Transcriptomic analysis of the trade-off between endurance and burst-performance in the frog Xenopus allofraseri
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ABSTRACT:
PROVIDER: PRJNA663331 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12638133_1.fastq.gz | Fastqsanger.gz | |||
| SRR12638133_2.fastq.gz | Fastqsanger.gz | |||
| SRR12638134_1.fastq.gz | Fastqsanger.gz | |||
| SRR12638134_2.fastq.gz | Fastqsanger.gz | |||
| SRR12638137_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Variation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach. Results: We obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥ 2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascade. Remarkably, we revealed transcripts isoforms of key genes with function in metabolism, apoptosis, nuclear export and as transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion. Conclusion: Locomotor performance trade-off in Xenopus allofraseri can be attributed to the differential expression of genes belonging to the different pathways of calcium signaling, endoplasmic reticulum stress response and striated muscle contraction, but also attributed to the use of alternative splicing and regulatory processes. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
2021-01-31 | GSE157915 | GEO
Project description:BackgroundVariation in locomotor capacity among animals often reflects adaptations to different environments. Despite evidence that physical performance is heritable, the molecular basis of locomotor performance and performance trade-offs remains poorly understood. In this study we identify the genes, signaling pathways, and regulatory processes possibly responsible for the trade-off between burst performance and endurance observed in Xenopus allofraseri, using a transcriptomic approach.ResultsWe obtained a total of about 121 million paired-end reads from Illumina RNA sequencing and analyzed 218,541 transcripts obtained from a de novo assembly. We identified 109 transcripts with a significant differential expression between endurant and burst performant individuals (FDR ≤ 0.05 and logFC ≥2), and blast searches resulted in 103 protein-coding genes. We found major differences between endurant and burst-performant individuals in the expression of genes involved in the polymerization and ATPase activity of actin filaments, cellular trafficking, proteoglycans and extracellular proteins secreted, lipid metabolism, mitochondrial activity and regulators of signaling cascades. Remarkably, we revealed transcript isoforms of key genes with functions in metabolism, apoptosis, nuclear export and as a transcriptional corepressor, expressed in either burst-performant or endurant individuals. Lastly, we find two up-regulated transcripts in burst-performant individuals that correspond to the expression of myosin-binding protein C fast-type (mybpc2). This suggests the presence of mybpc2 homoeologs and may have been favored by selection to permit fast and powerful locomotion.ConclusionThese results suggest that the differential expression of genes belonging to the pathways of calcium signaling, endoplasmic reticulum stress responses and striated muscle contraction, in addition to the use of alternative splicing and effectors of cellular activity underlie locomotor performance trade-offs. Ultimately, our transcriptomic analysis offers new perspectives for future analyses of the role of single nucleotide variants, homoeology and alternative splicing in the evolution of locomotor performance trade-offs.
| S-EPMC7986297 | biostudies-literature
Project description:Expression of known and predicted genes in tissues of Xenopus tropicalis (frog) pooled from multiple healthy individuals.
2009-04-16 | GSE12975 | GEO
Project description:Expression of known and predicted genes in tissues of Xenopus tropicalis (frog) pooled from multiple healthy individuals. Two-colour experiments with two different tissues hybridized to each array. Each tissue is arrayed in replicate with dye swaps. Tissues: Brain, Cartilage, Esophagus, Eye, Fat body, Femur, Gallbladder, Heart, Kidney, Large intestine, Liver, Lung, Muscle, Ovary, Oviduct, Skin, Small intestine, Spleen, Stomach, Testis
2010-06-19 | E-GEOD-12975 | biostudies-arrayexpress
Project description:This experiment contains the Xenopus tropicalis subset of data from the experiment E-GEOD-41338 (http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41338/). mRNA profiles of several organs (brain, liver, kidney, heart, skeletal muscle) in multiple vertebrate species (mouse, chicken, lizard, frog, pufferfish) were generated by deep sequencing using Illumina HiSeq to better understand how species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level.
2012-12-22 | E-MTAB-3726 | biostudies-arrayexpress
Project description:Frog gut microbiome transplant Green frog / Wood frog / Bullfrog Targeted loci environmental
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Project description:We provide a protocol to enable the mass spectrometry-based characterization of proteins in identified cell lineages in Xenopus laevis (frog) embryos. The experimental workflow leverages reproducible cell-fate maps and established technologies from developmental biology to identify, fluorescently label, track, and analyze cells and their progenies from this important biological model of vertebrate development. Proteins are identified and quantified via bottom-up proteomics. Microanalytical capillary electrophoresis or nanoflow liquid chromatography (nanoLC) are used to separate peptides, and electrospray ionization (ESI) high-resolution mass spectrometry (HRMS) are employed for detection.
2022-02-23 | PXD030059 | Pride
Project description:We sequenced allele-resolution single-cell transcriptomes from mouse primary fibroblasts and embryonic stem cells with the overall aim to infer transcriptional kinetics for each gene and allele. Inferred transcriptional burst kinetics revealed the genomic encoding of transcriptional burst frequencies and sizes within the genome. Core promoter elements were found to specify burst sizes, whereas burst frequencies were regulated by enhancers. In particular burst frequencies were found to account for cell-type differences in gene expression levels and were also mostly correlating with absolute expression levels in cells. Importantly, the patterns identified were not detectable at the level of mean expression demonstrating the need to investigate transcriptional dynamics at the level of burst kinetics.
2018-11-30 | E-MTAB-7098 | biostudies-arrayexpress