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52 results for “whole genome duplication”
Intercontinental dispersal and whole‐genome duplication contribute to loss of self‐incompatibility in a polyploid complex
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Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
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Alignments from: Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae)
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Data from: Whole-genome duplication and host genotype affect rhizosphere microbial communities
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Effects of glaciation and whole genome duplication on the distribution of the Campanula rotundifolia polyploid complex
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Data from: A meta-analysis of whole genome duplication and the effects on flowering traits in plants
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Data from: Genetic drift dominates genome-wide regulatory evolution following an ancient whole genome duplication in Atlantic salmon
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Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.
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Simulated data and results from "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data"
<p>This dataset contains all the simulated data and the results of all the considered methods in the benchmark presented in "Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data" [Zaccaria & Raphael, 2018]. All the data in this dataset and the corresponding formats are fully described at <a href="https://github.com/raphael-group/hatchet-paper">https://github.com/raphael-group/hatchet-paper</a>. The folder <em>simulations</em> which contains the entire dataset has been compressed with standard <em>zip</em>.</p>
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis
<p>Whole-genome duplication<b> </b>has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and a quantitative measure of their functional redundancy. Trigenic interaction analysis distinguishes two classes of paralogs, a more functionally divergent subset and another that retained more functional overlap. Gene feature analysis and modeling suggest that evolutionary trajectories of duplicated genes are dictated by combined functional and structural entanglement factors.</p>
Data from: Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size - 0.6pg to 4.4 pg per haploid cell. Firstly, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree - the first between 43-49 Mya (95% highest posterior density (HPD) 36.2-68.1 Mya) and the second at ~19 Mya (95% HPD 15.3-30.14 Mya). Secondly, RAD sequencing was used to identify potential WGD events and quantify transposable element abundance in different lineages. Evidence of two lineage scale WGDs were identified across the phylogeny, the first event occurring between 54-66 Mya (95% HPD 42.56-99.5 Mya) and the second at 20-30 Mya (95% HPD 15.3-45 Mya) based on haplotype numbers per contig and between 35-44 Mya (95% HPD 30.29-64.51 Mya) and 20-30 Mya (95% HPD 15.3-45 Mya) based on SNP read ratios. Transposable element abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20-30 Mya (95% HPD 15.3-45 Mya) and an older event at 35-44 Mya (95% HPD 30.29-64.51 Mya). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification
Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.
Evolution of binding preferences among whole-genome duplicated transcription factors
<p>Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge is known for only a few studied cases. To provide a genome-scale view, we considered the 35% of budding yeast TFs, classified as whole-genome duplication (WGD)-retained paralogs. Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed that ancestral preferences are unevenly split between duplicates, while new targets are acquired preferentially by the least conserved paralog (biased sub/neo-functionalization). Dimer-forming paralogs evolved mostly one-sided dependency, while other paralogs interacted through low-magnitude DNA-binding competition that minimized paralog interference. We discuss the implications of our findings for the evolutionary design of transcriptional networks.</p>
Chromosome-level genome of Capitulum mitella reveals an ancient whole-genome duplication event and intertidal adaptation of barnacles
<p><span>Barnacles are the only sessile crustaceans inhabiting intertidal zone, an extremely stressful environment for sessile organisms. Herein, we report the chromosome-level genome of a stalked barnacle, <em>Capitulum</em> <em>mitella</em>, which is a dominant intertidal cirripede of the west Pacific Ocean coast. After comprehensive comparative genomic analyses, it is the first time to find an ancient whole-genome duplication (WGD) event that preceded the divergence of Lepadomorpha and Sessilia approximately </span><span>237 million years ago. </span><span>The retained duplicated genes of WGD are primarily enriched in many environmental information processing pathways, shedding light on its adaptive evolution of intertidal sessile life. In addition, transcriptomic and metabolomic sequencing and analyses of <em>C</em>. <em>mitella</em> indicated that the upregulation of some expanded anti-stress factors and accumulation of acyl-carnitines help barnacles adapt to stressful intertidal conditions. Therefore, this study provides a valuable resource for understanding the unique intertidal adaptation mechanism of sessile crustaceans and reveals novel WGD events in invertebrates.</span></p>
Repeated shifts out of tropical climates preceded by whole genome duplication
<p>Inputs, outputs and scripts for performing anayses in the above mentioned article. </p>
Data from: Ancestral whole genome duplication in the marine chelicerate horseshoe crabs
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs—Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica
<p>Plant cells arose through the endosymbiotic engulfment of a cyanobacterium that subsequently formed the chloroplast genome, enabling plants to develop new critical functions. Almost all chloroplast proteins are now encoded in the nucleus, but some chloroplast protein complexes are jointly encoded by both nuclear and chloroplast genes, which interact to facilitate essential plant functions, such as the photosystems. Allopolyploidy, resulting from the hybridization and genome doubling of two divergent species, can disrupt these fine-tuned cytonuclear interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparental organelle inheritance. Such unequal genome inheritance may affect the conformation of the five cytonuclear complexes in allopolyploids. We used <em>Brassica</em> as a model to study the effects of paleopolyploidy and dichotomic divergence in parental species, as well as the effects of recent allopolyploidy in <em>Brassica napus</em>, on genes implicated in cytonuclear complexes. Because the <em>B. napus</em> parental diploid species are paleohexaploids, we first identified paleologous copies of cytonuclear complex genes. We found that these genes are preferentially retained in duplicates, are nearly all transcribed and are undergoing strong purifying selection, in accordance with the ‘gene balance hypothesis’. Subsequently, we compared expression patterns of cytonuclear complex homoeolog genes between resynthesized <em>B. napus </em>individuals and their respective diploid parents. The neo-polyploids showed neither biased sub-genome expression nor homogenization of homoeologs, due to highly conserved parental chloroplast genomes. These findings provide new insights and an innovative framework to understand the impact of cytonuclear interactions on interspecific hybridization and allopolyploid speciation.</p>
Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification
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Data from: Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers
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Data from: Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes
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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.