Genome-wide expression profiling of Octopus Arm and Hatchlings
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ABSTRACT:
ORGANISM(S): Octopus bimaculoides
PROVIDER: GSE188925 | GEO | 2022/06/30
REPOSITORIES: GEO
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Project description:Genome-wide expression profiling of Octopus Arm and Hatchlings
| PRJNA780781 | ENA
Project description:Three adult individuals of the Octopus vulgaris were collected from the Southern Tyrrhenian Sea (Italy). For each animal, total RNA was isolated from the supra- (SEM), sub- (SUB) esophageal masses, optic lobes (OL) and the arms (ARM). The RNA-sequencing has been performed using Illumina technology.
2022-04-15 | E-MTAB-3957 | biostudies-arrayexpress
Project description:Octopuses are mollusks that evolved intricate neural systems which are comparable with vertebrates in terms of cell number, complexity and size. Exactly how an octopus increases its neural cell number so dramatically and whether an increase in cell type diversity enables higher cognitive function and complex behavior is still unknown. To profile the cell diversity of the developing octopus brain we applied 10x Genomics’ single-cell/nuclei RNA sequencing technology. At hatching, the Octopus vulgaris brain possesses the main lobes and connections of an adult brain, but which cell types are present remains elusive. We were able to identify 42 robust cell types comprising mostly neural cells, as well as multiple glial subtypes and other non-neuronal populations such as endothelial cells and fibroblasts. In situ expression analysis of marker genes allowed spatial mapping of clusters, including vertical lobe cells and several optic lobe cell types. Investigation of cell type conservation indicated similar gene expression signatures between glial cells of mice, fly and octopus. Genes related to memory and learning were found enriched in vertical lobe cells, that showed molecular similarities with Kenyon cells in Drosophila but not to any mouse cell type. Lastly, we also analyzed the expression of newly expanded gene families (protocadherins, C2H2 zinc-finger transcription factors and G-protein coupled receptors) and found that these are enriched in specific cell types. Taken together, our data gives insight into cell type evolution and the composition of the complex octopus brain.
2022-01-31 | GSE193622 | GEO
Project description:Background:The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods. Findings:The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species. Conclusions:We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.
| S-EPMC6279123 | biostudies-literature
Project description:We performed paired end Illumina Hiseq on bulk tissues of Octopus bimaculoides sensory tissues, Libaries were sequenced on two different Lanes
2020-08-25 | GSE156748 | GEO
Project description:Cephalopods have a remarkable visual system, with a camera-type eye, high acuity vision, and a wide range of sophisticated visual behaviors. However, the cephalopod brain is organized dramatically differently from that of vertebrates, as well as other invertebrates, and little is known regarding the cell types and molecular determinants of their visual system organization beyond neuroanatomical descriptions. Here we present a comprehensive single-cell molecular atlas of the octopus optic lobe, which is the primary visual processing structure in the cephalopod brain. We combined single-cell RNA sequencing with RNA fluorescence in situ hybridization to both identify putative molecular cell types and determine their anatomical and spatial organization within the optic lobe. Our results reveal six major neuronal cell classes identified by neurotransmitter/neuropeptide usage, in addition to non-neuronal and immature neuronal populations. Moreover, we find that additional markers divide these neuronal classes into subtypes with distinct anatomical localizations, revealing cell type diversity and a detailed laminar organization within the optic lobe. We also delineate the immature neurons within this continuously growing tissue into subtypes defined by evolutionarily conserved fate specification genes as well as novel cephalopod- and octopus- specific genes. Together, these findings outline the organizational logic of the octopus visual system, based on functional determinants, laminar identity, and developmental markers/pathways. The resulting atlas presented here delineates the “parts list” of the neural circuits used for vision in octopus, providing a platform for investigations into the development and function of the octopus visual system as well as the evolution of visual processing.
2022-09-04 | GSE212528 | GEO
Project description:Coleoid cephalopods possess a highly complex nervous system and a rich behavioral repertoire that is unique within the invertebrates and is comparable to – but evolved independently from – the vertebrates (Shigeno et al. 2018). To explain this complexity, previous studies have implicated a unusually high level of mRNA editing in transcripts expressed in both the octopus and squid nervous system (Albertin et al. 2015; Alon et al. 2015; Liscovitch-Brauer et al. 2017). We have sequenced RNA across 18 tissues from the octopus O. vulgaris, and analyzed the extent of mRNA isoform usage as well as the expression of microRNAs in the nervous system in comparison to non-neuronal tissues.
2022-11-11 | GSE192550 | GEO
Project description:Common octopus, Octopus vulgaris, is an economically important cephalopod species. However, its rearing under captivity is currently challenged by massive mortalities previous to their juvenile stage due to nutritional and environmental factors. Dissecting the genetic basis and regulatory mechanism behind this mortality requires genomic background knowledge. A transcriptomic sequencing of 10 dph octopus paralarvae from different experimental conditions was constructed via RNA-seq. A total of 613,767,530 raw reads were filtered and de novo assembled into 363,527 contigs of which 82,513 were annotated in UniProt carrying also their GO and KEGG information. Differential gene expression analysis was carried out on paralarvae reared under different diet regimes and temperatures, also including wild paralarvae. Genes related to lipid metabolism exhibited higher transcriptional levels in individuals whose diet includes crustacean zoeas, which had an impact over their development and immune response capability. High temperature induces acclimation processes at the time that increase metabolic demands and oxidative stress. Wild individuals show an expression profile unexpectedly similar to Artemia fed individuals. Proteomic results support the hypothesis revealed by transcriptional analysis. The comparative study of the O. vulgaris transcriptomic profiles allowed the identification of genes that deserve to be further studied as candidates for biomarkers of development and health. The results obtained here on the transcriptional variations of genes caused by diet and temperature will provide new perspectives in understanding the molecular mechanisms behind nutritional and temperature requirements of common octopus that will open new opportunities to deepen in paralarvae rearing requirements.
2019-11-12 | PXD014141 | Pride