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25,372 results for “Transcriptomics”
Expression and comparison of unigene in the transcriptome in Siniperca chuatsi
<p>Muscle from 3-month old individuals of different sizes was used for transcriptome analysis. After screening, 39005 unigenes were annotated into four databases, including Nr (38833, 52.9%), Swissprot (337479, 46.0%), COG (10926, 14.8%) and KEGG (19791, 26.9%). Finally, the results was annotated by Nr database which defined the maximum number of unigenes.</p>
The transcriptomic response of murine thyroid to iodide overload and the role of the Nrf2 antioxidant system
<p>Wild-type and Nrf2(Nfe2l2) knockout male C57BL6J mice 3-4 months old were administred 0.05% NaI in their drinking water for 7 days. Control mice were administered regular drinking water. After this treatment mice were euthanized and thyroids were excised for RNA preparation and then for mRNA and miRNA RNAseq. </p> <p>The file titled "metadata RNAseq mRNA thyroid" contains the experimental information as well as the allocation of sample numbers to the relevant groups. Briefly, </p> <p>806 Knockout Iodide</p> <p>829 Wild type Iodide</p> <p>815 Knockout Control</p> <p>811 Knockout Control</p> <p>801 Knockout Iodide</p> <p>836 Wild type Control</p> <p>838 Wild type Control</p> <p>807 Knockout Iodide</p> <p>834 Wild type Control</p> <p>827 Wild type Iodide</p> <p>831 Wild type Iodide</p> <p>804 Knockout Iodide</p> <p>825 Wild type Iodide</p> <p>841 Wild type Control</p> <p>812 Knockout Control</p> <p>803 Knockout Iodide</p> <p>810 Knockout Control</p> <p>The fastq data have been uploaded. The ones with "miRNA" in their file name refer to miRNA sequencing. All the others refer to mRNA sequencing.</p>
Data from: Transcriptome profiling of maternal stress-induced wing dimorphism in pea aphids
Wing dimorphism, i.e., wingless and winged forms, can be induced by maternal stress signals and is an adaptive response of aphids to environmental changes. Here, we investigated the ecological and molecular effects of three kinds of stress, namely, crowding, predation, and aphid alarm pheromone, on wing dimorphism. These three stressors induced high proportion of up to 60% of winged morphs in offspring. Transcriptome analysis of stress-treated female aphids revealed different changes in maternal gene expression as induced by the three stressors. Crowding elicited widespread changes in the expression of genes involved in nutrient accumulation and energy mobilization. Distinct from crowding, predation caused dramatic expression changes in cuticle protein (CP) genes. Twenty-three CP genes that belong to CP RR2 subfamily and are highly expressed in legs and embryos were greatly repressed by the presence of ladybird. By contrast, application of alarm pheromone, E--farnesene, caused slight changes in gene expression. The three factors shared a responsive gene, cuticle protein 43. This study reveals the adaptive response of aphids to environmental stresses and provides a rich resource on genome-wide expression genes for exploring molecular mechanisms of ecological adaptation in aphids.
Transcriptome assembly for: Genetic compensation rather than genetic assimilation drives the evolution of plasticity in response to mild warming across latitudes in a damselfly
<p><span>Global warming is causing plastic and evolutionary changes in the phenotypes of ectotherms. Yet, we have limited knowledge on how the interplay between plasticity and evolution shapes thermal responses and underlying gene expression patterns. We assessed thermal reaction norm patterns across the transcriptome and identified associated molecular pathways in northern and southern populations of the damselfly <i>Ischnura elegans</i>. Larvae were reared<i> </i>in a common garden experiment at the mean summer water temperatures experienced at the northern (20 °C) and southern (24 °C) latitudes. This allowed a space-for-time substitution where the current gene expression levels at 24 °C in southern larvae are a proxy for the expected responses of northern larvae under gradual thermal evolution to the predicted 4 °C warming. Most differentially expressed genes showed fixed differences across temperatures between latitudes, suggesting that thermal genetic adaptation will mainly evolve through changes in constitutive gene expression. Northern populations also frequently showed plastic responses in gene expression to mild warming, while southern populations were much less responsive to temperature. Thermal responsive genes in northern populations showed to a large extent a pattern of genetic compensation, i.e. gene expression that was induced at 24 °C in northern populations remained at a lower constant level in southern populations, and were associated with metabolic and translation pathways. There was instead little evidence for genetic assimilation of an initial plastic response to mild warming. Our data therefore suggest that genetic compensation rather than genetic assimilation may drive the evolution of plasticity in response to mild warming in this damselfly species.</span></p>
Nicotiana benthamiana as a transient expression host to produce auxin analogues: Pisum sativum seed transcriptomic data
<p>Plant secondary metabolites have applications for the food, biofuel, and pharmaceutical industries. Recent advances in pathway elucidation and host expression systems now allow metabolic engineering of plant metabolic pathways to produce "new-to-nature" derivatives with novel biological activities, thereby amplifying the range of industrial uses for plant metabolites. Here we use a transient expression system in the model plant <i>Nicotiana benthamiana</i> to reconstitute the two-step plant-derived biosynthetic pathway for auxin (indole acetic acid) to achieve accumulation up to 500 ng/g fresh mass (FM). By expressing these plant-derived enzymes in combination with either bacterial halogenases and alternative substrates, we can produce both natural and new-to-nature halogenated auxin derivatives up to 990 ng/g FM. Proteins from the auxin synthesis pathway, tryptophan aminotransferases (TARs) and flavin-dependent monooxygenases (YUCs), could be transiently expressed in combination with four separate bacterial halogenases to generate halogenated auxin derivatives. Brominated auxin derivatives could also be observed after infiltration of the transfected <i>N. benthamiana</i> with<i> </i>potassium bromide and the halogenases. Finally, the production of additional auxin derivatives could also be achieved by co-infiltration of TAR and YUC genes with various tryptophan analogues. Given the emerging importance of transient expression in <i>N. benthamiana</i> for industrial scale protein and product expression, this work provides insight into the capacity of <i>N. benthamiana</i> to interface bacterial genes and synthetic substrates to produce novel halogenated metabolites.</p>
Data from: Integration of genomics and transcriptomics predicts diabetic retinopathy susceptibility genes
<p class="Normal1">We determined differential gene expression in response to high glucose in lymphoblastoid cell lines derived from matched individuals with type 1 diabetes with and without retinopathy. Those genes exhibiting the largest difference in glucose response were assessed for association to diabetic retinopathy in a genome-wide association study meta-analysis. Expression Quantitative Trait Loci (eQTLs) of the glucose response genes were tested for association with diabetic retinopathy. We detected an enrichment of the eQTLs from the glucose response genes among small association p-values and identified <i>FLCN</i> as a susceptibility gene for diabetic retinopathy. Expression of <i>FLCN </i>in response to glucose was greater in individuals with diabetic retinopathy. Independent cohorts of individuals with diabetes revealed an association of <i>FLCN</i> eQTLs to diabetic retinopathy. Mendelian randomization confirmed a direct positive effect of increased <i>FLCN</i> expression on retinopathy. Integrating genetic association with gene expression implicated <i>FLCN </i>as a disease gene for diabetic retinopathy.</p>
Dataset related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile"
<p>This record contains raw data related to the article "Human Cardiac Mesenchymal Stromal Cells From Right and Left Ventricles Display Differences in Number, Function, and Transcriptomic Profile". </p> <p><strong>Background:</strong> Left ventricle (LV) and right ventricle (RV) are characterized by well-known physiological differences, mainly related to their different embryological origin, hemodynamic environment, function, structure, and cellular composition. Nevertheless, scarce information is available about cellular peculiarities between left and right ventricular chambers in physiological and pathological contexts. Cardiac mesenchymal stromal cells (C-MSC) are key cells affecting many functions of the heart. Differential features that distinguish LV from RV C-MSC are still underappreciated.</p> <p><strong>Aim:</strong> To analyze the physiological differential amount, function, and transcriptome of human C-MSC in LV versus (vs.) RV.</p> <p><strong>Methods:</strong> Human cardiac specimens of LV and RV from healthy donors were used for tissue analysis of C-MSC number, and for C-MSC isolation. Paired LV and RV C-MSC were compared as for surface marker expression, cell proliferation/death ratio, migration, differentiation capabilities, and transcriptome profile.</p> <p><strong>Results:</strong> Histological analysis showed a greater percentage of C-MSC in RV vs. LV tissue. Moreover, a higher C-MSC amount was obtained from RV than from LV after isolation procedures. LV and RV C-MSC are characterized by a similar proportion of surface markers. Functional studies revealed comparable cell growth curves in cells from both ventricles. Conversely, LV C-MSC displayed a higher apoptosis rate and RV C-MSC were characterized by a higher migration speed and collagen deposition. Consistently, transcriptome analysis showed that genes related to apoptosis regulation or extracellular matrix organization and integrins were over-expressed in LV and RV, respectively. Besides, we revealed additional pathways specifically associated with LV or RV C-MSC, including energy metabolism, inflammatory response, cardiac conduction, and pluripotency.</p> <p><strong>Conclusion:</strong> Taken together, these results contribute to the functional characterization of RV and LV C-MSC in physiological conditions. This information suggests a possible differential role of the stromal compartment in chamber-specific pathologic scenarios.</p>
Good vs poor responder RNAseq transcriptome profiles in DBA/2J mice
<p>Major depressive disorder is the most prevalent mental illness worldwide, still its pharmacological treatment is limited by various challenges, such as the large heterogeneity in treatment response and the lack of insight into the neurobiological pathways underlying this phenomenon. To decode the molecular mechanisms shaping antidepressant response and to distinguish those from general paroxetine effects, we used a previously established approach targeting extremes (i.e. good vs. poor responder mice). Transcriptome profiling on micro-dissected DG granule cells as well as on peripheral blood samples was performed to <i>i</i>) reveal celltype specific changes in paroxetine-induced gene expression (paroxetine vs. vehicle) and <i>ii</i>) to identify molecular signatures of treatment response within a cohort of paroxetine-treated animals. In this datasheet, we provide the mapped and norm-counted RNAseq results of our experiments in an user-friendly excel file.</p>
Transcriptome analysis of ionic-liquid tolerant Bacillus amyloliquefaciens CMW1 and identification of a novel efflux pump
<p>Bacteria that exhibit ionic-liquid (IL) tolerance are useful in chemical industries using renewable carbon sources pretreated by ILs to produce biofuels and fine chemicals. Although an IL, 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), has a remarkable ability to solubilize wood components, [BMIM]Cl inhibits the growth of various bacterial hosts useful for bioconversion. We previously isolated a 10% [BMIM]Cl-tolerant bacterium Bacillus amyloliquefaciens CMW1. Here we report novel mechanisms of tolerance to [BMIM]Cl in strain CMW1 and a novel major facilitator superfamily (MFS) transporter coded by an ionic-liquid tolerance (ILT) gene. First, using CMW1 cells grown in the presence or absence of 10% [BMIM]Cl, whole-transcriptome analysis and differentially expressed gene analysis were performed. Probable mechanisms of tolerance to [BMIM]Cl include uptake of osmoprotectants from the culture medium toward CMW1 cells and the export of [BMIM] cations that accumulated in CMW1 cells. The finding represents a first step in elucidation of the mechanisms of IL resistance in Gram-positive bacteria. Second, we conferred tolerance to 5% [BMIM]Cl on [BMIM]Cl-susceptible Brevibacillus choshinensis using ILT gene. This finding provides a notable basis for engineering IL-tolerant bacterial hosts that are applicable for the effective and sustainable production of industrially important chemicals.</p>
BRCA1- and BRCA2- mutation associated transcriptome landscapes in breast and ovarian cancers: ml-SOM results
<p>This is the submission accompanying raw result files for multiple-layer SOM (ml-SOM) analysis for the paper "Transcriptome patterns of BRCA1- and BRCA2- mutated breast and ovarian cancers".</p> <p>The dataset contains the results of the ml-SOM analysis of RNA-sequencing data from TCGA-OV (ovarian cancer) and TCGA-BRCA (breast cancer) projects. </p> <p>The dataset is organized as follows:</p> <ul> <li>Folder <strong>"12.BC.40 - Results" </strong>- ml-SOM analysis of TCGA-BRCA (breast cancer) dataset</li> <li>Folder <strong>"12.OV.40 - Results"</strong> - ml-SOM analysis of TCGA-OV (ovarian cancer) dataset</li> <li>File <strong>"12.BC.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> <li>File <strong>"12.OV.40.RData"</strong> - R data file that contains ml-SOM environment for breast cancer</li> </ul> <p>For detailed instructions on browsing the results and their interpretation please refer to the oposSOM package manual [1], as well as original publications [2-4]. </p> <p><strong>References</strong></p> <ol> <li>Henry Loeffler-Wirth, Hoang Thanh Le and Martin Kalcheropos. SOM.Comprehensive analysis of transcriptome data. DOI: <a href="https://doi.org/doi:10.18129/B9.bioc.oposSOM">10.18129/B9.bioc.oposSOM</a> </li> <li>Löffler-Wirth H, Kalcher M, Binder H. oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on Bioconductor. Bioinformatics. 2015 Oct 1;31(19):3225-7. DOI: 10.1093/bioinformatics/btv342. Epub 2015 Jun 10.</li> <li>Wirth H, von Bergen M, Binder H. Mining SOM expression portraits: feature selection and integrating concepts of molecular function. BioData Min. 2012 Oct 8;5(1):18. DOI: 10.1186/1756-0381-5-18.</li> <li>Wirth H, Löffler M, von Bergen M, Binder H. Expression cartography of human tissues using self-organizing maps. BMC Bioinformatics. 2011 Jul 27;12:306. DOI: 10.1186/1471-2105-12-306.</li> </ol>
Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs
<p>Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid <em>Olkasia</em> as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by <em>Ploeotia</em> spp.), <em>Lentomonas</em>, and <em>Keelungia</em> form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes <em>Rapaza</em>, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (<em>Anisonema</em> and <em>Dinema</em> spp.), '<em>Heteronema</em> II' (represented by <em>H. vittatum</em>), and a clade of <em>Neometanema</em> plus Aphagea. Among 'peranemid' phagotrophs, <em>Chasmostoma</em> branches with included <em>Urceolus</em>, and <em>Peranema</em> with the undescribed '<em>Jenningsia</em> II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that <em>Entosiphon</em> is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.</p>
Transcriptomic data and analyses of shMeg3 muscle in vitro and in vivo
<p>Formation of skeletal muscle is among the most striking examples of cellular plasticity in animal tissue development, and while muscle progenitor cells are reprogrammed by epithelial-mesenchymal transition (EMT) to migrate during embryonic development, regulation of EMT in postnatal myogenesis remains poorly understood. Here, we demonstrate that the long noncoding RNA (lncRNA) <em>Meg3</em> regulates EMT in myoblast differentiation and skeletal muscle regeneration. Chronic inhibition of <em>Meg3</em> in C2C12 myoblasts induced EMT, and supressed cell state transitions required for differentiation. Furtheremore, adenoviral <em>Meg3</em> knockdown compromised muscle regeneration, which was accompanied by abnormal mesenchymal gene expression and interstitial cell proliferation. Transcriptomic and pathway analyses of <em>Meg3-</em>depleted C2C12 myoblasts and injured skeletal muscle revealed a significant dysregulation of EMT-related genes, and identified TGFβ as a key upstream regulator. Importantly, inhibition of TGFβR1 and its downstream effectors, and the EMT-related transcriptional repressor Snai2, restored many aspects of myogenic differentiation in <em>Meg3</em>-depleted myoblasts <em>in vitro</em>. We further demonstrate that reduction of <em>Meg3-</em>dependent Ezh2 activity results in epigenetic alterations associated with TGFβ activation. Thus, <em>Meg3</em> regulates myoblast identity to facilitate progression into muscle differentiation.</p>
Comparative transcriptome analysis reveals key genes potentially related to organic acid and sugar accumulation in loquat
<p class="MDPI17abstract">Organic acids and sugars are the primary components that determine the quality and flavor of loquat fruits. In the present study, major organic acids, sugar content, enzyme activities, and the expression of related genes were analyzed during fruit development in two loquat cultivars, 'JieFangZhong' (JFZ) and 'BaiLi' (BL). Our results showed that the sugar content increased during fruit development in the two cultivars; however, the organic acid content dramatically decreased in the later stages of fruit development. The differences in organic acid and sugar content between the two cultivars primarily occured in the late stage of fruit development and the related enzymes showed dynamic changes in activies during development. Phosphoenolpyruvate carboxylase (PEPC) and mNAD malic dehydrogenase (mNAD-MDH) showed higher activities in JFZ at 95 days after flowering (DAF) than in BL. However, NADP-dependent malic enzyme (NADP-ME) activity was the lowest at 95 DAF in both JFZ and BL with BL showing higher activity compared with JFZ. At 125 DAF, the activity of fructokinase (FRK) was significantly higher in JFZ than in BL. The activity of sucrose synthase (SUSY) in the sucrose cleavage direction (SS-C) was low at early stages of fruit development and increased at 125 DAF. SS-C activity was higher in JFZ than in BL. vAI and sucrose phosphate synthase (SPS) activities were similar in the two both cultivars and increased with fruit development. RNA-sequencing was performed to determine the candidate genes for organic acid and sugar metabolism. Our results showed that the differentially expressed genes (DEGs) with the greated fold changes in the later stages of fruit development between the two cultivars were phosphoenolpyruvate carboxylase 2 (<i>PEPC2</i>), mNAD-malate dehydrogenase (<i>mNAD-MDH</i>), cytosolic NADP-ME (<i>cyNADP-ME2</i>), aluminum-activated malate transporter (<i>ALMT9</i>), subunit A of vacuolar H<sup>+</sup>-ATPase (<i>VHA-A</i>), vacuolar H<sup>+</sup>-PPase (<i>VHP1</i>), NAD-sorbitol dehydrogenase (<i>NAD-SDH</i>), fructokinase (<i>FK</i>), sucrose synthase in sucrose cleavage (<i>SS-C</i>), sucrose-phosphate synthase 1 (<i>SPS1)</i>, neutral invertase (NI), and vacuolar acid invertase (<i>vAI)</i>. The expression of 12 key DEGs was validated by quantitative reverese transcription PCR (RT-qPCR). Our findings will help understand the molecular mechanism of organic acid and sugar formation in loquat, which will aid in breeding high-quality loquat cultivars.</p>
Data from: Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function
Background: Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their "unusual" energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results: We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions: The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of "model organism".
Data from: The transcriptomic and evolutionary signature of social interactions regulating honey bee caste development
The caste fate of developing female honey bee larvae is strictly socially regulated by adult nurse workers. As a result of this social regulation, nurse-expressed genes as well as larval-expressed genes may affect caste expression and evolution. We used a novel transcriptomic approach to identify genes with putative direct and indirect effects on honey bee caste development, and we subsequently studied the relative rates of molecular evolution at these caste-associated genes. We experimentally induced the production of new queens by removing the current colony queen, and we used RNA sequencing to study the gene expression profiles of both developing larvae and their caregiving nurses before and after queen removal. By comparing the gene expression profiles of queen-destined versus worker-destined larvae as well as nurses observed feeding these two types of larvae, we identified larval and nurse genes associated with caste development. Of 950 differentially expressed genes associated with caste, 82% were expressed in larvae with putative direct effects on larval caste, and 18% were expressed in nurses with putative indirect effects on caste. Estimated selection coefficients suggest that both nurse and larval genes putatively associated with caste are rapidly evolving, especially those genes associated with worker development. Altogether, our results suggest that indirect effect genes play important roles in both the expression and evolution of socially influenced traits such as caste.
Data from: Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species
C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.
Data from: Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle
Parenting in the burying beetle Nicrophorus vespilloides is complex and, unusually, the sex and number of parents that can be present is flexible. Such flexibility is expected to involve specialized behaviour by the two sexes under biparental conditions. Here, we show that offspring fare equally well regardless of the sex or number of parents present. Comparing transcriptomes, we find a largely overlapping set of differentially expressed genes in both uniparental and biparental females and in uniparental males including vitellogenin, associated with reproduction, and takeout, influencing sex-specific mating and feeding behaviour. Gene expression in biparental males is similar to that in non-caring states. Thus, being 'biparental' in N. vespilloides describes the family social organization rather than the number of directly parenting individuals. There was no specialization; instead, in biparental families, direct male parental care appears to be limited with female behaviour unchanged. This should lead to strong sexual conflict.
Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of Chalcidoid wasps
<p>Chalcidoidea (Hymenoptera) are a megadiverse superfamily of wasps with astounding variation in both morphology and biology. Most species are parasitoids and important natural enemies of insects in terrestrial ecosystems. In this study, we explored a transcriptome-based phylogeny of Chalcidoidea and found that poorly resolved relationships could only be marginally improved by adding more genes (a total of 5,591) and taxa (a total of 65), proof-checking for errors of homology and contamination, and decreasing missing data. Concatenation analyses consistently place Mymaridae and Trichogrammatidae sister to remaining Chalcidoidea. However, our coalescent analyses provide a different hypothesis with a grouping of (Mymaridae (((Trichogrammatidae, Eulophidae), (Encyrtidae, Aphelinidae)), remaining Chalcidoidea)). This hypothesis complicates our hypothesis of egg parasitism as being ancestral in Chalcidoidea. At the deeper nodes, the results uncovered a wide spectrum of gene discordance in the transcriptomic markers and identified a strong signal of functional bias in genes supporting alternative phylogenies. The basal nodes of the phylogeny are thus strongly influenced by biased support from different functional gene complexes. Shallower nodes showed similar gene discordance, but without strong functional bias. Understanding and identifying mechanisms that result in gene tree discordance may be beneficial and even essential for sorting out backbone relationships, especially for groups that have undergone extremely rapid radiation.</p>
Data from: AmpuBase: a transcriptome database for eight species of apple snails (Gastropoda: Ampullariidae)
Background: Gastropoda, with approximately 80,000 living species, is the largest class of Mollusca. Among gastropods, apple snails (family Ampullariidae) have members that are widely distributed in tropical and subtropical freshwater ecosystems and are ecologically and economically important. They exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying adaptation, population divergence, speciation, and larger-scale patterns of diversity, including biogeography of native and invasive populations. The limited availability of genomic data, however, hinders in-depth ecological and evolutionary studies of these non-model organisms. Results: Using Illumina Hiseq platforms, we sequenced 1,220 million reads for seven species of apple snails. Together with the RNA-Seq data of two apple snails, we conducted de novo transcriptome assembly of eight species covering five genera of Ampullariidae, including representatives of the Old World and New World lineages. There were 20,730 to 35,828 unigenes with predicted open read frames for the eight species, with N50 (shortest sequence length at 50% of the unigenes) ranging from 1,320 to 1,803 bp. 69.7 % to 80.2 % of these unigenes were functionally annotated by searching against databases of NCBI's non-redundant, Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes. With these data we developed AmpuBase, a relational database that features online BLAST for DNA/protein sequences, keyword search for unigenes/functional terms, and download functions for sequences and whole transcriptomes. Conclusions: In summary, we have generated comprehensive transcriptome data for multiple ampullariid genera and species, and created a publicly accessible database with a user-friendly interface to facilitate future basic and applied studies on ampullariids, and comparative molecular studies with other invertebrates.
Data from: MicroRNAs Shape Circadian Hepatic Gene Expression on a Transcriptome-Wide Scale
A considerable proportion of mammalian gene expression undergoes circadian oscillations. Post-transcriptional mechanisms likely make important contributions to mRNA abundance rhythms. We have investigated how microRNAs (miRNAs) contribute to core clock and clock-controlled gene expression using mice in which miRNA biogenesis can be inactivated in the liver. While the hepatic core clock was surprisingly resilient to miRNA loss, whole transcriptome sequencing uncovered widespread effects on clock output gene expression. Cyclic transcription paired with miRNA-mediated regulation was thus identified as a frequent phenomenon that affected up to 30% of the rhythmic transcriptome and served to post-transcriptionally adjust the phases and amplitudes of rhythmic mRNA accumulation. However, only few mRNA rhythms were actually generated by miRNAs. Overall, our study suggests that miRNAs function to adapt clock-driven gene expression to tissue-specific requirements. Finally, we pinpoint several miRNAs predicted to act as modulators of rhythmic transcripts, and identify rhythmic pathways particularly prone to miRNA regulation.
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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.