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90 results for “de novo transcriptome assembly”
DATASET: De novo assembly and functional annotation of the heart + hemolymph transcriptome in the Caribbean spiny lobster Panulirus argus
<p>The spiny lobster <em>Panulirus argus</em> is an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. This study reports, for the first time, the heart + hemolymph transcriptome of the Caribbean spiny lobster<em> Panulirus argus</em> assembled from short Illumina 150 bp PE raw reads. A total 80,152,094 raw reads were assembled using the Oyster River Protocol pipeline that aspires to become the standard protocol for <em>de novo</em> transcriptome assembly. The assembly resulted in a total of 254,773 transcripts. Functional gene annotation was conducted using the software package 'dammit' that also aspires to become the standard protocol for <em>de novo</em> transcriptome annotation. Lastly, gene enrichment analyses were conducted using the Gene Ontology (GO), KEGG pathway analyses (Kaas), and KOG (WebMGA) databases. This resource will be of utmost importance in future research aiming at exploring the effect of local and regional anthropogenic disturbances as well as global climate change on the molecular physiology of this overexploited species.</p>
Data From: The Oyster River Protocol: A multi assembler and kmer approach for de novo transcriptome assembly.
<p>Characterizing transcriptomes in non-model organisms has resulted in a massive increase in our understanding of biological phenomena. This boon, largely made possible via high-throughput sequencing, means that studies of functional, evolutionary and population genomics are now being done by hundreds or even thousands of labs around the world. For many, these studies begin with a <em>de novo</em> transcriptome assembly, which is a technically complicated process involving several discrete steps. The Oyster River Protocol (ORP), described here, implements a standardized and benchmarked set of bioinformatic processes, resulting in an assembly with enhanced qualities over other standard assembly methods. Specifically, ORP produced assemblies have higher Detonate and TransRate scores and mapping rates, which is largely a product of the fact that it leverages a multi-assembler and kmer assembly process, thereby bypassing the shortcomings of any one approach. These improvements are important, as previously unassembled transcripts are included in ORP assemblies, resulting in a significant enhancement of the power of downstream analysis. Further, as part of this study, I show that assembly quality is unrelated with the number of reads generated, above 30 million reads. Code Availability: The version controlled open-source code is available at <a href="https://github.com/macmanes-lab/Oyster_River_Protocol">https://github.com/macmanes-lab/Oyster_River_Protocol</a>. Instructions for software installation and use, and other details are available at <a href="http://oyster-river-protocol.rtfd.org/">http://oyster-river-protocol.rtfd.org/</a>.</p>
Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
<p>Six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of <em>in vitro</em> grown plants) were sequenced and <em>de novo</em> assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> .</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly.tar.gz">CE_Assembly.tar.gz</a> - Centaury referent transcriptome comprises of 160.839 Trinity transcripts grouped in 105.726 Trinity genes.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/CE_Assembly_fpkm.tar.gz">CE_Assembly_fpkm.tar.gz</a> - fpkm normalized read counts of the assembled transcripts in the six sequenced centaury tissues.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/nt.db_CE_assembly.tar.gz">nt.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (NT) database using BLASTn . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">swissprot.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against NCBI nucleotide (<a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/swissprot.db_CE_assembly.tar.gz">s</a>wissprot) database using BLASTx . The obtained results were filtered with E-value E ≤ 10<sup>-3</sup>.</p> <p><a href="https://zenodo.org/api/files/a0546879-e382-4cf9-8185-f188d1a0c5f0/pfam30.db_CE_assembly.tar.gz">pfam30.db_CE_assembly.tar.gz</a> - annotation of assembled transcripts by mapping them against Pfam30 domain database using hmmer3. The obtained results were filtered with independent E-value E ≤ 10<sup>-3</sup>.</p>
De novo transcriptome assembly of hyperaccumulating Noccaea praecox
<p>Trinity de novo assembly for hyperaccumulating plant species Noccaea praecox (syn. Thlaspi praecox), Brassicaceae. The dataset includes annotations from SwissProt, Pfam, Rfam databases and information on transmembrane regions and signal peptide cleavage sites (annotated using BLAST, HMMER, infernal, tmHMM and signalP through Trinotate). Detailed information on the preprocessing, assembly, post-processing and annotations are described in the ReadMe file.</p> <p>Supplementary material for Bočaj, V., Pongrac, P., Fischer, S. <em>et al.</em> <em>De novo</em> transcriptome assembly of hyperaccumulating <em>Noccaea praecox</em> for gene discovery. <em>Sci Data</em> <strong>10</strong>, 856 (2023). <a href="https://doi.org/10.1038/s41597-023-02776-x">https://doi.org/10.1038/s41597-023-02776-x</a></p>
Data from "Corset: enabling differential gene expression analysis for de novo assembled transcriptomes"
<p>This dataset contains de novo transcriptome assemblies for three publicly available RNA-seq dataset (SRA055442, SRR453566-SRR453571 and GSE37704 ). For each assembly we also provide a table with the read counts per contig, the output from corset (clusters and counts), and the results from a genome-based analysis. This dataset was used to assess the performance of the corset software. More detail is provided in the paper: Nadia M Davidson and Alicia Oshlack,<strong> </strong>Corset: enabling differential gene expression analysis for de novo assembled transcriptomes, <em>Genome Biology</em> 2014, <strong>15</strong>:410. http://genomebiology.com/2014/15/7/410/abstract</p>
De novo transcriptome assemblies for the spiny mouse (Acomys cahirinus)
<p>Transcriptome assemblies generated per https://dx.doi.org/10.1101/076067 (preprint) / https://dx.doi.org/10.17504/protocols.io.ghebt3e (protocol). Manuscript available at Scientific Reports.</p>
De novo transcriptome assembly and discovery of drought-responsive genes in eastern white spruce (Picea glauca)
<p>Forests face an escalating threat from the increasing frequency of extreme drought events driven by climate change. To address this challenge, it is crucial to understand how widely distributed species of economic or ecological importance may respond to drought stress. Here, we used RNA-sequencing to investigate transcriptome responses at increasing levels of water stress in white spruce (<em>Picea glauca</em> (Moench) Voss), distributed across North America. We began by generating an expanded transcriptome assembly emphasizing short-term drought stress at different developmental stages. We also analyzed differential gene expression at four time points over 22 days in a controlled drought stress experiment involving 2-year-old plants and three genetically unrelated clones. De novo transcriptome assembly and gene expression analysis revealed a total of 33,287 transcripts (18,934 annotated unique genes), with 4,425 unique drought-responsive genes. Many transcripts that had predicted functions associated with photosynthesis, cell wall organization, and water transport were down-regulated under drought conditions, while transcripts linked to abscisic acid response and defense response were up-regulated. Our study highlights a previously uncharacterized effect of drought stress on lipid metabolism genes in conifers and significant changes in the expression of several transcription factors, suggesting a regulatory response potentially linked to drought response or acclimation. Our research represents a fundamental step in unraveling the molecular mechanisms underlying short-term drought responses in white spruce seedlings. In addition, it provides a valuable source of new genetic data that could contribute to genetic selection strategies aimed at enhancing the drought resistance and resilience of white spruce to changing climates.</p>
Simulation data for benchmarking de novo long read transcriptome assembly software
<p>Method of simulation of differentially expressed biological replicates</p> <p>We first obtained a subset of transcripts that are widely expressed in the GTEx v9 dataset (92 samples) using Gencode comprehensive annotation (v44). We kept transcripts with more than 5 reads in at least 15 samples after Salmon quantification (18145 genes, 40509 transcripts), and stored their mean count per million (CPM) values as the control group’s baseline expression. We then generated a perturbed set of CPM values where transcript expression was changed by: (1) randomly selecting 1000 genes and changing all transcripts belonging to that gene concordantly (500 genes 2 fold up and 500 genes 2 fold down), (2) selected another 1000 genes randomly, and then select 2 random transcripts from the gene and swap their expression, (3) selected another 1000 genes randomly, and then select 1 random transcript to change its expression (500 transcripts 2 fold up and 500 transcripts 2 fold down). The updated CPM were stored as the perturbed group baseline expression. We then generated a count matrix and CPM matrix for 3 control replicates and 3 perturbed replicates with gamma distribution, followed by a Poisson distribution <a href="https://www.zotero.org/google-docs/?cUP4ui">(Baldoni et al., 2024)</a>. Both long-read and short-read FASTQ files were simulated using SQANTI-SIM with default settings and ONT R9.4 cDNA error profile (v 0.2.1) <a href="https://www.zotero.org/google-docs/?Qyopst">(Mestre-Tomás et al., 2023)</a>. The long read data contained 6 million reads in total, and an average read length of 1085 bp, and short read data was 100 bp paired-end. We then subsampled the short-read data to match the total number of base pairs in the long read data (6.5 billion bases). The simulated data was non-stranded, and contains 2000 DE genes, 2000 genes with DTU, 5927 transcripts with DTU and 6933 DE transcripts.</p> <p> </p>
de novo transcriptome assemblies for Peperomia dahlstedtii and Peperomia pellucida
<p><em>De novo</em> transcriptome assemblies generated using Trinity using young leaf tissue from <em>Peperomia dahlstedtii</em> and <em>Peperomia pellucida</em>. </p>
De novo transcriptome assembly from the killifish, Fundulus rathbuni (gill epithelium)
<p>De novo transcriptome assembly from the killifish, Fundulus rathbuni. Fish were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge. Transcriptome data from gill epithelium tissue were collected. A reference transcriptome assembly was generated from all individuals then used to analyze transcriptional responses to salinity.</p>
De novo transcriptome assembly and discovery of drought-responsive genes in eastern white spruce (Picea glauca)
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De novo transcriptome assembly Aegilops cylindrica
<p>De novo transcriptome assembly of Aegilops cylindrica was created using trinity v. 2.15.1. The assembly contains 285000 transcripts encoding for 174040 genes.</p>
De novo transcriptome assembly of the rockrose Helianthemum marifolium
<p>Illumina paired-end RNA sequences from leaves of 16 individuals of Helianthemum marifolium (four individuals from each of the four recognised taxonomic subspecies) were cleaned and assembled de novo using Trinity and Oases. EvidentialGene provides the curated assembled transcriptome containing 122002 transcripts, which are contained in the file Helianthemum_marifolium_transcriptome.fa.</p> <p>The predicted peptide sequences obtained with TransDecoder are in the file Helianthemum_marifolium_fa_transdecoder.pep.</p> <p>Gene ontology annotations from Trinotate are in the file Helianthemum_marifolium_trinotate_annotation.xls.</p>
Error, noise and bias in de novo transcriptome assemblies
<p><i>De novo</i> transcriptome assembly is a powerful tool, widely used over the last decade for making evolutionary inferences. However, it relies on two implicit assumptions: that the assembled transcriptome is an unbiased representation of the underlying expressed transcriptome, and that expression estimates from the assembly are good, if noisy approximations of the relative abundance of expressed transcripts. Using publicly available data for model organisms, we demonstrate that, across assembly algorithms and data sets, these assumptions are consistently violated. Bias exists at the nucleotide level, with genotyping error rates ranging from 30-83%. As a result, diversity is underestimated in transcriptome assemblies, with consistent under-estimation of heterozygosity in all but the most inbred samples. Even at the gene level, expression estimates show wide deviations from map-to-reference estimates, and positive bias at lower expression levels. Standard filtering of transcriptome assemblies improves the robustness of gene expression estimates but leads to the loss of a meaningful number of protein-coding genes, including many that are highly expressed. We demonstrate a computational method, length-rescaled CPM, to partly alleviate noise and bias in expression estimates. Researchers should consider ways to minimize the impact of bias in transcriptome assemblies.</p>
Error, noise and bias in de novo transcriptome assemblies
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Data from: "De novo transcriptome assembly of the mountain fly Drosophila nigrosparsa using short RNA-seq reads" in Genomic Resources Notes Accepted 1 August 2014-30 September 2014
Drosophila (Drosophila) nigrosparsa is a habitat specialist restricted to the European montane/alpine zone (Bächli 2008). Mountain biodiversity is considered highly vulnerable to ongoing climate warming (IPCC 2013), and organisms at high altitudes have only limited possibility to shift to cooler habitats at elevations above (Pertoldi & Bach 2007). For such species, rapid evolution may offer a solution for long-term survival. We are establishing D. nigrosparsa as a model system to test the extent and tempo of adaptive evolution under thermal stress in the laboratory. In this study, we used Illumina high-throughput sequencing to assemble the species' transcriptome using the pooled mRNA from 22 developmental and physiological stages.
Data from: De novo assembly of the transcriptome of an invasive snail and its multiple ecological applications
Studying how invasive species respond to environmental stress at the molecular level can help us assess their impact and predict their range expansion. Development of markers of genetic polymorphism can help us reconstruct their invasive route. However, to conduct such studies requires the presence of substantial amount of genomic resources. This study aimed to generate and characterize genomic resources using high throughput transcriptome sequencing for Pomacea canaliculata, a non-model gastropod indigenous to Argentina that has invaded Asia, Hawaii and southern United States. De novo assembly of the transcriptome resulted in 128,436 unigenes with an average length of 419 bp (range: 150 to 8,556 bp). Many of the unigenes (2,439) contained transposable elements, showing the existence of a source of genetic variability in response to stressful conditions. A total of 3,196 microsatellites were detected in the transcriptome; among 20 of the randomly tested microsatellites, 10 were validated to exhibit polymorphism. A total of 15,412 single-nucleotide polymorphisms (SNPs) were detected in the ORFs. LC-MS/MS analysis of the proteome of juveniles revealed 878 proteins, of which many are stress-related. This study has demonstrated the great potential of high throughput DNA sequencing for rapid development of genomic resources for a non-model organism. Such resources can facilitate various molecular ecological studies, such as stress physiology and range expansion.
Data from: "De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild population of the rostrum dace (Leuciscus burgiladensis) that is infected by Tracheliastes polycolpus, an emerging freshwater ectoparasite copepod. We used next generation Illumina sequencing technology to sequence the transcriptome of eight L. burdigalensis adult individuals collected in natura from the same sampling site. Four individuals were non-infected and four individuals were infected by T. polycolpus. We specifically focused on the spleen, the head kidney and epithelial cells and mucus from the fins, three tissues known to be involved in the immune response of fish. We used the Trinity methodology to reconstruct a de novo full-length transcriptome for L. burdigalensis. The resulting transcriptome will serve as an important broad-scale genomic resource for further studying the response of local population of L. burdigalensis to T. polycolpus pressures.
Data from: "De novo assembled transcriptome of organs involved in reproduction in an endangered endemic Iberian cyprinid fish (Squalius pyrenaicus)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
Sex determination systems are diverse, especially among fish, and include genetic and/or environmental components. Unexpectedly for such a basic aspect of development, sex determination systems change rapidly during evolution and gonadal fate is not ultimate, being actively maintained lifelong. Here, sequences of expressed genes involved in maintenance of gonad identity and reproduction processes were obtained through transcriptome assembly of the brain-gonadal axis tissues of a freshwater fish inhabiting highly variable environments, the gonochoristic Iberian fish Squalius pyrenaicus. Through Illumina total RNA-sequencing, male and female transcriptomes of brain and gonad tissues were assembled with Trans-ABySS software and merged to produce a more comprehensive S. pyrenaicus transcriptome. Coding sequences (CDS) predicted by TransDecoder were annotated using blastx. By means of read mapping against the reference transcriptome and CDS datasets, using Bowtie2, the accuracy of read mapping was assessed. This first endemic Iberian cyprinid transcriptome of organs involved in reproduction processes may serve as a valuable genomic resource for studying sexual mechanisms and other aspects of evolution, such as speciation and responses to environmental changes, and may be a useful tool for conservation studies since S. pyrenaicus is an endangered species.
Data from: De novo transcriptome assembly for the lobster Homarus americanus and characterization of differential gene expression across nervous system tissues
Background: The American lobster, Homarus americanus, is an important species as an economically valuable fishery, a key member in marine ecosystems, and a well-studied model for central pattern generation, the neural networks that control rhythmic motor patterns. Despite multi-faceted scientific interest in this species, currently our genetic resources for the lobster are limited. In this study, we de novo assemble a transcriptome for Homarus americanus using central nervous system (CNS), muscle, and hybrid neurosecretory tissues and compare gene expression across these tissue types. In particular, we focus our analysis on genes relevant to central pattern generation and the identity of the neurons in a neural network, which is defined by combinations of genes distinguishing the neuronal behavior and phenotype, including ion channels, neurotransmitters, neuromodulators, receptors, transcription factors, and other gene products. Results: Using samples from the central nervous system (brain, abdominal ganglia), abdominal muscle, and heart (cardiac ganglia, pericardial organs, muscle), we used RNA-Seq to characterize gene expression patterns across tissues types. We also compared control tissues with those challenged with the neuropeptide proctolin in vivo. Our transcriptome generated 34,813 transcripts with known protein annotations. Of these, 5,000-10,000 of annotated transcripts were significantly differentially expressed (DE) across tissue types. We found 421 transcripts for ion channels and identified receptors and/or proteins for over 20 different neurotransmitters and neuromodulators. Results indicated tissue-specific expression of select neuromodulator (allostatin, myomodulin, octopamine, nitric oxide) and neurotransmitter (glutamate, acetylcholine) pathways. We also identify differential expression of ion channel families, including kainite family glutamate receptors, inward-rectifying K+ (IRK) channels, and transient receptor potential (TRP) A family channels, across central pattern generating tissues. Conclusions: Our transcriptome-wide profiles of the rhythmic pattern generating abdominal and cardiac nervous systems in Homarus americanus reveal candidates for neuronal features that drive the production of motor output in these systems.
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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)
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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.