mRNA editing analysis of Doryteuthis pealeii
Cite this dataset
Medina Ruiz, Sofia et al. (2022). mRNA editing analysis of Doryteuthis pealeii [Dataset]. Dryad. https://doi.org/10.6078/D15X38
Abstract
Cephalopods are known for their large nervous systems, complex behaviors and morphological innovations. To investigate the genomic underpinnings of these features, we assembled the chromosomes of the Boston market squid Doryteuthis (Loligo) pealeii and the California two-spot octopus, Octopus bimaculoides, and compared them with those of the Hawaiian bobtail squid, Euprymna scolopes. The genomes of the soft-bodied (coleoid) cephalopods are highly rearranged relative to other extant molluscs, indicating an intense, early burst of genome restructuring. The coleoid genomes feature multi-megabase, tandem arrays of genes associated with brain development and cephalopod-specific innovations. We find that another coleoid hallmark, extensive A-to-I mRNA editing, displays two fundamentally distinct patterns: one exclusive to the nervous system and concentrated in genic sequences, the other widespread and directed toward repetitive elements. We conclude that coleoid novelty is mediated in part by substantial genome reorganization, gene family expansion, and tissue-dependent mRNA editing.
Methods
Files provided on this repository are used as inputs for the analysis of the RNA-editing in Doryteuthis (Loligo) pealeii.
Usage notes
Raw transcriptome sequence data used in the current study (SRA as Bioproject PRJNA641326) is identified by 'Albertin' tag on the file name (for reference, alternate, depth, and annotation files). Analysis of a separate Doryteuthis pealeii specimen[1] following our analysis pipeline has the *Alon* identifier.
All files presented on this repository are tabulated.
Citation:
[1] Alon, S. et al. The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. eLife https://elifesciences.org/articles/05198 (2015) doi:10.7554/eLife.05198.
Funding
FWF Austrian Science Fund, Award: P30686-B29
National Science Foundation of Sri Lanka, Award: IOS-1354898
National Center for Advancing Translational Sciences, Award: 5UL1TR002389-02
National Center for Advancing Translational Sciences, Award: UL1 TR000430
Grass Foundation
University of Chicago, Award: Hibbitt Early Career Fellowship
University of Chicago, Award: Whitman Fellowship
Chan-Zuckerberg BioHub