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Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

ABSTRACT: Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

PROVIDER: PRJNA1162559 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30716651.fastq.gz	Fastqsanger.gz
	SRR30716652.fastq.gz	Fastqsanger.gz
	SRR30716653.fastq.gz	Fastqsanger.gz
	SRR30716654.fastq.gz	Fastqsanger.gz
	SRR30716655.fastq.gz	Fastqsanger.gz

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Single-cell transcriptomics reveals evolutionary reconfiguration of embryonic cell fate specification in the sea urchin Heliocidaris erythrogramma

Project description:Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a “natural experiment” in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of scRNA-seq developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states respectively) reveals numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events, and the primary signaling center are co-localized in the ancestral dGRN but remarkably, in H. erythrogramma they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.

2024-10-05 | GSE277517 | GEO

Proteomic analysis of sea urchin egg provisioning and development

Project description:Here we present LC-MS/MS proteomic datasets of Heliocidaris erythrogramma, Heliocidaris tuberculata, and Lytechinus variegatus eggs and larvae. We find dramatic proteomic differences likely associated with life history evolution and between developmental stages. This study provides a complimentary dataset to previous transcriptomic analyses of the same three sea urchin species.

2019-03-04 | PXD007065 | Pride

Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin Heliocidaris erythrogramma.

Project description:Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a "natural experiment" in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of single-cell transcriptome analysis (scRNA-seq) developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states, respectively) reveal numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events and the primary signaling center are co-localized in the ancestral developmental gene regulatory network; remarkably, in H. erythrogramma, they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.

| S-EPMC11719709 | biostudies-literature

Heliocidaris erythrogramma

Project description:Heliocidaris erythrogramma overview

| PRJNA886777 | ENA

Heliocidaris erythrogramma

Project description:Heliocidaris erythrogramma Transcriptome or Gene expression

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Heliocidaris erythrogramma isolate:PLD85

Project description:Heliocidaris erythrogramma isolate:PLD85 Genome sequencing and assembly

| PRJNA827916 | ENA

Lipidomics data for "Marine invertebrate life history evolution: a comparative analysis of sea urchin egg provisioning using mass spectrometry"

Project description:We performed untargeted, high-resolution liquid chromatography-tandem mass spectrometry to generate lipidomic and proteomic profiles of eggs and larvae from three sea urchin species: the lecithotroph Heliocidaris erythrogramma, the closely-related planktotroph Heliocidaris tuberculata, and the more distantly-related planktotroph Lytechinus variegatus. We identify numerous molecular changes involving several previously undescribed physiological adaptations possibly associated with the evolution of lecithotrophic development including upregulated carbohydrate metabolism during embryonic development and long-term storage of maternally-derived diacylglycerol ether lipids for post-metamorphic survivorship. These findings demonstrate how mass spectrometry can enrich our understanding of life history evolution by identifying specific molecules associated with distinct life history strategies.

2018-06-25 | MSV000082501 | MassIVE

Heliocidaris crassispina

Project description:Heliocidaris crassispina overview

| PRJNA1058733 | ENA

Heliocidaris crassispina

Project description:Heliocidaris crassispina Genome sequencing

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Heliocidaris crassispina

Project description:Heliocidaris crassispina Raw sequence reads

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