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429 results for “multiple genes”
Data from: Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)
<p>Global climate change is predicted to increase the co-occurrence of high pCO2 and hypoxia in upwelling zones worldwide. Yet, few studies have examined the effects of these stressors on economically and ecologically important fishes. Here, we investigated short-term responses of juvenile blue rockfish (Sebastes mystinus) to independent and combined high pCO2 and hypoxia at the molecular level, using changes in gene expression and metabolic enzymatic activity to investigate potential shifts in energy metabolism. Fish were experimentally exposed to conditions associated with intensified upwelling under climate change: high pCO2 (1200 μatm, pH~7.6), hypoxia (4.0 mg O2/L), and a combined high pCO2/hypoxia treatment for 12 h, 24 h or two weeks. Muscle transcriptome profiles varied significantly among the three treatments, with limited overlap among genes responsive to both the single and combined stressors. Under elevated pCO2, blue rockfish increased expression of genes encoding proteins involved in the electron transport chain and muscle contraction. Under hypoxia, blue rockfish up regulated genes involved in oxygen and ion transport and down regulated transcriptional machinery. Under combined high pCO2 and hypoxia, blue rockfish induced a unique set of ionoregulatory and hypoxia responsive genes not expressed under the single stressors. Thus, high pCO2 and hypoxia exposure appears to induce a non-additive transcriptomic response that cannot be predicted from single stressor exposures alone, further highlighting the need for multiple stressor studies at the molecular level. Overall, lack of a major shift in cellular energetics indicates that blue rockfish may be relatively resistant to intensified upwelling conditions in the short term.</p>
Joint representation of molecular networks from multiple species improves gene classification - Data
<p>This is the data the accompanies the manuscript <em>Joint representation of molecular networks from multiple species improves gene classification</em></p> <p>Below is the license agreement for each of the publicly available datasets </p> <ul> <li><a href="https://wiki.thebiogrid.org/doku.php/terms_and_conditions">BioGRID</a></li> <li><a href="http://geneontology.org/docs/go-citation-policy/">GO</a></li> <li><a href="https://www.disgenet.org/legal">DisGeNet</a></li> <li><a href="https://monarchinitiative.org/about/licensing">Monarch</a></li> <li><a href="http://eggnog-mapper.embl.de">eggNOG</a></li> </ul> <p>No license agreement was available on <a href="http://imp.princeton.edu">IMP web site</a>, however we have obtained permission from the owner of the material to redistribute the network.</p>
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
<p>The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species <em>Formica polyctena</em> and <em>F. aquilonia</em>. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from <em>F. aquilonia</em> to <em>F. polyctena</em> until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.</p>
Figure 1 in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 1 Geographic location of the A. aegypti populations included in this study and gene-flow models evaluated. In both graphics, circles indicate the populations and arrows represent the gene flow between populations. A) Scale at American continent level (N = 2,996 specimens from six locations: Mexico – North America (M-NA), Venezuela (VZ), Peru (PE), Brazilian Amazon (BrAm), southeastern Brazil (SEBr), and Colombia (CO). B) Scale at South America level (N = 1,083 specimens from six locations: Venezuela, Peru, Brazilian Amazon (5 locations; Brazilian Amazon (BrAM), Manaus (MAO), Belém (BL). Boa Vista (BV), Rio Branco (RB), Porto Velho (PV)), Southeastern Brazil (SEBr) and Colombia (2 locations; Sucre (S), Quindio (Q)).
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 4. Phylogeny constructed through Bayesian inference estimated from the 35H found of the ND4 gene for the A. aegypti populations in the American continent. The blue horizontal bars above the branches reflect the 95% CI for the branch supports. The color bars (blue, green, and red) on the tree terminals indicate which haplotypes are exclusive for a specific population. The dotted lines on the right side of the tree and numbers I or II indicate to what clade each of the terminals belong. H1-Col (Colombia (Sucre and Quindio), Venezuela, Peru, M-NA, Brasil (MA-O, RBPV, SEBr, BE-L)), H4 (Venezuela, M-NA, Brasil (MA-O, RBPV, BEL)), H3 (Venezuela, M-NA, Brazil (RBPV, SEBr, BE-L)), H2-Col (Colombia (Sucre), Venezuela, Peru, M-NA, Brazil (RBPV, SEBr, BE-L)), H13 (M-NA, Brazil (SEBr)), H8 (Venezuela, Brazil (SEBr)).
Figure 3 in Gene Flow Patterns of the Aedes aegypti (Diptera: Culicidae) Mosquito in Colombia: a Continental Comparison Suggests Multiple Invasion Routes and Gene Exchange
Figure 3. Representation of the gene-flow model with greater subsequent probability in the scenarios of the Americas and South America.A. Scale at American continent level (N = 2,996 specimens from six locations: Mexico–North America, Venezuela, Peru, Brazilian Amazon, southeastern Brazil, and Colombia. Within the continent context, the Stepping Stone 1 model shows through the green vectors the way the gene flow occurs among the different populations evaluated. B. Scale at South America level; the Full-migration model indicates migration among all the populations, hence, plotting of the potential migration routes through passive land transport (Pan-American highway) and riverine paths (principal rivers).
Data platform (genotyping data set) related to ERDF postdoctoral project No. 1.1.1.2/VIAA/4/20/718 "The role of vitamin D gene polymorphisms and its receptors in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis".
<p><strong>Data platform </strong><strong>(genotyping dataset)</strong> <strong>related to the ERDF postdoctoral project No. </strong><strong>1.1.1.2/VIAA/4/20/718</strong><strong> “</strong><strong>The role of vitamin D and its receptor gene polymorphisms in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis</strong><strong>”.</strong></p> <p><strong>About the project and gathered data:</strong></p> <p>The dataset contains genotyping data on 289 sex-balanced samples (approximately 60% women / 40% men)) were created at the the multiple sclerosis (MS) Clinic of the Latvian Maritime Medical Center (LMMC) in 2011 (disease duration of 1-51 years); the collection was updated within the framework of the ERDF MS project (2017-2020) and replenished during the ERDF postdoctoral project No. 1.1.1.2/VIAA/4/20/718 “The role of vitamin D and its receptor gene polymorphisms in the modulation of intestinal inflammation in patients with relapsing and progressive forms of multiple sclerosis” (2021-2023).</p> <p>For the <strong>Genotyping dataset </strong>relevant information for each patient from the MS disease cohort, referring to proteasomal gene genetic variations (microsatellites and SNPs): (HSMS006 <em>(PSMA6),</em> HSMS602 <em>(FAM177A1),</em> HSMS701 <em>(KIAA0391)</em>, HSMS702 <em>(KIAA0391)</em> HSMS801 <em>(KIAA0391)</em>, rs11543947<em>(PSMB5), </em>rs2277460 (mi110), rs1048990 (mi8)<em> (PSMA6),</em> rs1048990 (mi8)<em> (PSMA6),</em> rs2295826/rs2295827<em>(PSMC6),</em> rs2348071 <em>(PSMA3),</em> rs2071543, rs9357155 <em>(PSMB8),</em> rs17587<em>(PSMB9),</em> rs74421874 <em>(PSMD9); </em>rs9275596 from HLA region; vitamin D-related genes (VDR and GC) polymorphisms: rs2228570, rs1544410, rs7975232, rs731236 (<em>VDR</em>) and rs7041, rs4588 <em>(GC).</em></p>
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
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Data from: Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)
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Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers
<p>Species radiations have long served as model systems in evolutionary biology. However, it has only recently become possible to study the genetic bases of the traits responsible for diversification, and only in a small number of model systems. Here we use genomes of 36 species of North, Central, and South American warblers to highlight the role of pigmentation genes—involved in melanin and carotenoid processing—in the diversification of this group. We show that <i>agouti signaling protein</i> (<i>ASIP</i>) and <i>beta-carotene oxygenase 2</i> (<i>BCO2</i>) are predictably divergent between species that differ in the distribution of melanin and carotenoid in their plumages, respectively. Among species, sequence variation at <i>ASIP</i> broadly mirrors the species' phylogenetic history, consistent with repeated, independent mutations generating melanin-based variation. In contrast, <i>BCO2</i> variation is highly discordant from the species tree, with evidence of cross-lineage introgression among species like the yellow warbler (<i>Setophaga petechia</i>) and magnolia warbler (<i>S. magnolia</i>) with extensive carotenoid-based coloration. We also detect introgression of a small part of the <i>BCO2</i> coding region (<3 kb) in <i>S. discolor</i> and <i>S. vitellina, </i>including an amino acid substitution that is unique to warblers but otherwise highly conserved across birds. Lateral transfer of carotenoid-processing genes has been documented in arthropods, but introgression of <i>BCO2</i> as demonstrated here—presumably adaptive—represents the first example of carotenoid gene transfer among vertebrates. These contrasting genomic patterns show that both independent evolution in a common set of genes and past gene flow have fueled plumage diversification in this colorful avian radiation.</p>
Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones
<p>The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognised pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or <em>de</em> <em>novo</em> mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six <em>Triturus</em> newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of <em>Triturus</em> species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple <em>Triturus</em> hybrid zones, indicating that MHC introgression between divergent hybridising species may be widespread and adaptive.</p>
Data for: Self-cleaving 2A peptides allow for expression of multiple genes in Dictyostelium discoideum
<p>The social amoeba <em>Dictyostelium discoideum</em> is a model for a wide range of biological processes including chemotaxis, cell-cell communication, phagocytosis, and development. Interrogating these processes with modern genetic tools often requires the expression of multiple transgenes. While it is possible to transfect multiple transcriptional units, the use of separate promoters and terminators for each gene leads to large plasmid sizes and possible interference between units. In many eukaryotic systems this challenge has been addressed through polycistronic expression mediated by 2A viral peptides, permitting efficient, co-regulated gene expression. Here, we screen the most commonly used 2A peptides, porcine teschovirus-1 2A (P2A), <em>Thosea asigna</em> virus 2A (T2A), equine rhinitis A virus 2A (E2A), and foot-and-mouth disease virus 2A (F2A), for activity in <em>D. discoideum</em> and find that all the screened 2A sequences are effective. However, combining the coding sequences of two proteins into a single transcript leads to notable strain-dependent decreases in expression level, suggesting additional factors regulate gene expression in <em>D. discoideum</em> that merit further investigation. Our results show that P2A is the optimal sequence for polycistronic expression in <em>D. discoideum</em>, opening up new possibilities for genetic engineering in this model system.</p>
Data for: Self-cleaving 2A peptides allow for expression of multiple genes in Dictyostelium discoideum
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Pigmentation Genes Show Evidence of Repeated Divergence and Multiple Bouts of Introgression in Setophaga Warblers
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Interspecific introgression of MHC genes in Triturus newts: Evidence from multiple contact zones
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Data from: Orthogonal transcriptional modulation and gene editing using multiple CRISPR/Cas systems
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Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype
<p>Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across ~7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (<em>CYP2J19</em>) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wings and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.</p>
Data from: Combinations of Spok genes create multiple meiotic drivers in Podospora
Meiotic drive is the preferential transmission of a particular allele during sexual reproduction. The phenomenon is observed as spore killing in multiple fungi. In natural populations of Podospora anserina, seven spore killer types (Psks) have been identified through classical genetic analyses. Here we show that the Spok gene-family underlies the Psks. The combination of Spok genes at different chromosomal locations defines the spore killer types and creates a killing hierarchy within the same population. We identify two novel Spok homologs located within a large (74-167 kbp) region (the Spok block) that resides in different chromosomal locations in given strains. We confirm that the SPOK protein performs both killing and resistance functions and show that these activities are dependent on distinct domains, a predicted nuclease and kinase domain. Genomic and phylogenetic analyses across ascomycetes suggest that the Spok genes disperse via cross-species transfer, and evolve by duplication and diversification within lineages.
Additive and mostly adaptive plastic responses of gene expression to multiple stress in Tribolium castaneum
Gene expression is known to be highly responsive to the environment and important for adjustment of metabolism but there is also growing evidence that differences in gene regulation contribute to species divergence and differences among locally adapted populations. However, most studies so far investigated populations when divergence had already occurred. Selection acting on expression levels at the onset of adaptation to an environmental change has not been characterized. Understanding the mechanisms is further complicated by the fact that environmental change is often multivariate, meaning that organisms are exposed to multiple stressors simultaneously with potentially interactive effects. Here we use a novel approach by combining fitness and whole-transcriptome data in a large-scale experiment to investigate responses to drought, heat and their combination in Tribolium castaneum . We found that fitness was reduced by both stressors and their combined effect was almost additive. Expression data showed that stressor responses were acting independently and did not interfere physiologically. Since we measured expression and fitness within the same individuals, we were able to estimate selection on gene expression levels. We found that variation in fitness can be attributed to gene expression variation and that selection pressures were environment dependent and opposite between control and stress conditions. We could further show that plastic responses of expression were largely adaptive, i.e. in the direction that should increase fitness.
Multiple paths to cold tolerance: the role of environmental cues, morphological traits and the circadian clock gene vrille
<p><strong>Background</strong>: Tracing the association between insect cold tolerance and latitudinally and locally varying environmental conditions, as well as key morphological traits and molecular mechanisms, is essential for understanding the processes involved in adaptation. We explored these issues in two closely-related species, Drosophila montana and Drosophila flavomontana, originating from diverse climatic locations across several latitudes on the coastal and mountainous regions of North America. We also investigated the association between sequence variation in one of the key circadian clock genes, vrille, and cold tolerance in both species. Finally, we studied the impact of vrille on fly cold tolerance and cold acclimation ability by silencing it with RNA interference in D. montana.</p> <p><strong>Results</strong>: We performed a principal component analysis (PCA) on variables representing bioclimatic conditions on the study sites and used latitude as a proxy of photoperiod. PC1 separated the mountainous continental sites from the coastal ones based on temperature variability and precipitation, while PC2 arranged the sites based on summer and annual mean temperatures. Cold tolerance tests showed D. montana to be more cold-tolerant than D. flavomontana and chill coma resistance (CT<sub>min</sub>) of this species showed an association with PC2. Chill coma recovery time (CCRT) of both species improved towards northern latitudes, and in D. flavomontana this trait was also associated with PC1. D. flavomontana flies were darkest in the coast and in the northern mountainous populations, but coloration showed no linkage with cold tolerance. Body size decreased towards cold environments in both species, but only within D. montana populations largest flies showed fastest recovery from cold. Finally, both the sequence analysis and RNAi study on vrille suggested this gene to play an essential role in D. montana cold resistance and acclimation, but not in recovery time.</p> <p><strong>Conclusions</strong>: Our study demonstrates the complexity of insect cold tolerance and emphasizes the need to trace its association with multiple environmental variables and morphological traits to identify potential agents of natural selection. It also shows that a circadian clock gene vrille is essential both for short- and long-term cold acclimation, potentially elucidating the connection between circadian clock system and cold tolerance.</p> <p> </p>
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.