Ontology highlight
ABSTRACT:
PROVIDER: PRJNA664650 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12681100_1.fastq.gz | Fastqsanger.gz | |||
| SRR12681100_2.fastq.gz | Fastqsanger.gz | |||
| SRR12681101_1.fastq.gz | Fastqsanger.gz | |||
| SRR12681101_2.fastq.gz | Fastqsanger.gz | |||
| SRR12681102_1.fastq.gz | Fastqsanger.gz |
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Project description:Molting is an essential biological process occurring characteristic times throughout the life cycle of holometabolous insects. However, it is not clear how insects determine whether the direction of molting is to remain status quo or to initiate metamorphosis. Here, we used liquid chromatography-mass spectrometry to identify the molecules involved in larval and metamorphic molting, and compare the differentially expressed proteins (DEPs) in the two processes, to explore the functional factors that determine the direction of molts. There were 322 and 1140 DEPs identified in larval and metamorphic molting process, respectively. Bioinformatics analyses show that the amino sugar pathway was up-regulated in both processes. The up-regulated protease contributed to the metamorphosis. In addition, several proteins with different expression patterns in larval-larval and larval-pupal transitions, including Endochitinase, GRIM-19 (Genes associated with retinoid-IFN-induced mortality-19), IDE (Insulin-degrading enzyme), Sorcin (Soluble resistance related calcium binding protein), OBP (Odorant-binding protein-2 precursor), TRAP1(Tumor necrosis factor receptor associated protein-1), etc., were further identified by parallel reaction monitoring, which may play diverse functions in the determination of molting properties. These results provide a proteomic insight into molecules involved in larval and metamorphic molts, and will likely improve the current understanding of determination of direction of molts.
2020-10-30 | PXD020414 | Pride
Project description:Differentially expressed genes at molting and metamorphosis stages in Bombyx fat body
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Project description:Why is metamorphosis so pervasive? Does it facilitate the independent (micro)evolution of quantitative traits in distinct life-stages, like it does for discrete characters such as limbs and organs? We tested this hypothesis by measuring the expression of 6400 genes in 41 Drosophila melanogaster inbred lines at larval and adult stages. Only 32% of the genes showed significant genetic correlations between larval and adult expression. By contrast, 44% of the traits showed some level of independence between stages. Gene ontology terms enrichment of the functions most and least constrained among stages revealed that traits related to immunity emerged as largely correlated between larvae and adults. Direct comparisons with other datasets showed that inter-stage constraints were lower than inter-sexual or cross-environment genetic constraints. These results show that metamorphosis enables a large part of the transcriptome to evolve independently at different life-stages and identify biological functions under high and low genetic constraints.
2024-02-27 | GSE226174 | GEO
Project description:RNA sequencing of A.japonica during larval metamorphosis
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Project description:In order to analyse gene expression during metamorphosis of Sycon ciliatum (Calcispongiae), we generated a series of RNA-Seq libraries representing subsequent stages of metamorphosis, ranging from freshly settled postlarvae (stage I) to functional ascon-grade juveniles (stage V).
2014-10-25 | E-MTAB-2890 | biostudies-arrayexpress
Project description:The monitoring of global transcription patterns during development is a useful first step to understand mechanisms underlying growth, differentiation and patterning in a given species. However such large scale developmental studies are so far only available from a few selected model organisms such as mouse, Drosophila and the nematode C. elegans. Genomic scale information from the lophotrochozoa is now emerging. The recently characterized neuronal transcriptome of the sea hare Aplysia californica (~200’000 ESTs and ~40,000 unique non-redundant sequences representing about 55-70% of all neuronal transcripts including splice forms and non-coding RNAs) provides new insights and opportunities into problems of molluscan development and specifically neurogenesis. Regulatory genes used in development are recruited for the functions of adult nervous systems such as synaptogenesis, specific wiring in networks and structural changes underlying synaptic plasticity. While this similarity reflects a basic concept in biology, namely the recruitment of the same genes for different functions, it has never been tested on a large scale genomic level. We used representative oligo-arrays constructed from transcripts obtained from the Aplysia nervous system to explore the following two questions: 1) What neuronal genes are differentially expressed during embryonic development of the sea hare Aplysia. 2) What gene expression changes can be observed in correlation with gastrulation, metamorphosis, and larval neurogenesis. For this purpose we hybridized RNA from 3 embryonic (64 cells, gastrula, trochophore) and 4 larval stages (pre-hatching, post-hatching, pre-metamorphosis, postmetamorphosis) against a reference sample consisting of equal contributions from all stages. Our analysis revealed that all embryonic and larval stages can be distinguished based on their transcription profiles. A comparison of the Aplysia atlas with similar studies in Drosophila and mouse reveals interesting differences. We identified several new transcription factors which are differentially expressed during early embryonic development. Various other transcripts involved in metabolism and differentiation were characterized. These genes can be candidate targets for understanding neuronal growth, synaptogenesis and memory mechanisms. We conclude that the microarray technology provides us with a powerful tool for efficient survey and functional annotation of the neuronal transcriptome in Aplysia. We used a reference design for this study where we hybridized each of the 8 developmental stages of Aplysia (cleavage, gastrula, trochophore, first veliger, hatching veliger, pre-metamorphosis (stage 6), post-metamorphosis (stage 7), post-metamorphosis 60 hours (pm60)
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Project description:the chromatin accessibility and gene expression of muscle in E. sinensis in pre-molt (D) and post-molt (A) stages were sequenced by Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) and RNA-seq, respectively.The differntial peaks in ATAC-seq and differntial genes in RNA-seq were analzed. The data was used to analysis the differentially expressed genes (DEGs) in muscle before and after molting by combining ATAC-seq and RNA-seq
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Project description:IMolting, a special period during which the old cuticle is shed and a new one is produced, is crucial to insect development. During their life cycles, insects that undergo complete metamorphosis may experience several larva-to-larva moltings to become larger, followed by larva-to-pupa and pupa-to-adult moltings to become adults. During the larva-to-larva molting stage, insect larvae stop consuming food and become restful. Whether any changes occur within the molting midgut before ecdysis remains known.
2016-02-01 | GSE65522 | GEO
Project description:Larval settlement and metamorphosis is a vital transition period for marine invertebrates and can have far-reaching effects on the ecology and evolution of a species. To explore the molecular mechanisms of this critical process in a non-model organism, the tropical abalone Haliotis asinina, we employed cDNA microarray methods. By comparing gene expression profiles through mid to late larval development and metamorphosis, we identified 144 genes as likely candidates for a role in competence and/or metamorphosis. Gene characterization showed that ~60% of these were significantly similar to previously described genes from other taxa, while ~40% had no significant similarities to any known genes. A high 49.3% of genes were gastropod- or abalone-specific, but none appear to be Lophotrochozoan-specific, despite the fact that metamorphosis is thought to have had a separate origin in this group. Based on temporal expression profiles, the differentially expressed larval and postlarval genes can be clustered into 5 categories that reveal there are strikingly different transcriptional patterns occurring during this phase of development. Some classes of gene activation are contingent upon exogenous cues and correlate with the initiation of settlement and metamorphosis. Importantly, there is also extensive gene activity associated with the endogenous attainment of competence, which occurs prior to, and independent of, the exogenous induction of settlement. Our results show that as the haliotid veliger larva matures, it requires the coordinated regulation of temporally different batteries of genes involved in a wide range of physiological and developmental processes associated with colonisation of the benthos. Although the signalling pathways operating at metamorphosis may be conserved across the animal kingdom, it appears they are regulating the expression of novel genes specific to abalone, gastropods and molluscs during H. asinina metamorphosis. Keywords: timecourse; metamorphosis; marine ecology Each microarray slide contained a different combination of 2 of the 9 developmental stages used in the experiment (66 hpf, 78 hpf, 90 hpf, 108 hpf, 120 hpf, 144 hpf, 12 hpi, 24 hpi, 48 hpi). Each developmental stage was subjected to 4 hybridisations â amounting to 4 technical replicates per stage - in a loop design (Churchill 2002; Oleksiak et al. 2002). This design led to raw data consisting of 72 measurements - 9 stages with 8 replicates (including 2 replicates per chip) - for each of 5541 spots.
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