Contrasting the development of larval and adult body plans during the evolution of biphasic lifecycles in sea urchins
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1162557 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30716641.fastq.gz | Fastqsanger.gz | |||
| SRR30716642.fastq.gz | Fastqsanger.gz | |||
| SRR30716643.fastq.gz | Fastqsanger.gz | |||
| SRR30716644.fastq.gz | Fastqsanger.gz | |||
| SRR30716645.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:Sea urchins are a unique system for studying developmental transistions because of the stark differences between their bilateral larval and pentaradial adult body plans. Here, we use single cell RNA-sequencing to analyze the development of Heliocidaris erythrogramma (He), a sea urchin species with an accelerated, non-feeding mode of larval development. The sequencing time course extends from early embryogenesis to roughly a day before the onset of metamorphosis in He larvae, which is a period that has not been covered by previous datasets. We find that the non-feeding developmental strategy of He is associated with several changes in the specification of larval cell types compared to sea urchins with feeding larvae, such as the loss of a larva-specific skeletal cell population. Furthermore, the development of the larval and adult body plans in sea urchins may utilize largely different sets of regulatory genes. These findings lay the groundwork for extending existing developmental gene regulatory networks to cover additional stages of biphasic lifecycles.
2024-09-23 | GSE277518 | GEO
Project description:We use mRNA-seq to transcriptionally profile larval fat body and midgut tissues from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts.
2010-11-02 | GSE25025 | GEO
Project description:We use mRNA-seq to transcriptionally profile larval fat body and midgut tissues from Drosophila third instar larvae. These data provide insights into tissue physiology and can be used to identify tissue specific transcripts. Fat bodies from wandering third instar larvae were dissected from ~50 male larvae and gonads were removed to eliminate contaminating transctips from the gonads. Larval midguts were dissected from ~50 wandering third instar larvae. Larval tissues were removed to Graces unsupplemented medium on ice prior to RNA extraction with TRIzol reagent. mRNA-seq samples were prepared from 5ug of total RNA and subject to Illumina based sequencing.
2010-11-02 | E-GEOD-25025 | biostudies-arrayexpress
Project description:Sea urchins are emblematic marine animals with a rich fossil record and represent instrumental models for developmental biology. As echinoderms, sea urchins display several characteristics that set them apart from other deuterostomes such as their highly regulative embryonic development and their unique pentaradial adult body plan. To determine whether these characteristics are linked to particular genomic rearrangement or gene regulatory rewiring, we introduce a chromosome-scale genome assembly for sea urchin Paracentrotus lividus as well as extensive transcriptomic and epigenetic profiling during its embryonic development. We found that sea urchins show opposite modalities of genome evolution as compared to those of vertebrates: they retained ancestral chromosomal linkages that otherwise underwent mixing in vertebrates, while their intrachromosomal gene order has evolved much faster between sea urchin species that split 60 Myr ago than it did in vertebrates. We further assessed the conservation of the cis-regulatory program between sea urchins and chordates and identified conserved modules despite the developmental and body plan differences. We documented regulatory events underlying processes like zygotic genome activation and transition to larval stage in sea urchins. We also identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes are involved in organismal novelties, such as Aristotle's lantern, tube feet, or in the specification of lineages through for instance the pmar1 and pop genes. Altogether, our results suggest that gene regulatory networks controlling development can be conserved despite extensive gene order rearrangement.
2023-02-09 | GSE202034 | GEO
Project description:Evolutionary history of deuterostomes has remained unsolved and is intimately related to how chordates originated. Within the clade of deuterostomes, hemichordates and echinoderms (together called Ambulacraria) are sister groups of chordates; comparative studies among the three are insightful for understanding deuterostome evolution. Indirect-developing hemichordates, such as Ptychodera flava, develop into planktonic larvae, which are morphologically similar to echinoderm larvae, before metamorphosing into the adult body plan that retains an anteroposterior polarity homologous to that of chordates. Therefore, deciphering developmental programmes of indirect-developing hemichordates may provide a key for understanding the evolution of deuterostomes and chordate origins. Here, we characterise transcriptomes and chromatin accessibility across multiple developmental stages of P. flava and uncover biphasic developmental programmes controlled by different sets of transcription factors and their corresponding cis-regulatory elements. Transcriptome age and network analyses reveal that the gastrula transcriptome is relatively ancient and highly connected. By comparing developmental transcriptomes of hemichordate, sea urchin and amphioxus, a high conservation of gene expression during gastrulation is identified and extended to neurula stages of amphioxus, in addition to the highly similar larval transcriptomes among the three species. Moreover, P. flava possesses conserved interactions of transcription factors required for the development of echinoderm endomesoderm and chordate axial mesoderm. These results suggest a deuterostome phylotypic stage during gastrulation (corresponding to amphioxus gastrulation and neurulation) controlled by gene regulatory networks with conserved cis-regulatory interactions, and support the hypothesis that the deuterostome ancestor is an indirect-developer.
2024-07-31 | GSE207834 | GEO
Project description:Evolutionary history of deuterostomes has remained unsolved and is intimately related to how chordates originated. Within the clade of deuterostomes, hemichordates and echinoderms (together called Ambulacraria) are sister groups of chordates; comparative studies among the three are insightful for understanding deuterostome evolution. Indirect-developing hemichordates, such as Ptychodera flava, develop into planktonic larvae, which are morphologically similar to echinoderm larvae, before metamorphosing into the adult body plan that retains an anteroposterior polarity homologous to that of chordates. Therefore, deciphering developmental programmes of indirect-developing hemichordates may provide a key for understanding the evolution of deuterostomes and chordate origins. Here, we characterise transcriptomes and chromatin accessibility across multiple developmental stages of P. flava and uncover biphasic developmental programmes controlled by different sets of transcription factors and their corresponding cis-regulatory elements. Transcriptome age and network analyses reveal that the gastrula transcriptome is relatively ancient and highly connected. By comparing developmental transcriptomes of hemichordate, sea urchin and amphioxus, a high conservation of gene expression during gastrulation is identified and extended to neurula stages of amphioxus, in addition to the highly similar larval transcriptomes among the three species. Moreover, P. flava possesses conserved interactions of transcription factors required for the development of echinoderm endomesoderm and chordate axial mesoderm. These results suggest a deuterostome phylotypic stage during gastrulation (corresponding to amphioxus gastrulation and neurulation) controlled by gene regulatory networks with conserved cis-regulatory interactions, and support the hypothesis that the deuterostome ancestor is an indirect-developer.
2024-07-31 | GSE207833 | GEO
Project description:Regeneration is pervasive among the metazoa, but to vastly varying degrees. Platyhelminthes, Cnidaria, and Echinodermata are examples of phyla whose members are capable of whole-body regeneration (WBR). While planaria and hydra have been exemplary models of this phenomenon, the molecular details of echinoderm WBR are less established. It remains unclear to what degree such a dramatic regenerative capacity is due to the operation of conserved mechanisms and, in particular, whether any of these are involved in a regenerating Deuterostome. We characterize regeneration in the larval sea star (Patiria miniata) via transcriptome assessment. Transcriptome profiling highlight functions common to regeneration, such as wound healing, axis patterning and proliferation. This dataset was used as a basis for comparison to published Platyhelminth and Cnidarian regeneration datasets. These analyses show that sea star larvae undergo regeneration through a trajectory including wound response, axis respecification, and blastemal proliferation. Commonalities between this Deuterostome model and other WBR models suggest a deep conservation of whole-body regeneration among the metazoa.
2018-11-21 | GSE97230 | GEO
Project description:Analysis of the larval fat bodies overexpressing AKH, which activates AKH signaling in the fat body in an autocrine manner. As a homolog of human glucagon, AKH causes dysregulation of carbohydrate metabolism and hyperglycemia. Results provide insight into the AKH effects on metabolic gene expression.
2017-03-18 | GSE92350 | GEO
Project description:We compared four transcription factor knockdowns using transgenic RNAi expressed in the larval fat body. FOXO, Tfb1, p53, and Stat92E-dependent gene expression in the Drosophila fat body was quantified on control and high-sugar diets in order to generate expression profiles via RNA-seq. These expression data were used to build a gene regulatory network to predict novel roles for these and other genes during caloric overload.
2018-03-13 | GSE111728 | GEO
Project description:mRNA-seq and ORC2 ChIP-seq in Drosophila larval fat body
| PRJNA356316 | ENA