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Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.
Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).
Supporting data for: A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence
<p>This upload contains genome assemblies and annotation files for four planarian species. </p> <h2>Genome assemblies</h2> <p>The genome assemblies are deposited as FASTA files with the ending '.fa.gz'.</p> <h2>Genome annotations</h2> <p>The genome annotations are deposited as gff3 files and contain the 'ENCODE' keyword.</p> <p>Integration into Wormbase are currently ongoing to provide userfriendly access.</p> <h2>Transposable element annotation</h2> <p>Transposable element annotation performed with the EDTA pipeline are deposited as GFF3 files with the file ending '.EDTA.TEanno.gff3.gz'.</p> <h2>Satellite DNA</h2> <p>Repetitive satellite regions annotated using RepeatExplorer and SRF are deposited as GFF3 files with the ending 'satDNA.gff3'.</p>
Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between <i>trnS1</i> and <i>trnL1</i></td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between <i>rrnL</i> and <i>trnE</i></td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
Genomic population structure of striped bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River
<p>Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada to the Cape Fear River, United States (US). We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (1) evidence of admixture within Saint John River, indicating that migrants from the US and from Shubenacadie River occasionally spawn in the Saint John River; (2) Striped Bass collected in the Mira River, Cape Breton, Canada were found to be of both Miramichi River and US origin ; (3) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (4) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.</p>
Data from: Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure
Populus trichocarpa is an ecologically important tree across western North America. We used a large population sample of 498 accessions over a wide geographical area genotyped with a 34K Populus SNP array to quantify geographical patterns of genetic variation in this species (landscape genomics). We present evidence that three processes contribute to the observed patterns: (1) introgression from the sister species P. balsamifera (2) isolation-by-distance and (3) natural selection. Introgression was detected only at the margins of the species' distribution. Isolation-by-distance was significant across the sampled area as a whole, but no evidence of restricted gene flow was detected in a core of drainages from southern British Columbia. We identified a large number of FST outliers. GO analyses revealed that FST outliers are overrepresented in genes involved in circadian rhythm and response to red/far-red light when the entire dataset is considered, while in southern British Columbia heat response genes are overrepresented. We also identified strong correlations between geoclimate variables and allele frequencies at FST outlier loci that provide clues regarding the selective pressures acting at these loci.
Structural 3D domain reconstruction of the RNA genome from viruses from a secondary structure model
<p>Fragments and final models of reconstructed STMV genome from in virio and in vitro secondary structures reported in Larman et al. (2017).</p> <p>Simulation scripts for simulations of genome and fragments.</p> <p>Full code of SPQR package for performing simulations.</p>
Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the Chocolate Tree
<p>Genomic structural variants (SVs) can play important roles in adaptation and speciation. Yet, the overall fitness effects of SVs are poorly understood, partly because accurate population-level identification of SVs requires multiple high-quality genome assemblies. Here, we use 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao – an outcrossing, long-lived tree species that is the source of chocolate – to investigate the fitness consequences of SVs in natural populations. Among the 31 accessions, we find over 160 thousand SVs, which together cover eight times more of the genome than SNPs and short indels (125 Mb vs. 15 Mb). Our results indicate that a vast majority of these SVs are deleterious: they segregate at low frequencies and are depleted from functional regions of the genome. We show that SVs influence gene expression, which likely impairs gene function and contributes to the detrimental effects of SVs. We also provide empirical support for a theoretical prediction that SVs, particularly inversions, increase genetic load through the accumulation of deleterious nucleotide variants as a result of suppressed recombination.<br> Despite the overall detrimental effects, we identify individual SVs bearing signatures of local adaptation, several of which are associated with genes differentially expressed between populations. Genes involved in pathogen resistance are strongly enriched among these candidates, highlighting the contribution of SVs on this important local adaptation trait. Beyond revealing new empirical evidence for the evolutionary importance of SVs, these 31 de novo assemblies provide a valuable resource for genetic and breeding studies in T. cacao. </p>
Data from: Genomics detects population structure within and between ocean basins in a circumpolar seabird: the white-chinned petrel
<p>The Southern Ocean represents a continuous stretch of circumpolar marine habitat, but the potential physical and ecological drivers of evolutionary genetic differentiation across this vast ecosystem remain unclear. We tested for genetic structure across the full circumpolar range of the white-chinned petrel (<i>Procellaria aequinoctialis</i>) to unravel the potential drivers of population differentiation and test alternative population differentiation hypotheses. Following range-wide comprehensive sampling, we applied genomic (genotyping-by-sequencing or GBS; 60,709 loci) and standard mitochondrial-marker approaches (cytochrome b and 1st domain of control region) to quantify genetic diversity within and among island populations, test for isolation by distance, and quantify the number of genetic clusters using neutral and outlier (non-neutral) loci. Our results supported the multi-region hypothesis, with a range of analyses showing clear three-region genetic population structure, split by ocean basin, within two evolutionary units. The most significant differentiation between these regions confirmed previous work distinguishing New Zealand and nominate subspecies. Although there was little evidence of structure within the island groups of the Indian or Atlantic oceans, a small set of highly-discriminatory outlier loci could assign petrels to ocean basin and potentially to island group, though the latter needs further verification. Genomic data hold the key to revealing substantial regional genetic structure within wide-ranging circumpolar species previously assumed to be panmictic.</p>
A classification framework for Bacillus anthracis defined by global genomic structure
<p><i>Bacillus anthracis</i>, the causative agent of anthrax, is a considerable global health threat affecting wildlife, livestock, and the general public. In this study whole-genome sequence analysis of over 350 <i>B. anthracis</i> isolates was used to establish a new high-resolution global genotyping framework that is both biogeographically informative, and compatible with multiple genomic assays. The data presented in this study shed new light on the diverse global dissemination of this species and indicate that many lineages may be uniquely suited to the geographic regions in which they are found. In addition, we demonstrate that plasmid genomic structure for this species is largely consistent with chromosomal population structure, suggesting vertical inheritance in this bacterium has contributed to its evolutionary persistence. This classification methodology is the first based on population genomic structure for this species and has potential use for local and broader institutions seeking to understand both disease outbreak origins and recent introductions. In addition, we provide access to a newly developed genotyping script as well as the full whole genome sequence analyses output for this study, allowing future studies to rapidly employ and append their data in the context of this global collection. This framework may act as a powerful tool for public health agencies, wildlife disease laboratories, and researchers seeking to utilize and expand this classification scheme for further investigations into <i>B. anthracis</i> evolution.</p>
Data from: Structural variation and its potential impact on genome instability: novel discoveries in the EGFR landscape by long-read sequencing
<p>Studies of structural variation (SV) have been challenging due to technological contraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examime SV in the <em>EGFR </em>landscape of four haplotypes derived from two human samples. We analyzed the <em>EGFR</em> gene and its landscape (+/- 500,000 base pairs) using this sequencing approach and were able to identify regions of non-coding DNA which had relatively high similarity to the most common activating <em>EGFR</em> mutation in non-small cell lung cancer. We discovered that reverse complements to the exon 19 deletion mutation which had at least 60% homology to the <em>EGFR</em> exon 19 canonical deletion and were within ± 421,000 bp of the deletion varied across the five haploid genomes examined (4 patient landscapes and hg38). Although the sample size is limited in this study, the estimated variation observed in genomic stability between the five <em>EGFR</em> haplotypes examined is novel and encourages further work to examine structural variation in larger cohorts.</p>
Genomic assessment of global population structure in a highly migratory and habitat versatile apex predator, the tiger shark (Galeocerdo cuvier)
<p>Understanding the population dynamics of highly mobile, widely distributed, oceanic sharks, many of which are overexploited, is necessary to aid their conservation management. We investigated the global population genomics of tiger sharks (<i>Galeocerdo cuvier</i>), a circumglobally distributed, apex predator displaying remarkable behavioral versatility in its diet, habitat use (near coastal, coral reef, pelagic), and individual movement patterns (spatially resident to long-distance migrations). We genotyped 242 tiger sharks from 10 globally distributed locations at more than 2000 single nucleotide polymorphisms. Although this species often conducts massive distance migrations, the data show strong genetic differentiation at both neutral (<i>F</i><sub>ST</sub>=0.125-0.144) and candidate outlier loci (<i>F</i><sub>ST</sub>=0.570-0.761) between western Atlantic and Indo-Pacific sharks, suggesting the potential for adaptation to the environments specific to these oceanic regions. Within these regions, there was mixed support for population differentiation between northern and southern hemispheres in the western Atlantic, and none for structure within the Indian Ocean. Notably, the results demonstrate a low level of population differentiation of tiger sharks from the remote Hawaiian archipelago compared to sharks from the Indian Ocean (<i>F</i><sub>ST</sub>=0.003-0.005, <i>P</i><0.01). Given concerns about biodiversity loss and marine ecosystem impacts caused by overfishing of oceanic sharks in the midst of rapid environmental change, our results suggest it imperative that international fishery management prioritize conservation of the evolutionary potential of the highly genetically differentiated Atlantic and Indo-Pacific populations of this unique apex predator. Furthermore, we suggest targeted management attention to tiger sharks in the Hawaiian archipelago based on a precautionary biodiversity conservation perspective.</p>
FIGURE 14 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 14. Living specimens of Gastrotheca of the fissipes group: (A) Gastrotheca recava sp. nov. (Wenceslau Guimarães, BA), (B) G. fissipes (Maceió, AL); (C) G. prasina sp. nov. (Jequitinhonha, MG), and (D) G. megacephala (Guarapari, ES).
FIGURE 11 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 11. Advertisement call of Gastrotheca recava sp. nov.: (A) Oscillogram containing two calls and; (B) An oscillogram of a section comprising a single call; (C) Spectrogram of the same call; (D) Amplitude spectrum of the same call. Calls were recorded about 20:00h on 8th December 2011, air temperature was about 22ºC.
FIGURE 10 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 10. Living specimen of Gastrotheca recava sp. nov. (A), perching over a fern, where they were commonly find (B), a juvenile (C), an ovigerous female (D) and a male calling with extended vocal sac (E).
FIGURE 6 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 6. Habitats occupied by Gastrotheca prasina sp. nov.: (A) A general view of the landscape at RBME; note hills slopes covered with forests and patches of open sparse vegetation on their top; (B) a detail of the open vegetation that dominate the summit, showing the sandy soil with bare ground, and dense clusters of bromeliads; (C) and the bromeliad in which individuals of Gastrotheca prasina sp. nov. were found.
FIGURE 3 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 3. Living holotype (MZUSP 147059) of Gastrotheca prasina sp. nov. (A), living paratopotypes hiding inside a bromeliad (B), calling with extended vocal sac (C), and a female carrying eggs on its pouch (D).
FIGURE 13 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 13. Bayesian Inference tree and posterior probabilities based on ND1, cmyc, cryBA, rhodopsin, and SIA sequences. Published sequences of Scinax, Flectonotus, and Fritziana were used as outgroup (not shown).
FIGURE 5 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 5. Comparison of posterior edge of skull in (A) Gastrotheca megacephala, (B) G. prasina sp. nov., (C) G. recava sp. nov., and (D) G. fissipes, externally (left) and internally (right). Externally visible edge of skull bones represented by a black dashed line. Bones: 1= sphenethmoid; 2=nasal; 3=frontoparietal; 4=squamosal.
FIGURE 12 in Solution NMR Structure of CalU16 from Micromonospora echinospora, Northeast Structural Genomics Consortium (NESG) Target MiR12
FIGURE 12. Habitats occupied by Gastrotheca recava sp. nov. at EEEWG. (A) view of the interior of the forest; (B) external view of a hill covered with forest; and (C) an anthropized area in regeneration.
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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.