• To define the divergence in gene expression modules between C(3) and C(4) photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C(4)) and Tarenaya hassleriana (C(3)), by RNA sequencing. (nih.gov)
  • We have provided a comprehensive transcriptome library of CCM disease across species and for the first time to our knowledge in Ccm1/Krit1 versus Ccm3/Pdcd10 genotypes. (jci.org)
  • Therefore, a well-assembled, accurate, and comprehensive transcriptome is a prerequisite for the subsequent analysis. (biomedcentral.com)
  • Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. (plos.org)
  • Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. (nature.com)
  • On the basis of whole-transcriptome analyses, we identify many genes that are expressed in a sex- or life stage-specific manner and characterize the transcriptional landscape of a morphological region with unique biological adaptations, namely, bacillary band and stichosome, found only in whipworms and related parasites. (nature.com)
  • Differential gene expression analyses between closely related C 3 and C 4 species have significantly increased our understanding of C 4 functioning and evolution. (nih.gov)
  • The purpose of this study was to determine important genes, functions, and networks contributing to the pathobiology of cerebral cavernous malformation (CCM) from transcriptomic analyses across 3 species and 2 disease genotypes. (jci.org)
  • Cross-comparisons of DEGs between species and genotypes, as well as network and gene ontology (GO) enrichment analyses, were performed. (jci.org)
  • Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. (bvsalud.org)
  • To explore the underlying molecular events that are associated with the progression of PGD, we sampled Atlantic salmon from three different marine production sites in Scotland and examined the gill tissue at three different levels of organization: gross morphology with the use of PGD scores (macroscopic examination), whole transcriptome (gene expression by RNA-seq) and histopathology (microscopic examination). (frontiersin.org)
  • In parallel, multiple technologies and manual finishing were used to produce an 85-Mb reference genome assembly from the more readily available mouse parasite species T. muris (Online Methods and Supplementary Note ). (nature.com)
  • De novo transcriptome assembly is the de novo sequence assembly method of creating a transcriptome without the aid of a reference genome. (wikipedia.org)
  • Prior to the development of transcriptome assembly computer programs, transcriptome data were analyzed primarily by mapping on to a reference genome. (wikipedia.org)
  • For an organism that lacks a high-quality reference genome, the de novo assembly of its transcriptome is a useful method for researchers to find the transcripts or genes responsive to various treatments and to better understand the expression patterns of the candidate genes. (biomedcentral.com)
  • Here we present the first reference genome and transcriptome of C. personatum to support studies in phylogenetics, genetic diversity, pathogenicity, and metabolites of this peanut pathogen. (biomedcentral.com)
  • Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology. (nature.com)
  • The study of specialized tissue domains and their interactions is essential for a comprehensive understanding of the function of biological systems, including the wide variety of plant species. (nature.com)
  • For many temperate plant species, a period of exposure to chilling temperatures increases plant tolerance to subsequent freezing conditions in a phenomenon known as "cold acclimation" [ 7 ]. (biomedcentral.com)
  • Currently, the common way to prepare celastrol is direct extraction of wild plant resources, which has endangered the continuation of the wild plant species and has brought adverse effects on the environment. (techscience.com)
  • However, the occurrence of polpunonic acid (friedelin 29-carboxylic acid) in several plant species of Celastraceae (e.g. (techscience.com)
  • Comparison to other dormancy microarray studies indicated that nearly half of the genes identified in our study were also differentially expressed in at least two other plant species during dormancy transitions. (usda.gov)
  • These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes. (biomedcentral.com)
  • These novel genetic resources were then analyzed to provide a better understanding of differential gene expression between C 3 , C 2 and C 4 species. (nih.gov)
  • Furthermore, a function of PEP-CK in C 2 photosynthesis appears likely, since PEP-CK gene expression is not only increased in S. divaricata but also in C 2 species of other groups. (nih.gov)
  • Overall, the gene expression profiles appear remarkably similar between the C(3) and C(4) species. (nih.gov)
  • Unlike genome sequence coverage levels - which can vary randomly as a result of repeat content in non-coding intron regions of DNA - transcriptome sequence coverage levels can be directly indicative of gene expression levels. (wikipedia.org)
  • Along with the molecular species identification, an analysis of the ciliates' stop codons was carried out, which revealed a relationship where TGA stop codon frequency decreased with increasing gene expression levels. (bournemouth.ac.uk)
  • Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. (bioconductor.org)
  • Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. (bioconductor.org)
  • 2020. Dataset for the combined transcriptome assembly of and functional annotation. . (ncbs.res.in)
  • There was considerable discussion of adding value to the transcriptome by way of annotation methods, yet none of the annotations can be tied to actual sequence data. (peerj.com)
  • We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. (nature.com)
  • Here, we combine spatial transcriptomics and scRNA-Seq datasets to define the transcriptome of tumor-proximal and tumor-distal cancer-associated fibroblasts (CAFs) and link this to clinical outcome. (elifesciences.org)
  • 2021. On the systematics and the phylogenetic position of the poorly known, montane dragon-lizard species Pseudocalotes austeniana (Annandale, 1908) (Squamata, Agamidae, Draconinae) . (ncbs.res.in)
  • A draft genome will also allow for a more robust phylogenetic analysis of this species, and perhaps settle its systematic placement, which has changed in recent years. (biomedcentral.com)
  • Transcriptome analysis is a powerful tool that enables a deep understanding of complicated physiological pathways, including immune responses. (frontiersin.org)
  • RNA sequencing (RNA-Seq)-based transcriptome analysis and various bioinformatics tools have also been used to study non-model animals, including aquaculture species for which reference genomes are not available. (frontiersin.org)
  • Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L. (usda.gov)
  • These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. (usda.gov)
  • Analysis of the transcriptome indicates that S. semivirescens potentially uses rhodoquinol-dependent fumarate reduction to respire in the oxygen-depleted habitats where it lives. (bournemouth.ac.uk)
  • Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
  • Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy. (cdc.gov)
  • In the two populations of the C 2 species S. divaricata transcript abundance of several C 4 genes are slightly increased, however, a C 4 cycle is not detectable in the carbon isotope values. (nih.gov)
  • Third, transcriptome assembly is more challenging because transcript variants from the same gene can share exons and are difficult to resolve unambiguously. (wikipedia.org)
  • We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. (biomedcentral.com)
  • The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. (biomedcentral.com)
  • Many alternatively spliced transcript were present in out transcriptome. (stanford.edu)
  • Each representative transcript has been classified based on most probable species of origin based on TopSort (a machine-learning algorithm) and genomic read alignment (.txt file). (stanford.edu)
  • 2022. Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.). . Sci Rep. 12(1):13534. (ncbs.res.in)
  • De novo transcriptome assembly is often the preferred method to studying non-model organisms, since it is cheaper and easier than building a genome, and reference-based methods are not possible without an existing genome. (wikipedia.org)
  • These repeated sequences also create ambiguities in the formation of contigs in genome assembly, while ambiguities in transcriptome assembly contigs usually correspond to spliced isoforms, or minor variation among members of a gene family. (wikipedia.org)
  • Genome assembler can't be directly used in transcriptome assembly for several reasons. (wikipedia.org)
  • Although these programs have been generally successful in assembling genomes, transcriptome assembly presents some unique challenges. (wikipedia.org)
  • A total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. (biomedcentral.com)
  • We performed de novo transcriptome assembly using deep RNA sequencing data from 11 distinct tissues from one male and one female bat. (columbia.edu)
  • This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry. (biomedcentral.com)
  • These contigs were uploaded to the NCBI Transcriptome Assembly Shotgun Sequence Database, accession numbers JV077153-JV134524. (stanford.edu)
  • We demonstrated that only 39 differentially expressed genes (DEGs) were present in all species. (frontiersin.org)
  • The DEGs in different fish species were also representative of specific immune-related pathways. (frontiersin.org)
  • Among hundreds of DEGs identified in each model, common genes and 1 GO term (GO:0051656, establishment of organelle localization) were commonly identified across the different species and genotypes. (jci.org)
  • In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. (biomedcentral.com)
  • A Heidelberg University-led team analyzed bulk transcriptome data from half a dozen organs and species to examine developmental dynamics. (genomeweb.com)
  • More information available in: "Conserved developmental transcriptomes in evolutionarily divergent species. (dictybase.org)
  • This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. (biomedcentral.com)
  • Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. (bl.uk)
  • The data also shows that despite large geographical distances (over 1,600 km) between the sampling sites investigated, a morphologically-identical species can share an exact molecular signature, suggesting that some ciliate species, even those over 1mm in size, could have a global biogeographical distribution. (bournemouth.ac.uk)
  • Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. (biorxiv.org)
  • We assembled the transcriptome of a clonal population of adult, aposymbiotic (dinoflagellate-free) Aiptasia pallida from ~208 million reads, yielding 58,018 contigs. (stanford.edu)
  • The transcriptomes of these organisms can thus reveal novel proteins and their isoforms that are implicated in such unique biological phenomena. (wikipedia.org)
  • Most of the core enzymes of photorespiration are highly increased in the C 2 species compared to both C 3 and C 4 species, confirming a successful establishment of the C 2 photosynthetic pathway. (nih.gov)
  • The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome. (biomedcentral.com)
  • The ICE1-CBF-COR transcriptional cascade (inducer of CBF expression 1 and C-repeat binding factor transcriptional cascade) is the best characterized pathway for gene regulation under cold conditions in many species [ 8 ]. (biomedcentral.com)
  • Interactions between species introduce spurious associations in microbiome studies. (cdc.gov)
  • Homey presented the results of a study of 61 patients designed to look at how ivermectin might be working in the treatment of people with rosacea and investigate if there was any relation to the skin microbiome and transcriptome of patients. (medscape.com)
  • mRNA from assimilating organs of each species was sequenced in triplicates, and sequence reads were de novo assembled. (nih.gov)
  • Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a transcriptome, they may indicate abundance. (wikipedia.org)
  • Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. (bl.uk)
  • Sequences were preprocessed with adapter trimming and alignment-free quantification with Kallisto using Ensembl v96 transcriptomes. (cdc.gov)
  • Our results indicate that machine learning algorithms can detect and quantify microglial cells in all the three mammalian species in a precise manner, equipotent to the one observed following manual counting. (lu.se)
  • Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. (lu.se)
  • In conclusion, our results provide cross-species in planta models for identifying common virulence factors, which can be useful for the protection of crops against diverse pathogens. (figshare.com)
  • Fourth, we present a comparison of transcriptomic datasets and identify 175 genes that share common responses to heat stress across Mytilus species. (biologists.com)
  • Species in the genus Ocimum are native to Africa, South America, and Asia, and are valued as aromatic and medicinal plants. (biomedcentral.com)
  • On the systematic status of the genus Oriocalotes Günther, 1864 (Squamata: Agamidae: Draconinae) with the description of a new species from Mizoram state, Northeast India. (ncbs.res.in)
  • 2017. Taxonomic overview of the hyperdiverse ant genus Tetramorium Mayr (Hymenoptera, Formicidae) in India with descriptions and X-ray microtomography of two new species from the Andaman Islands. . (ncbs.res.in)
  • The genus contains the species Corynebacterium diphtheriae and the nondiphtherial corynebacteria, collectively referred to as diphtheroids. (medscape.com)
  • Although only one SFFF sample (F) caused robust increased intracellular reactive oxygen species, several AFFF and PFAS species showed decreased antioxidant capacity. (cdc.gov)
  • In Chenopodiaceae, a family that is rich in C 4 origins and photosynthetic types, the anatomy, physiology and phylogeny of C 4 , C 2 , and C 3 species of Salsoleae has been studied in great detail, which facilitated the choice of six samples of five representative species with different photosynthetic types for transcriptome comparisons. (nih.gov)
  • Toxicity and transcriptome comparisons of different firefighting foam exposures in human renal proximal tubule epithelial cells. (cdc.gov)
  • Although it is known that accessions of Lens ervoides possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in L. ervoides . (biomedcentral.com)
  • Molecular investigation of the ciliate Spirostomum semivirescens, with first transcriptome and new geographical records. (bournemouth.ac.uk)
  • The species has been rarely recorded and it lacks any molecular investigations. (bournemouth.ac.uk)
  • Advancements in bioinformatics has significantly supported RNA-Seq technology to accelerate the knowledge on transcriptomes ( 1 ). (frontiersin.org)
  • A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C(4) leaf. (nih.gov)
  • The abundance of photorespiratory transcripts is decreased compared to the C 3 and C 2 species. (nih.gov)
  • In addition, unlike genome sequencing, transcriptome sequencing can be strand-specific, due to the possibility of both sense and antisense transcripts. (wikipedia.org)
  • 2020. Distinct Evolutionary Origins of Intron Retention Splicing Events in Antiporter Transcripts Relate to Sequence Specific Distinctions in Species. . (ncbs.res.in)
  • However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. (biomedcentral.com)
  • Experimental varieties or clones are cultivated in pure stands (a species A or a species B) and in mixed stands (species A and species B). Eight genotypes of species A are combined with three genotypes of species B. Combinations are arranged in blocks with four replications. (uni-goettingen.de)
  • 2020. The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera). . (ncbs.res.in)
  • . pilosum and compared the transcriptomes of plants grown under normal and low temperatures. (biomedcentral.com)
  • The Tolerome: A Database of Transcriptome-Level Contributions to Diverse Escherichia coli Resistance and Tolerance Phenotypes. (cdc.gov)
  • Based on degenerated primers, expressed orthologous genes previously tested in other insect species (V-ATPase A, Ecdisone Receptor, and Arginine Kinase) were cloned,whilegenes with specific function (Juvenile Hormone Epoxide Hydrolase, Neverland, and Chitin Synthase) were identified from an in-house assembled transcriptome of D. saccharalis and cloned. (usp.br)
  • Transcriptome profiling of two Moringa species and insights into their antihyperglycemic activity. (ncbs.res.in)
  • Species and sex identification by hyperspectral imaging Identifying mosquitoes is important for the prevention of mosquito-borne diseases, effective pest control, and environmental monitoring. (lu.se)
  • Even though their distributions are largely disjunct, it has been suggested the two species may hybridize to form P. edulis var. (bioone.org)
  • CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison. (bioconductor.org)
  • Using a multi-omics approach, we demonstrate that TEs introduce a layer of transcriptome complexity to the human brain. (lu.se)
  • Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function ( CCR7 , CD27 , IL7R , CAMK4 , CD28 ), mitochondrial ribosomal proteins ( MRPS27 , MRPS9 , MRPS31 ), and DNA replication and repair ( WRN ). (biomedcentral.com)
  • Toxicogenomics: new strategies for ecotoxicology studies in autochthonous species I. A glade in the entangled path towards the 'fingerprint' of environmental impact? (inderscience.com)
  • Toxicogenomics: new strategies for ecotoxicology studies in autochthonous species II. (inderscience.com)
  • We undertook a transcriptome-scale approach (454 pyrosequencing) as a baseline for future studies addressing the physiological response of krill to short-term food shortage and natural UV-B stress. (ualg.pt)
  • The Egyptian Rousette bat (Rousettus aegyptiacus), a common fruit bat species found throughout Africa and the Middle East, was recently identified as a natural reservoir host of Marburg virus. (columbia.edu)
  • Our results suggest that cold temperature significantly affects genes related to protein translation and cellular metabolism in this chilling sensitive species. (biomedcentral.com)
  • All AFFF caused significantly greater cytotoxicity than legacy PFAS species, including PFOS, on a total fluorine dose basis. (cdc.gov)
  • Cnidaria is a group of primarily marine invertebrates composed of about 11,000 described species [ 1 ] that include reef-forming corals, sea anemones, soft corals, jellyfish, marine hydroids, and freshwater Hydra ( Fig 1 ). (plos.org)