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399 results for “gene family”
Evolution of repetitive genomic content and gene families over geo-climatic gradients in Brassicaceae
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Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
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Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa
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A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
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Comparative genomic analysis of chemosensory-related gene families in gastropods
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Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution
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Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane
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Data from: The effect of copy number hemiplasy on gene family evolution
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Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
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Structural evolution drives diversification of the large LRR-RLK gene family
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Data from: Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)
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Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species
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Among‐family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish
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Mating preferences can drive expansion or contraction of major histocompatibility complex gene family
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The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
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Evolution of chemosensory and detoxification gene families across herbivorous Drosophilidae
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Supplementary tables S5, S7, S9, S10, original protein models fasta files used for alignments, aligned and manually curated protein modes files used for phylogenies (PHYLIP format), and phylogenetic trees of plant cell wall decomposition gene families from 44 basidiomycete genomes (.tre files)
<p><span><span><span><span><span><span><span><span><span><span><span>Litter-decomposing Agaricales play key role in terrestrial carbon cycling, but little is known about their decomposition mechanisms. We assembled datasets of 42 gene families involved in plant-cell-wall decomposition from seven newly sequenced litter decomposers and 35 other Agaricomycotina members, mostly white-rot and brown-rot species. Using sequence similarity and phylogenetics, we split the families into phylogroups and compared their gene composition across nutritional strategies. Subsequently, we used Raman spectroscopy to examine the ability of litter decomposers, white-rot fungi, and brown-rot fungi to decompose crystalline cellulose. Both litter decomposers and white-rot fungi share the enzymatic cellulose decomposition, whereas brown-rot fungi possess a distinct mechanism that disrupts cellulose crystallinity. However, litter decomposers and white-rot fungi differ with respect to hemicellulose and lignin degradation phylogroups, suggesting adaptation of the former group to the litter environment. Litter decomposers show high phylogroup diversity, which is indicative of high functional versatility within the group, whereas a set of white-rot species shows adaptation to bulk-wood decomposition. In both groups, we detected species that have unique characteristics associated with hitherto unknown adaptations to diverse wood and litter substrates. Our results suggest that the terms white-rot fungi and litter decomposers mask a much larger functional diversity.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita
<p>By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include <i>de novo</i> gene birth, horizontal gene transfer and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the molecular dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM <i>Amanita</i> fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM <i>Amanita </i>species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared to genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either <i>de novo</i> gene birth (two gene families), horizontal gene transfer (four), and gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes an ACC deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene. Ethylene is a common negative regulator of plant-microbial mutualisms.</p>
Gene family data from the PhyloGenes (release version 2.2, phylogenes.org)
<p>About the two zip files: </p> <p>1. phyloXML.zip</p> <p>PhyloGenes gene family trees in PhyloXML format, one file per family (e.g. <family_ID>.xml).</p> <p>The following information is provided for each node of a tree:<br> 1) leaf node:<br> branch length<br> name <gene_id><br> taxonomy scientific_name<br> sequence accession <UniProt ID></p> <p>2) non-leaf node:<br> branch length<br> events <duplication or speciation></p> <p><br> 2. CSV.zip</p> <p>Functional information of family members in CSV format, one file per family (e.g. <family_ID>.csv). </p> <p>A CSV file includes the following columns:<br> Uniprot ID<br> Gene <Gene name. If none then Gene ID><br> Gene ID<br> Gene name<br> Organism<br> Subfamily name</p> <p>The columns displayed after 'Subfamily name', if any, are GO annotations. Each column is a GO molecular function or biological process term that is annotated to at least one member of the gene family AND the annotation is supported by an experimental evidence (indicated by 'EXP') or phylogenetic inference (indicated by 'IBA'). A '0' indicates absence of either annotations.</p>
Data from: The origin of the odorant receptor gene family in insects
The origin of the insect odorant receptor (OR) gene family has been hypothesized to have coincided with the evolution of terrestriality in insects. Missbach et al. (2014) suggested that ORs instead evolved with an ancestral OR co-receptor (Orco) after the origin of terrestriality and the OR/Orco system is an adaptation to winged flight in insects. We investigated genomes of the Collembola, Diplura, Archaeognatha, Zygentoma, Odonata, and Ephemeroptera, and find ORs present in all insect genomes but absent from lineages predating the evolution of insects. Orco is absent only in the ancestrally wingless insect lineage Archaeognatha. Our new genome sequence of the zygentoman firebrat Thermobia domestica reveals a full OR/Orco system. We conclude that ORs evolved before winged flight, perhaps as an adaptation to terrestriality, representing a key evolutionary novelty in the ancestor of all insects, and hence a molecular synapomorphy for the Class Insecta.
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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.