Molecular characterization of cell types in the squid Loligo vulgaris
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA823009 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18593507_1.fastq.gz | Fastqsanger.gz | |||
| SRR18593507_2.fastq.gz | Fastqsanger.gz | |||
| SRR18593508_1.fastq.gz | Fastqsanger.gz | |||
| SRR18593508_2.fastq.gz | Fastqsanger.gz | |||
| SRR18593509_1.fastq.gz | Fastqsanger.gz |
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Project description:Cephalopods have long been getting a lot of attention for their fascinating behavioral abilities and for the complexity of their nervous systems that set them apart from other mollusks. Because of the great evolutionary distance that separates vertebrates from mollusks, it is evident that higher cognitive features have evolved independently in this clade although they sometimes resemble cognitive functions of vertebrates. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Gaining a better understanding of the biology of various species of cephalopods can significantly improve our knowledge of how these animals evolved and better identify the mechanisms that drive the astonishing faculties of their nervous systems. In this study, we performed single-cell transcriptomics of whole heads of Loligo vulgaris pre-hatchlings. We characterized the different cell types in the head of these animals and explored the expression patterns of core cell type markers by hybridization chain reaction. We were able to thoroughly describe some major components of the squid nervous that play important roles for the maintenance, development and sensory function in the nervous system of these animals.
2022-04-07 | GSE200108 | GEO
Project description:Cephalopods are set apart from other mollusks by their advanced behavioral abilities and the complexity of their nervous systems. Because of the great evolutionary distance that separates vertebrates from cephalopods, it is evident that higher cognitive features have evolved separately in these clades despite the similarities that they share. Alongside their complex behavioral abilities, cephalopods have evolved specialized cells and tissues, such as the chromatophores for camouflage or suckers to grasp prey. Despite significant progress in genome and transcriptome sequencing, the molecular identities of cell types in cephalopods remain largely unknown. We here combine single-cell transcriptomics with in situ gene expression analysis to uncover cell type diversity in the European squid Loligo vulgaris. We describe cell types that are conserved with other phyla such as neurons, muscles, or connective tissues but also cephalopod-specific cells, such as chromatophores or sucker cells. Moreover, we investigate major components of the squid nervous system including progenitor and developing cells, differentiated cells of the brain and optic lobes, as well as sensory systems of the head. Our study provides a molecular assessment for conserved and novel cell types in cephalopods and a framework for mapping the nervous system of L. vulgaris.
| S-EPMC9839350 | biostudies-literature
Project description:The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained.
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Project description:The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are missing. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium. A broad comparison of wild type and bud bloomer’s flowers was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using next generation 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances in wild type and bud bloomer’s libraries were compared and 365 differentially expressed genes detected. Among these differentially genes, CvPI was identified which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) and considered as the most promising candidate gene. Quantitative PCR was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and CvAP3 in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the flowers of bud blooming cultivars. Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause characteristics of flower morphology in C. vulgaris wild type and bud blooming flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in the wild type and the “bud flowering” phenotype. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers. However, the complete loss of stamens in bud blooming flowers remains to be explained. two samples were analysed, each representing a flower type
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Project description:Bacterial strains within a species can differ in traits that shape host–microbe interactions. Using the squid–vibrio symbiosis, we examined how strain-level variation influences host responses. Strains from squid and fish light organs were compared for their effects on Euprymna scolopes gene expression and development. Non-native strains showed reduced colonization success and delayed host phenotypes. Transcriptomic responses were most similar with native isolates and most divergent with a fish-derived strain. These findings demonstrate that fine-scale strain differences shape host compatibility and underscore the importance of strain-level diversity in the establishment of beneficial symbioses.
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Project description:Integrated characterization of cell types, states and molecular programs in disseinated appendiceal neoplasms
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Project description:The light-organ symbiosis between the squid Euprymna scolopes and the luminous bacterium Vibrio fischeri offers the opportunity to decipher the hour-by-hour events that occur during the natural colonization of an animal's epithelial surface by its microbial partners. To determine the genetic basis of these events, a glass-slide microarray was used to characterize the light-organ transcriptome of juvenile squid in response to the initiation of symbiosis. Patterns of gene expression were compared between animals not exposed to the symbiont, exposed to the wild-type symbiont, or exposed to a mutant symbiont defective in either of two key characters of this association: bacterial luminescence or autoinducer (AI) production. Hundreds of genes were differentially regulated as a result of symbiosis initiation, and a hierarchy existed in the magnitude of the host's response to three symbiont features: bacterial presence > luminescence > AI production. Putative host receptors for bacterial surface molecules known to induce squid development are up-regulated by symbiont light production, suggesting that bioluminescence plays a key role in preparing the host for bacteria-induced development. Further, because the transcriptional response of tissues exposed to AI in the natural context (i.e., with the symbionts) differed from that to AI alone, the presence of the bacteria potentiates the role of quorum signals in symbiosis. Comparison of these microarray data with those from other symbioses, such as germ-free/conventionalized mice and zebrafish, revealed a set of shared genes that may represent a core set of ancient host responses conserved throughout animal evolution. Six experimental treatments of juvenile animals were performed for the microarray matrix: uncolonized (Apo); uncolonized, but supplemented with AI (Apo + AI); colonized by wild-type V. fischeri (wild type); colonized by a mutant defective in luciferase synthesis (luxA); colonized by a mutant defective in AI synthesis (luxI); and, colonized by the luxI mutant, but supplemented with AI (luxI + AI). At 18 h postinoculation, animals were anesthetized in 2% ethanol in HOSW, and the light organs were removed into RNAlater (Ambion Biosystems).
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