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399 results for “gene family”
Datset related to article "G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"
<p><strong>NGS_analysis performed at Fondazione Besta carried out as part of the study reported at title</strong></p>
Dataset related to article"G507D MUTATION IN FUS GENE CAUSES FAMILIAL AMYOTROPHIC LATERAL SCLEROSIS WITH A SPECIFIC GENOTYPE-PHENOTYPE CORRELATION"
<p>NGS Analyses of patients included in the study reported at title followed at Fondazione Besta</p>
Data from: The multilocus multispecies coalescent: a flexible new model of gene family evolution
<p>Incomplete lineage sorting (ILS), the interaction between coalescence and speciation, can generate incongruence between gene trees and species trees, as can gene duplication (D), transfer (T) and loss (L). These processes are usually modelled independently, but in reality, ILS can affect gene copy number polymorphism, i.e., interfere with DTL. This has been previously recognised, but not treated in a satisfactory way, mainly because DTL events are naturally modelled forward-in-time, while ILS is naturally modelled backwards-in-time with the coalescent. Here we consider the joint action of ILS and DTL on the gene tree/species tree problem in all its complexity. In particular, we show that the interaction between ILS and duplications/transfers (without losses) can result in patterns usually interpreted as resulting from gene loss, and that the realised rate of D, T and L becomes non-homogeneous in time when ILS is taken into account. We introduce algorithmic solutions to these problems. Our new model, the <em>multilocus multispecies coalescent</em> (MLMSC), which also accounts for any level of linkage between loci, generalises the multispecies coalescent model and offers a versatile, powerful framework for proper simulation and inference of gene family evolution.</p>
Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa
<p>As organisms are faced with intense rapidly changing selective pressures, new genetic material is required to facilitate adaptation. Among sources of genetic novelty, gene duplications and transposable elements (TEs) offer new genes or new regulatory patterns that can facilitate evolutionary change. With advances in genome sequencing it is possible to gain a broader view of how gene family proliferation and TE content evolve in non-model species when populations become threatened. Freshwater bivalves (Unionidae) currently face severe anthropogenic challenges. Over 70% of species in the United States are threatened, endangered or extinct due to pollution, damming of waterways, and overfishing. We have created a reference genome for M. nervosa to determine how genome content has evolved in the face of these widespread environmental challenges. We observe a burst of recent transposable element proliferation causing a 382 Mb expansion in genome content. Gene family expansion is common, with a duplication rate of 1.16 x 10^-8 per gene per generation. Cytochrome P450, ABC transporters, Hsp70 genes, von Willebrand proteins, chitin metabolism genes, mitochondria eating proteins, and opsin gene families have experienced significantly greater amplification and show signatures of selection. We use evolutionary theory to assess the relative contribution of SNPs and duplications in evolutionary change. Estimates suggest that gene family evolution may offer an exceptional substrate of genetic variation in M. nervosa, with Psgv=0.185 compared with Psgv=0.067 for single nucleotide changes. Hence, we suggest that gene family evolution is a source of "hopeful monsters" within the genome that facilitate adaptation.</p>
Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)
Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (∼2200 species) that includes the cacti and harbors many evolutionary transitions to C4 and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C4 and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C4 and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75–218 loci across 74 taxa, with ∼50% matrix completeness across datasets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.
FESNov gene families
<p>Functionally and Evolutionarily Significant Novel (FESNov) gene family predictions. This repository includes:</p><ul><li>GTBD r202 taxonomic labels for all the genomes analyzed (genome2taxonomy.r202.tab)</li><li>Plasflow and Seeker predictions for all the genomes analyzed (plasflow.json.gz<a href="https://zenodo.org/uploads/10242439"> </a>and<a href="https://zenodo.org/uploads/10242439"> </a>seeker.json.gz)</li><li>Fasta files for each FESNov gene family (FESNov_families.fasta.tar.gz)</li><li>Gene family trees for each FESNov gene family (FESNov_families.trees.tar.gz)</li><li>HMM profiles for each FESNov gene family (FESNov_families.hmm.tar.gz)</li><li>FESNov gene family statistics (FESNov_fams_stats.tab)</li><li>Functional predictions and habitat distribution of all FESNov gene families (FESNov_fams_funct_hab_info.json.gz)</li><li>FESNov gene family PDB files with structure predictions by AlphaFold (FESNov_families.pdb.tar.gz), and their associated pLDDT values (pLDDT_values.tab)</li></ul>
PRKN gene Introns in families from Order Primates show common Open Reading Frames
<p>Supplementary material:</p> <p><strong>01 Supplementary material. </strong>Contains Table 1, named: “<u>PRKN</u><em> gene determined in Primates in Gene database NCBI. Supplementary material</em>”. Data are shown for the primate species identified for this study. In addition, a Folder with title “<em>PRKN</em> database”, that contains the subfolders of the 34 primate species for which the <em>PRKN</em> gene was reported until April 2023. Species used for this study are indicated with the title “0 Selected-species”, and those not used only with the species name. In turn, all have four subfolders:</p> <ul> <li><strong>01 <em>PRKN</em> gene and mRNA variants-Fasta format</strong>: contains the sequences of the mRNA variants in FASTA format and of the <em>PRKN</em> gene.</li> <li><strong>02 Alignment <em>PRKN</em> gene and mRNA variants</strong>: contains the <em>PRKN</em> gene and mRNA sequences in FASTA format and the result of the alignment between the gene and the variants. Additionally, a Word document with the manual verification of the previous result. This document is not included in the primate species folders that were not used in this study.</li> <li><strong>03 <em>PRKN</em> aminoacid variants-Fasta format: </strong>contains the amino acid sequences of the <em>PRKN </em>gene variants in FASTA format.</li> <li><strong>04 PRKN Protein variants domains</strong>: contains documents with the graphical representation of the PRKN isoform domains, in Scalable Vector Graphic (SVG) format.</li> </ul> <p><strong>02 Supplementary material.</strong> Table 2 in Excel document containing the positions of the introns and exons of <em>PRKN </em>gene the 16 primate species used in this study. The first sheet contains the size of the introns/exons and their location by species. In the following sheets, the species name, intron/exon position and size are indicated.</p> <p><strong>03 Supplementary material. </strong>Contains two files:</p> <ul> <li><strong>Figure 1.</strong> Document with the alignments of the Primate PRKN proteins encoded by each mRNA variant. Also, are indicated the amino acids whose codons contain the intron with their respective phase.</li> <li><strong>Table 3, named “<em>Intron Phase for </em>PRKN<em> gene</em>”</strong>, in Excel document containing the phases, codons, their respective amino acids and the location of the introns of the primate <em>PRKN</em> gene. The first sheet contains the consensus data for each species, grouped according to families. In the following sheets, the species name, the Phases, the codon and the respective amino acid for each intron are indicated. Phases 0, 1, and 2 are indicated in purple, red, and green letters, respectively. To Phases 1 and 2, the position of the intron in the codon is indicated with a vertical bar, whereas, for Phase 0, each codon is in separate boxes. The mRNA variants that showed loss or fusion of introns are indicated as “Non determine”. Variants with alternatively spliced mRNA and phase change are indicated in yellow boxes.</li> </ul> <p><strong>04 Supplementary material. </strong>Contains two Excel documents and a subfolder with the putative <em>PRKN</em> introns Open Reading Frame (ORF):</p> <ul> <li><strong>Excel file: Table 4, named “<em>Positive ORFs</em>”</strong>. The first sheet contains the general data of 5’-3’ and 3’-5’ ORFs, characterized for each species by intron and organized by families. The second sheet corresponds to the total number of exons determined for each ORF, with the previously mentioned organization. The additional sheets are divided by intron and the species are organized by families along with the different characterized ORFs.</li> <li><strong>Excel file: Table 5 named “<em>ORFs Introns</em>”</strong>. In the first sheet, the number of ORFs of the introns is indicated, according to the grouping performed in this study. The other Sheets correspond to both unique and common ORFs determined for each species per intron, organized by family.</li> <li><strong>Subfolder named “<em>ORFs alignments</em>”</strong>: Contains the alignments between the ORFs of each intron by species. Exclusive and common ORFs are also indicated.</li> </ul> <p><strong>05 Supplementary material.</strong> Contains two Excel documents with putative functional sites of PRKN introns ORFs protein:</p> <ul> <li><strong>Excel file: Table 6 named “<em>Family Common Functional Sites</em>”</strong>. The first sheet contains the general information of the functional sites characterized in the ORFs, determined in the introns of each species ordered by family. Also, the total count of ORFs per family. The other sheets correspond to the categories of cellular processes. Within these are the functional site according to the species that presented it, ordered by family and the total count of each site.</li> <li><strong>Excel file: Table 7 named “<em>Protein Domain ORFs</em>”</strong>. Functional sites determined only for ORFs common to two or more species are found. The position of each functional site is indicated according to the amino acid sequence and in relation to each species.</li> </ul> <p><strong>06 Supplementary material. </strong>Contains two subfolders that comprise BLAST and Protein Data Bank search from mRNA and PRKN ORF intron proteins:</p> <ul> <li><strong>BLAST subfolder comprises a Word document and 7 plain text documents. </strong>The Word document corresponds to the sequences reported in the Transcriptome Shotgun Assembly protein (tsa_nr) and Expressed sequence tags (est) databases, for ORFs that are common between Homo sapiens and the other species, according to the intron. The plaintext-like documents correspond to BLAST analyses that yielded more than six sequences similar to the reference ORF. The documents are named according to the sequences analyzed: the ORF name and database (Protein or Nucleotide).</li> <li><strong>Protein Data Bank subfolder. </strong>Contains 6 files in .PDF format, that correspond to protein structures that showed similarities with human ORFs 32 and 11, from Introns 6 and 9, respectively. Each document contains the protein structure information indicated in the Protein Data Bank (PDB) and the amino acid alignment between the Intron ORF sequence and the PDB protein sequence. The documents are named according to the protein ID obtained in the PDB and the respective ORF.</li> </ul>
Data from: Analysis of the PEBP gene family and identification of a novel FLOWERING LOCUS T orthologue in sugarcane
<p>Sugarcane (<i>Saccharum</i> spp.) is an important economic crop for both sugar and biomass, the yields of which are negatively affected by flowering. The molecular mechanisms controlling flowering in sugarcane are nevertheless poorly understood. RNA-seq data analysis and database searches have enabled a comprehensive description of the PEBP gene family in sugarcane. It is shown to consist of at least 13 <i>FLOWERING LOCUS T </i>(<i>FT</i>)-like genes, two <i>MOTHER OF FT AND TFL </i>(<i>MFT</i>)<i>-</i>like genes, and four <i>TERMINAL FLOWER </i>(<i>TFL</i>)-like genes. As expected, these genes all show very high homology to their corresponding genes in <i>Sorghum</i>, and also to <i>FT</i>-like, <i>MFT-</i>like, and <i>TFL</i>-like genes in maize, rice, and Arabidopsis. Functional analysis in Arabidopsis showed that the sugarcane <i>ScFT3</i> gene can rescue the late flowering phenotype of the Arabidopsis <i>ft-10</i> mutant, whereas <i>ScFT5</i> cannot. High expression levels of <i>ScFT3</i> in leaves of short day-induced sugarcane plants coincided with initial stages of floral induction in the shoot apical meristem as shown by histological analysis of meristem dissections. This suggests that <i>ScFT3</i> is likely to play a role in floral induction in sugarcane; however, other sugarcane <i>FT</i>-like genes may also be involved in the flowering process.</p>
The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approach
<p>The plant genus <em>Oenothera</em> has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 <em>Oenothera</em> species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching for orthologous genes and performed gene family evolution analysis. We found wide heterogeneity in gene family evolution across the genus, with section <em>Oenothera </em>exhibiting the most pronounced evolutionary changes. Overall, more significant expansions occurred than contractions. We also analyzed the molecular evolution of phenolic metabolism by retrieving proteins annotated for phenolic enzymatic complexes. We identified 1,568 phenolic genes arranged into 83 multigene families that varied widely across the genus. All taxa experienced rapid phenolic evolution involving 33 gene families, which exhibited large expansions, gaining about 2-fold more genes than they lost. Upstream enzymes phenylalanine ammonia-lyase (PAL) and 4-coumaroyl: CoA ligase (4CL) accounted for most of the significant expansions and contractions. Our results suggest that adaptive responses to environmental stress coupled with non-adaptive evolutionary forces have contributed to <em>Oenothera </em>diversification and rapid gene family evolution.</p>
Data from: The effect of copy number hemiplasy on gene family evolution
<p>The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH).</p> <p>In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models --- MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not --- approximate the Wright-Fisher process with duplication and loss.</p> <p>We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.}</p>
Dataset of gene family analysis for Gekko japonicus and other sauropsids
<p>We assembled a chromosome-level genome of <em>Gekko japonicus</em> and then performed a series of gene family analyses on it and other representative sauropsids generated a dataset containing predicted sequences, sequence alignments and phylogenetic trees of the corresponding genes.</p>
Fig. 3 in Phylogenomics of the tropical plant family Ochnaceae using targeted enrichment of nuclear genes and 250+ taxa
Fig. 3. Continues. For caption, see next part.
Mating preferences can drive expansion or contraction of MHC gene family
MHC-based mating rules can evolve as a way to avoid inbreeding or to increase offspring immune competence. While the role of mating preference in the MHC diversity in vertebrates has been acknowledged, its impact on individual MHC diversity has not been considered. Here, we use computer simulations to investigate how simple mating rules favouring MHC-dissimilar partners affect the evolution of the number of MHC variants in individual genomes, accompanying selection for resistance to parasites. We showed that the effect of such preferences could sometimes be dramatic. If preferences are aimed at avoiding identical alleles, e.g. under strong selection against sib-mating, the equilibrium number of MHC alleles is much smaller than under random mating. However, if the mating rule minimises the ratio of shared to different alleles in partners, MHC number is higher than under random mating. Additionally, our simulations revealed that a negative correlation between the numbers of MHC variants in mated individuals can arise from simple rules of MHC-disassortative mating. Our results reveal unexpected potential of MHC-based mating preferences to drive MHC gene family expansions or contractions and highlight the need to study the mechanistic basis of such preferences.
Gene family data from the PhyloGenes (release version 4.0, phylogenes.org)
<p>The data files were generated from the PhyloGenes 4.0 release (see release notes <a href="https://conf.arabidopsis.org/display/PHGSUP/About+PhyloGenes">here</a>).</p> <p>About the two zip files: </p> <p>1. phyloXML.zip (these are different and updated from the immediately preceding PhyloGenes 3.2 release)</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>
A new genome of an African weakly electric fish (Campylomormyrus compressirostris, Mormyridae) indicates rapid gene family evolution in Osteoglossomorpha
Background <p>Teleost fishes comprise more than half of the vertebrate species. Within teleosts, most phylogenies consider the split between Osteoglossomorpha and Euteleosteomorpha/Otomorpha as basal, preceded only by the derivation of the most primitive group of teleosts, the Elopomorpha. While Osteoglossomorpha are generally species-poor, the taxon contains the African weakly electric fish (Mormyroidei), which have radiated into numerous species. Within the mormyrids, the genus <em>Campylomormyrus</em> is mostly endemic to the Congo Basin. <em>Campylomormyrus</em> serves as a model to understand mechanisms of adaptive radiation and ecological speciation, especially with regard to its highly diverse species-specific electric organ discharges (EOD). Currently, there are few well-annotated genomes available for electric fish in general and mormyrids in particular. Our study aims at producing a high-quality genome and to use this to examine genome evolution in relation to other teleosts. This will facilitate further understanding of the evolution of the osteoglossomorph fish in general and of electric fish in particular.</p> Results <p>A high-quality weakly electric fish (<em>C. compressirostris</em>) genome was produced from a single individual with a genome size of 862Mb, consisting of 1,497 contigs with an N50 of 1,399 kb and a GC-content of 43.69%. Gene predictions identified 34,492 protein-coding genes, which is a higher number than in the two other available Osteoglossomorpha genomes of <em>Paramormyrops</em> <em>kingsleyae</em> and <em>Scleropages</em> <em>formosus</em>. A CAFE5 analysis of gene family evolution comparing 33 teleost fish genomes suggests an overall faster gene family turnover rate in Osteoglossomorpha than in Otomorpha and Euteleosteomorpha. Moreover, the ratios of expanded/contracted gene family numbers in Osteoglossomorpha are significantly higher than in the other two taxa, except for species that had undergone an additional genome duplication (<em>Cyprinus</em> <em>carpio</em> and <em>Oncorhynchus</em> <em>mykiss</em>). As potassium channel proteins are hypothesized to play a key role in EOD diversity among species, we put a special focus on them, and manually curated 16 Kv1 genes. We identified a tandem duplication in the KCNA7a gene in the genome of <em>C</em>. <em>compressirostris</em>.</p> Conclusions <p>We present the fourth genome of an electric fish and the third well-annotated genome for Osteoglossomorpha, enabling us to compare gene family evolution among major teleost lineages. Osteoglossomorpha appears to exhibit rapid gene family evolution, with more gene family expansions than contractions. The curated Kv1 gene family showed seven gene clusters, which is more than in other analyzed fish genomes outside Osteoglossomorpha. The KCNA7a, encoding for a potassium channel central for EOD production and modulation, is tandemly duplicated which may related to the diverse EOD observed among <em>Campylomormyrus</em> species.</p>
Comparative transcriptomics reveals divergence in pathogen response gene families amongst twenty forest tree species
<p>Forest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. <span>In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, </span>we used the RNA-seq data of twenty co-occurring forest tree species from genera including <em>Acer, Alnus, Amelanchier, Betula, Cornus, Corylus, Dirca, Fraxinus, Ostrya, Populus, Prunus, Quercus, Ribes, Tilia, </em>and<em> Ulmus </em>sampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.</p>
Comparative genomic analysis of chemosensory-related gene families in gastropods
<p>Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and spiders, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann–Pick type C2 (NPC2) proteins, and lipocalins, although much smaller in size. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) large gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a huge number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.</p>
Data from: Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae)
<p>A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly <em>Neodiprion lecontei</em>, a non-eusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor (GR), clan 3 cytochrome P450 (CYP3), olfactory receptor (OR), and antimicrobial peptide (AMP) subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.</p>
Tudor genes of Holozoa: Early evolution and within Metazoa diversification of a multifaceted protein family
<p>Early metazoan evolution was characterized by the expansion of many gene families involved in novel multicellularity-related functions, like the Tudor family. In eukaryotes, Tudor genes are numerous and heterogeneous, mostly associated with gene expression regulation. However, the family underwent a lineage-specific expansion in animals, with novel elements almost exclusively involved in the germline-specific regulation of retrotransposons through piRNAs (as spatiotemporal regulators of the key-element Piwi, another previously supposedly animal-specific gene). In the present analysis, we used online-available proteomes for a total of 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, and we confirmed the apomorphic expansion of piRNA-related Tudor genes in animals. However, we could also interestingly observe the presence of elements of the piRNA pathway, both Tudor and Piwi genes, in some Ichthyosporea species, suggesting that some elements of the pathway were already present in the last common ancestor of Holozoa. Moreover, we observed an outstanding variability (34-fold) of Tudor gene number both between and within metazoan phyla, that could be associated with convergent genomic and phenotypic evolutions. Expansions were usually sided by whole genome duplications and/or life history traits such as parthenogenesis, possibly leading to the expansion of retrotransposon silencing pathways. Reductions were instead mostly associated with overall phenotypic and genomic simplifications, like almost all endoparasites of our dataset. Lastly, we phylogenetically tested a previously proposed model for the evolution of the three possible secondary structures of the Tudor domains and we could mostly (but not completely) confirm the model.</p>
CYP19A1 (Cytochrome P450 Family 19 Subfamily A Member 1) Gene and Pharmacogenetics of Response to Testosterone Therapy
ClinicalTrials.gov study NCT01378299. IPD Sharing: YES. Countries: 1. Publications: 2.
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.