Figure 3 in Genomic survey sequencing and complete mitochondrial genome of the elkhorn coral crab Domecia acanthophora (Desbonne in Desbonne & Schramm, 1867) (Decapoda: Brachyura: Domeciidae)
Figure 3. Secondary structure of the 22 tRNA genes in Domecia acanthophora.
Supplementary Info for manuscript "A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)" - F1000 Research
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Genome sequencing and assembly of Phytophthora oleae, isolate VK10A, NCBI sequences annotation.
<p>Annotation of the first draft of genome assembly of Phytophthora oleae, isolate code: VK10A.</p> <p>This isolate has been found in rot of mature olive drupes (Olea europaea var. sylvestris), from a tree located in Sicily: Complesso Speleologico Villasmundo S. Alfio Nature Reserve (NR) (Melilli, Siracusa, Italy); DATUM WGS 84, 37°13'17.2"N 15°06'22.3"E.</p> <p>Supplementary materials related to the manuscript: </p> <p><strong>Genome sequencing and assembly of <em>Phytophthora oleae</em>, isolate VK10A, causative agent of rot of olive drupes.</strong></p> <p><span>The Whole Genome Shotgun (WGS) of <em>P. oleae</em> genome assembly project has been deposited at DDBJ/ENA/GenBank under the accession JBIMZQ000000000 (assembly DJ1425, https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_046127205.1/).</span></p> <p> </p>
Supplementary Material for Ph.D. thesis: "Development of a data-intensive centralized system for surveillance and outbreak investigation of bacterial pathogens using whole-genome sequencing""
<p>Supplementary material for Ph.D. thesis.</p>
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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.
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.