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399 results for “gene family”
cDNA sequence of E2 gene family in Arabidopsis thaliana and data of statistical analysis
<p>E2 ubiquitin-conjugating enzymes act as a heart role in the ubiquitination process and are responsible for catalysis ubiquitin transfer. Although the function of ubiquitin-protein ligases (E3s) in plant response to diverse abiotic stress by targeting specific substrates has been well studied, the E2s' involvement in environmental responses and their downstream targets are not well understood. Here, we demonstrated that the E2 ubiquitin-conjugating enzyme 18 (UBC18) regulates the stability of FREE1 to modulate iron deficiency stress. UBC18 affects the ubiquitination of FREE1 and promotes its degradation, overexpression of<em> UBC18</em> in plants decreases their sensitivity to iron deficiency by reducing the level of FREE1, and high accumulation of FREE1 in<em> </em>the<em> ubc18</em> mutant resulted in sensitivity to iron deficiency. In addition, we demonstrated the lysine residues K227, K295, K315, and K540 are required for FREE1 ubiquitination and stability regulation, and mutation of these lysines of FREE1 residues resulted in sensitivity to iron starvation in plants. Taken together, our findings reveal a mechanism of UBC18 in response to iron deficiency stress by altering the abundance of FREE1, and further elucidate the role of ubiquitination sites in FREE1 stability regulation and the plant iron deficiency response.</p>
GMPipe: A gene mining pipeline for identifying olfactory receptor repertoires and other multicopy gene families from genomes
<p>This repository contains the code and tutorial for the GMPipe algorithm. GMPipe is a gene mining pipeline designed to maximize the identification of multicopy gene family homologs in genome assemblies (for intronless genes) or lists of protein sequences. GMPipe has been validated for mining olfactory receptor genes from vertebrate genomes. This algorithm uses custom ingroup and outgroup sequence lists to distinguish between members of a gene family of interest from close off-target relatives. Overall, GMPipe uses HMMER as an initial screening step, paired with phylogenetic clustering to test whether passing sequences are more closly related to "ingroup" than "outgroup" sequences. The result is a pipeline with a low false negative rate, with minimal impact on the false positive rate, especially when paired with additional family-specific filtering steps.</p>
Figure 4 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 4. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 28 concatenated individual mtDNA gene sequences, i.e. 14 from female-type (12 protein-coding and 2 rRNA genes) and 14 (12 protein-coding and 2 rRNA genes) from male-type mitochondria. Values for branch support above each node represent Bayesian posterior probabilities percentage/ maximum likelihood bootstrap.
Figure 3 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 3. Phylogenetic tree of the Unionidae+Margaritiferidae estimated from 14 concatenated individual mtDNA gene sequences (12 protein-coding and 2 rRNA genes). Values for branch support above each node represent Bayesian posterior probabilities percentage/maximum likelihood bootstrap support. *Supported values ≥ 95 are represented by an asterisk.
Figure 1 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 1. Recent multi-locus phylogenetic hypotheses on Gonideinae sensu Pfeiffer et al. (2019). Vertical bars indicate subfamilies recognized in respective publications. Note that Froufe et al. (2020) adopted a new systematic framework with three instead of two family-group levels, and thus, traditional tribes (ending -ini) are considered subtribes (ending -ina) in that study.
Figure 6 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 6. Relationship between (A) mean Ka/Ks and substitution rate (μ) per female-type (full circles) and male-type (empty circles) mtDNA protein-coding gene; and (B) differences between male- and female-type K a /K s and μ per proteincoding mtDNA gene.
Figure 2 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 2. Gene maps of the F- and M-type mitochondrial genomes of Lens contradens, Physunio superbus, Hyriopsis bialata and Rectidens sumatrensis. Genes positioned inside the circle are encoded on the heavy strand, and genes outside the circle are encoded on the light strand. Colour codes: small and large ribosomal RNAs (red); transfer RNAs (purple); M-orf, F-specific open reading frame (yellow); M-orf, M-specific open reading frame (yellow); protein-coding genes (green).
Figure 5 in Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)
Figure 5. Fossil-calibrated ultrametric chronogram of the Unionidae calculated under a lognormal relaxed clock model and a Yule process speciation implemented in BEAST v.1.10.1 and obtained for the complete F-type mitogenome data set. The newly sequenced tribe-level taxa are coloured red. An outgroup sample (Margaritiferidae) has been removed for better visualization (but see original BEAST tree in Supporting Information, Fig. S1A). Bars indicate 95% confidence intervals of the estimated divergence times between lineages (Mya). Black numbers near nodes are mean ages (Mya). Colour labels indicate the F-mtDNA gene order (UF1, UF2, and UF3). Stratigraphic chart according to the International Commission on Stratigraphy v.2018/08 (www.stratigraphy.org). Abbreviations: J, Jurassic; K, Cretaceous; N, Neogene; Pg, Palaeogene; Q, Quaternary.
Sergestidae shrimp family single- and multi-gene alignments and tree files
<p>Deep-sea shrimp belonging to the family Sergestidae provide a unique system for studying the evolution of bioluminescence. Most species within the family possess autogenic bioluminescent photophores in one of three distinct forms: lensed photophores, non-lensed photophores, or internal organs of Pesta. This morphological diversity across Sergestidae has resulted in recent major taxonomic revisions, dividing the two major genera (<em>Sergia </em>and<em> Sergestes</em>) into 15. Here, we capitalize on molecular data to construct an updated genus-level phylogeny of sergestid shrimp. DNA was successfully extracted from approximately 87 individuals belonging to 13 of the 15 newly proposed genera. We implemented a "genome skimming" approach, allowing us to capture mitochondrial genomic data across 19 Sergestidae species. Additional individuals have been incorporated into the phylogeny through Sanger sequencing of both nuclear (H3, NAK) and mitochondrial (16S and COI) genes. The resulting molecular phylogeny is compared with previous morphological trees with specific attention to genus-level relationships. The -<em>sergestes</em> group was rendered non-monophyletic, and the -<em>sergia</em> group was recovered as monophyletic. Ancestral state reconstructions of light organ type indicate the organs of Pesta is the ancestral state for the family. Non-lensed photophores evolved once across the -<em>sergia</em> group, but were later lost in the deepest living genus, <em>Sergia</em>. Lensed photophores also evolved once within the genera <em>Prehensilosergia</em>, <em>Lucensosersgia</em>, and <em>Challengerosergia</em>. Our findings identify preliminary patterns across light organ type and species' depth distributions, however future research that incorporates finer-scale depth data and more species is needed to confirm our findings. </p>
Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes - orthogroups dataset
<p>Orthogroups clustering and analysis of pines and spruces, as reported in Gagalova et al., 2022</p>
High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae
<p>Annotations, aligned rthologoious gene sets and CAFE outputs used in the article "High rate of gene family evolution in close proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae."</p>
Evolution and amplification of the trehalose-6-phosphate synthase gene family in Theaceae
Open the record for dataset details and reuse information.
Figure 1 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 1. Mitochondrial genome synteny in Cubaris murina and closely related species. A dash (-) before the gene name means that the gene is encoded on the light strand. NCR means a non-coding region that is longer than 100 bp. Cubaris murina is marked in bold black and shades of grey.
Figure 2 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
Figure 2. Secondary structure of each transfer RNA (tRNA) visualised in Forna (http://rna.tbi.univie.ac. at/forna).
Table 3 in Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures
<p><b>Table 3.</b> Characteristic (AT content, repeat, number of predicted secondary structure, range of <i>ΔG</i> value (kcal/mol)) of control region of <i>Cubaris murina</i> by RNAstructure.</p><table><tbody><tr><th></th><th></th><th></th><th></th><th>Length</th><th></th><th></th><th></th><th>Number of predicted</th><th></th></tr></tbody><tbody><tr><th>Species [reference]</th><td>Name</td><td>Start</td><td>Stop</td><td>(bp)</td><td>Location</td><td>%AT</td><td>Repeat</td><td>secondary structures</td><td><i>ΔG</i> value (kcal/mol)</td></tr><tr><th><i>Cubaris murina</i></th><td>NCR1</td><td>5219</td><td>5360</td><td>142</td><td>Between <i>nad1</i> and <i>trnN</i></td><td>52.80%</td><td></td><td>7</td><td>−16.9 to −15.4</td></tr><tr><th>[present study]</th><td>NCR2</td><td>6297</td><td>6666</td><td>370</td><td>Between <i>trnS1</i> and <i>trnL1</i></td><td>59.70%</td><td>CT-rich & AT-loop</td><td>20</td><td>−103.7 to −101.0</td></tr><tr><th></th><td>NCR3</td><td>12,550</td><td>12,753</td><td>204</td><td>Between <i>rrnL</i> and <i>trnE</i></td><td>71.10%</td><td>poly-A</td><td>7</td><td>−17.5 to −17.1</td></tr><tr><th></th><td>NCR4</td><td>12,813</td><td>12,950</td><td>138</td><td>Between <i>trnE</i> and <i>trnV</i></td><td>71.70%</td><td>AG-rich</td><td>5</td><td>−13.4 to −12.3</td></tr><tr><th><i>Panulirus argus</i> [Baeza, 2018]</th><td>NCR</td><td>13,525</td><td>14,326</td><td>801</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>69.60%</td><td>AT-rich</td><td>7</td><td>−99.20 to −94.52</td></tr><tr><th><i>Synalpheus microneptunus</i> [Chak <i>et al.</i>, 2020]</th><td>NCR</td><td>13,365</td><td>14,198</td><td>834</td><td>Between <i>rrnS</i> and <i>trnI</i></td><td>79.50%</td><td>AT-rich</td><td>20</td><td>− 104 (lowest)</td></tr></tbody></table>
Genomic regions associated with adaptation to predation in Daphnia often include members of expanded gene families
<p>Predation has been a major driver of the evolution of prey species, which consequently develop antipredator adaptations. However, little is known about the genetic basis underpinning the adaptation of prey to intensive predation. Here, we describe a high-quality chromosome-level genome assembly (approx. 145 Mb, scaffold N50 11.45 Mb) of <em>Daphnia mitsukuri</em>, a primary forage for many fish species. Transcriptional profiling of <em>D. mitsukuri</em> exposed to fish kairomone revealed that this cladoceran responds to predation risk through regulating activities of Wnt signalling, cuticle pattern formation, cell cycle regulation and anti-apoptosis pathways. Genes differentially expressed in response to predation risk are more likely to be members of expanded families. Our results suggest that expansions of multiple gene families associated with chemoreception and vision allow<em> Daphnia</em> to enhance detection of predation risk, and that expansions of those associated with detoxification and cuticle formation allow <em>Daphnia</em> to mount an efficient response to perceived predation risk. This study increases our understanding of the molecular basis of prey defences, being important evolutionary adaptations playing a stabilizing role in community dynamics.</p>
Gene family data from the PhyloGenes (release version 3.2, phylogenes.org)
<p>The data files were generated from the PhyloGenes 3.2 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 (there is no change from the PhyloGenes 3.0 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>
Figure 6 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 6. Hypothetical radiation schemes for Uromastyx and possibly relevant geological events. Approximate distribution range for each taxon (Wilms, 2001) is shown with its abbreviated name: Hard (Uromastyx hardwickii), Aca (U. acanthinura), Mali (U. d. maliensis), Gey (U. geyri), Dis (U. d. dispar), Oce (U. ocellata), Mac (U. macfadyeni), Aeg (U. a. aegyptia), Mic (U. a. microlepis), Orn (U. ornata) and Ben (U. benti).
Figure 5 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 5. Neighbour-joining tree constructed based on maximum likelihood distances from 1503 alignable nucleotide sites (the HKY model and transition/transversion ratio of 3.48). The tree was rooted with Chamaeleo africanus as an outgroup. Bootstrap probabilities are shown for neighbour joining, maximum likelihood and maximum parsimony analyses (from left to right). Underlined values mean that the branch was not reconstructed in the best tree topology by the corresponding analyses. Note that two distinct sequence haplotypes are included for Uromastyx acanthinura and U. ocellata. See Material and methods for more details on the analytical conditions. The nucleotide sequences taken from the database are: Chamaeleo africanus (accession No., AF448743), Chlamydosaurus kingii (AF128469), Physignathus lesueurii (AF128463), Acanthosoura capra (AF128498), Salea horsfieldii (AF128490), Trapelus savignii (AF128512), Leiolepis guentherpetersi (AF128461), Leiolepis belliana (U82689), Laudakia caucasia (AF028681) and Laudakia lehmanni (AF028677).
Figure 4 in Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements
Figure 4. Secondary structures of the inserted sequences found between tRNAGln and tRNAIle genes. The 128 bp insert for Uromastyx ornata can assume alternative secondary structures either with an extremely stable and long stem region (A) or with a clover-leaf structure for the second tRNAGln gene (or pseudogene) and a stable stem-and-loop structure (B). The 59 bp inserted for U. ocellata may also assume a somewhat less stable stem-and-loop structure (C). Heavy-strand sequences are shown and numbers refer to the corresponding positions in their light-strand sequences shown in Fig. 3A. Bars in stems represent Watson–Crick base pairs and dots stand for wobble G–U pairs for RNA.
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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.