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Mesocentrotus franciscanus

ABSTRACT: Low coverage whole genome sequencing for red sea urchin

PROVIDER: PRJNA20313 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR000321.fastq.gz	Fastqsanger.gz
	SRR000322.fastq.gz	Fastqsanger.gz
	SRR000323.fastq.gz	Fastqsanger.gz
	SRR000324.fastq.gz	Fastqsanger.gz
	SRR000325.fastq.gz	Fastqsanger.gz

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Mesocentrotus franciscanus

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Project description:The red sea urchin, Mesocentrotus franciscanus, is one the earth’s longest-lived animals, reported to live more than 100 years with indeterminate growth, life-long reproduction and no increase in mortality rate with age. To explore the idea that transcriptional stability is a key determinant of longevity and negligible senescence, age-related gene expression was examined in three tissues of the red sea urchin (Aristotle’s lantern muscle, esophagus and radial nerve cord). Genome-wide transcriptional profiling using RNA-Seq revealed remarkable stability in muscle and esophagus with very few age-related changes in gene expression. In contrast, expression of more than 900 genes was significantly altered with age in radial nerve cord including genes involved in nerve function, signaling, metabolism, cytoskeleton, transcriptional regulation and chromatin modification. Notably, there was an upregulation in expression of genes involved in synaptogenesis and axonogenesis suggesting enhanced nervous system activity with age. Among the signaling pathways affected by age, there was a downregulation in expression of key components of the mTOR signaling pathway and an upregulation of negative regulators of this pathway. This was accompanied by a reduction in expression of genes involved in protein synthesis and mitochondrial function and an increase in expression of genes that promote autophagy. Downregulation of the mTOR pathway together with the other observed changes reveals a unique age-related gene expression profile in the red sea urchin nervous system that may contribute to mitigation of the detrimental effects of aging in this long-lived animal.

2020-06-08 | GSE136352 | GEO

A high-resolution transcriptome map of the sea urchin embryo

Project description:The sea urchin S. purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low leveles in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process. Keywords: high-resolution tiling array, sea urchin, embryo Keywords: other

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Deep conservation of cis-regulatory elements and chromatin organization in echinoderms uncover ancestral regulatory features of animal genomes [Hi-C]

Project description:we generated new reference genome assemblies for two species belonging to two different echinoderm classes: the bat sea star Patiria miniata and the purple sea urchin Strongylocentrotus purpuratus

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Project description:Red Sea Urchin (Mesocentrotus franciscanus) Genome

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The sea urchin larval response to immune challenge with Vibrio diazotrophicus

Project description:Seawater exposure to the gram negative marine bacterium Vibrio diazotrophicus induces a robust cellular response in sea urchin larvae that includes the migration of pigment cells to the gut epithelium, changes in cell behavior and altered gut morphology (Ho et al., 2016; PMID 27192936). To investigate the transcriptional underpinnings of this response, whole transcriptome sequencing was performed on mRNA isolated from larval samples collected at 0, 6, 12 and 24 hr of exposure to V. diazotrophicus. The morphological simplicity of the sea urchin larva provides a systems-level model for identifying biologically relevant transcriptional state changes in response to dysbiosis in the gut lumen.

2017-03-24 | GSE96940 | GEO

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