Project description:Coleoid cephalopods (squids, cuttlefish, octopus) have the largest nervous system among invertebrates that together with many lineage-specific morphological traits enables complex behaviors. The genomic basis underlying these innovations remains unknown. Using comparative and functional genomics in the model squid Euprymna scolopes, we reveal the unique genomic, topological, and regulatory organization of cephalopod genomes. We show that cephalopod genomes have been extensively restructured compared to other animals leading to the emergence of hundreds of tightly linked and evolutionary unique gene clusters (microsyntenies). Such novel microsyntenies correspond to topological compartments with a distinct regulatory structure and contribute to complex expression patterns. In particular, we identified a set of microsyntenies associated with cephalopod innovations (MACIs) broadly enriched in cephalopod nervous system expression. We posit that the emergence of MACIs was instrumental to cephalopod nervous system evolution and propose that microsyntenic profiling will be central to understand cephalopod innovations.
Project description:To test the conservation and evolution of long non-coding RNAs across multiple rodent species by transcriptome sequencing and histone modification mapping. Part of experiment series: E-MTAB-867 RNA-Seq, E-MTAB-959 ChIP-Seq.
Project description:The saliva of the common octopus (Octopus vulgaris) has been the subject of biochemical study for over a century. A combination of bioassays, behavioural studies and molecular analysis on O. vulgaris and related species suggests that it should contain a mixture of highly potent neurotoxins and degradative proteins. However, a lack of genomic and transcriptomic data has meant that the amino acid sequences of these proteins remain almost entirely unknown. To address this, we assembled the salivary gland transcriptome of O. vulgaris and combined it with high resolution mass spectrometry data from the posterior and anterior salivary glands of two adults, the posterior salivary glands of six paralarvae and the saliva from a single adult. We identified a total of 2810 protein groups from across this range of salivary tissues and age classes, including 84 with homology to known venom protein families. Additionally, we found 21 short secreted cysteine rich protein groups of which 12 were specific to cephalopods. By combining protein expression data with phylogenetic analysis we demonstrate that serine proteases expanded dramatically within the cephalopod lineage and that cephalopod specific proteins are strongly associated with the salivary apparatus.
2018-09-24 | PXD010298 | Pride
Project description:Transcriptome sequencing of multiple Actiniaria species