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669 results for “comparative genomics”
Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, 3 of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease-resistance. Parallel comparisons using a wild, non-founder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
Data from: Comparative species divergence across eight triplets of spiny lizards (Sceloporus) using genomic sequence data
Species divergence is typically thought to occur in the absence of gene flow, but many empirical studies are discovering that gene flow may be more pervasive during species formation. Although many examples of divergence with gene flow have been identified, only few clades have been investigated in a comparative manner, and fewer have been studied using genome-wide sequence data. We contrast species divergence genetic histories across eight triplets of North American Sceloporus lizards using a maximum likelihood implementation of the isolation–migration (IM) model. Gene flow at the time of species divergence is modeled indirectly as variation in species divergence time across the genome or explicitly using a migration rate parameter. Likelihood ratio tests (LRTs) are used to test the null model of no gene flow at speciation against these two alternative gene flow models. We also use the Akaike information criterion to rank the models. Hundreds of loci are needed for the LRTs to have statistical power, and we use genome sequencing of reduced representation libraries to obtain DNA sequence alignments at many loci (between 340 and 3,478; mean 1⁄4 1,678) for each triplet. We find that current species distributions are a poor predictor of whether a species pair diverged with gene flow. Interrogating the genome using the triplet method expedites the comparative study of species divergence history and the estimation of genetic parameters associated with speciation.
Data from: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges
Background: The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. Results: The strains from each pathotype form monophyletic clades, with a short branch shared by the Aw and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, Aw and A/Aw clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and Aw are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences. Conclusions: The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them.
Data from: Selection and genomic differentiation during ecological speciation: isolating the contributions of host association via a comparative genome scan of Neochlamisus bebbianae leaf beetles
This study uses a comparative genome scan to evaluate the contributions of host plant related divergent selection to genetic differentiation and ecological speciation in maple- and willow-associated populations of Neochlamisus bebbianae leaf beetles. For each of 15 pairwise population comparisons, we identified "outlier loci" whose strong differentiation putatively reflects divergent selection. Of 447 AFLP loci, 15% were outliers across multiple population comparisons, and low linkage disequilibrium indicated that these outliers derived from multiple regions of the genome. Outliers were further classified as "host-specific" if repeatedly observed in "different-host" population comparisons but never in "same-host" comparisons. Outliers exhibiting the opposite pattern were analogously classified as "host-independent." Host-specific outliers represented 5% of all loci and were more frequent than host-independent outliers, thus revealing a large role for host-adaptation in population genomic differentiation. Evidence that host-related selection can promote divergence despite gene flow was provided by population trees. These were structured by host-association when datasets included host-specific outliers, but not when based on neutral loci, which united sympatric populations. Lastly, three host-specific outliers were highly differentiated in all nine different-host comparisons. Because host-adaptation promotes reproductive isolation in these beetles, these loci provide promising candidate gene regions for future molecular studies of ecological speciation.
Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica
The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here we address the question whether two highly different methods - Fst outlier analysis and admixture analysis - detect largely the same set of non-neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves Macoma balthica rubra and M. b. balthica descend from two independent trans-Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca 8000 years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak, M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non-neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism (AFLP) markers as significant Fst outliers. Genomic clines analysis detects 31 out of 84 markers as non-neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non-neutral effects.
FIGURE 4 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes
FIGURE 4. Phylogenetic reconstruction of the Ensifera using mitochondrial PCGs and rRNAs concatenated dataset. (A) Maximum likelihood result; (B) Bayesian result.
FIGURE 3 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes
FIGURE 3. Mitogenome organization across sequenced Ensifera. Genome organization of (A) most sequenced ensiferans and proposed insect ancestor; (B) Gryllinae species; (C) the two Sinochlora species; (D) Phyllomimus detersus of Pseudophyllinae; (E) Ruidocollaris obscura of Phaneropterinae. The circular mitogenomes are linearized to do better presentation. The translocated regions are highlighted in color. Gene lengths are not to scale.
FIGURE 2 in Complete mitochondrial genomes of three crickets (Orthoptera: Gryllidae) and comparative analyses within Ensifera mitogenomes
FIGURE 2. Potential stem-loop structures and their location of Gryllidea. (A) the location of the predicted stem-loop in the mitogenome of Gryllidea, (B) potential stem-loop structures of cricket mitogenomes from Gryllidea
FIGURE 8 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 8. Tree showing the phylogenetic relationships among Lepidopteran insects, constructed using (A) Bayesian inference (BI). (B) Maximum Likelihood method (ML). Bootstrap values (1000 repetitions) of the branches are indicated. Drosophila melanogaster (U37541.1) and Anopheles gambiae (L20934.1) were used as outgroups.
FIGURE 6 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 6. Alignment of overlapping region between atp8 and atp6 across Lepidoptera and other insects. The numbers on the right refer to intergenic nucleotides.
FIGURE 7 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 7. (A) Alignment of the intergenic spacer region between trnS2 (UCN) and nad1 of several Lepidopteran insects. The shaded 'ATACTAA' motif is conserved across the Lepidoptera order. (B) Features present in the A+T-rich region of A. suspecta. The sequence is shown in the reverse strand. The ATATG motif is shaded. The poly-T stretch is underlined while the poly-A stretch is double underlined. The single microsatellite T/A repeats sequence are indicated by dotted underlining.
FIGURE 4 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 4. The Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of five superfamilies in the Lepidoptera. Codon families are plotted on the X axis. Codons indicated above the bar are not present in the mitogenome.
FIGURE 2 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 2. Comparison of codon usage within the mitochondrial genome of members of the Lepidoptera. Lowercase letters (a, b, c, d and e) above species name represent the superfamily to which the species belongs (a: Geometroidea, b: Bombycoidea, c: Noctuoidea, d: Tortricoidea, e Hepialoidea:).
FIGURE 1 in Mitochondrial genome of Abraxas suspecta (Lepidoptera: Geometridae) and comparative analysis with other Lepidopterans
FIGURE 1. Map of the mitogenome of A. suspecta. The tRNA genes are labeled according to the IUPAC-IUB single-letter amino acids: cox1, cox2 and cox3 refer to the cytochrome c oxidase subunits; cob refers to cytochrome b; nad1-nad6 refer to NADH dehydrogenase components; rrnL and rrnS refer to ribosomal RNAs.
High genomic plasticity and unique features of Xanthomonas translucens pv. graminis revealed through comparative analysis of complete genome sequences
<p><strong>Background:</strong> <i>Xanthomonas</i> <i>translucens</i> pv. <i>graminis</i> (<i>Xtg</i>) is a major bacterial pathogen of economically important forage grasses, causing severe yield losses. So far, genomic resources for this pathovar consisted mostly of draft genome sequences, and only one complete genome sequence was available, preventing comprehensive comparative genomic analyses. Such comparative analyses are essential in understanding the mechanisms involved in the virulence of pathogens and to identify virulence factors involved in pathogenicity.</p><p><strong>Results:</strong> In this study, we produced high-quality, complete genome sequences of four strains of <i>Xtg</i>, complementing the recently obtained complete genome sequence of the <i>Xtg </i>pathotype strain. These genomic resources allowed for a comprehensive comparative analysis, which revealed a high genomic plasticity with many chromosomal rearrangements, although the strains were highly related, with 99.9 to 100% average nucleotide identity. A high number of transposases were exclusively found in <i>Xtg </i>and corresponded to 413 to 457 insertion/excision transposable elements per strain. These mobile genetic elements are likely to be involved in the observed genomic plasticity and may play an important role in the adaptation of <i>Xtg</i>. The pathovar was found to lack a type IV secretion system, and it possessed the smallest set of type III effectors in the species. However, three XopE and XopX family effectors were found, while in the other pathovars of the species two or less were present. Additional genes that were specific to the pathovar were identified, including a unique set of minor pilins of the type IV pilus, 17 TonB-dependent receptors (TBDRs), and 11 degradative enzymes. </p><p><strong>Conclusion:</strong> These results suggest a high adaptability of <i>Xtg</i>, conferred by the abundance of mobile genetic elements, which may have led to the loss of many features. Conserved features that were specific to <i>Xtg </i>were identified, and further investigation will help to determine genes that are essential to pathogenicity and host adaptation of <i>Xtg</i>.</p>
Three genomes of Pseudomonas syringae pv. actinidiae and their annotation files were used for comparative genomic studies
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Sequence and functional analyses of native plasmids from plant pathogenic Gammaproteobacteria: comparative genomics, conjugative mobilization and fitness effects
<p>These data tables are part of the Supplementary Material for Chapter I of the thesis titled <em>"Sequence and Functional Analyses of Native Plasmids from Plant-Pathogenic Gammaproteobacteria: Comparative Genomics, Conjugative Mobilization, and Fitness Effects."</em></p>
Comparative genomics of Nectriaceae, including freshwater fungi show environment adaptations and conservation strate-gies for fungi
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Comparative genomics of Nectriaceae, including freshwater fungi show environment adaptations and conservation strategies for fungi - Supplementary Material
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Comparative mitochondrial genome and phylogenetic analysis of malaria mosquitoes Anopheles hyrcanus and Anopheles messeae supplementary files
<p><strong>T</strong><strong><span>able</span></strong><strong> S1.</strong> This study encompassed 105 species, along with their corresponding taxonomy and GenBank registration numbers.</p> <p><strong>Figure S1</strong> Inferred secondary structures of tRNAs in the mt genome of <em>An. </em><em><span>h</span></em><em>yrcanus</em><em> </em><span>(A)</span><em> </em><span>and </span><em>An. </em><em><span>m</span></em><em>esseae</em><em> </em><span>(B)</span>, with corresponding amino acids labeled next to the tRNAs.</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.