mRNA editing analysis of Doryteuthis pealeii

Medina Ruiz, Sofia 1 ; Albertin, Caroline2 ; Mitros, Therese1 ; Schmidbaur, Hannah3; Sanchez, Gustavo4; Wang, Z.Y.5; Grimwood, Jane6; Rosenthal, Joshua2; Ragsdale, Clifton5; Simakov, Oleg3; Rokhsar, Daniel1

Published Mar 16, 2022 on 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.

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.

File	Description
Source_Editing_Albertin.tab	Main RNA editing annotation table used to create all the manuscript figures (edit sites overlapping genic features that do not overlap with genomic variants). The columns integrate the annotation from PFAM, TMHMM, Repeat overlap. Each row corresponds to a unique edit site identified by {Chr:Position}. Find the column description: README_Source_Editing_Albertin.txt

ADAR_Albertin.tab, ADAR_Alon.tab	Annotation of ADAR target sites on the Doryteuthis pealeii reference genome.
EF_Albertin.tab, EF_Alon.tab	Edit frequencies. The A>G edit sites (rows) and individual tissues samples (columns). Refer to README_Tissue_sampleID.tab
Ref_Albertin.tab, Ref_Alon.tab	Number of reads with reference nucleotide 'A' for all edit sites (rows) and individual tissues samples (columns). Refer to README_Tissue_sampleID.tab
Alt_Albertin.tab, Alt_Alon.tab	Number of reads with alternate/edited nucleotide 'G' for all edit sites (rows) and individual tissues samples (columns). Refer to README_Tissue_sampleID.tab
DP_Albertin.tab, DP_Alon.tab	Sum of reads with 'A' or 'G' for a given edit site (rows) and individual tissues samples (columns). Refer to README_Tissue_sampleID.tab
Weighted_values_Albertin.tab	Weighted average edit frequencies and read depth for Neural and Non-neural samples for each edit target (rows).
Counts_edits_by_Etype_Repeat_Not_Edited.tab	Number of Adenosines in genic regions, categorized by genomic feature (3', 5', Intron, Rec/recoding), SJ/splice junction, and Syn/synonymous) and subcategorized by the presence of repeats (True: Overlapping repeat; False: Non-overlapping repeat). The gene orientation strand orientation was is taken into account for these calculations. The numbers were obtained from the genomic variant calls.
Edit_prot_pos_intersect.bed	bedtools intersect output from Edited aminoacids and PFAM domains. Columns = ['GeneID', 'Prot_pos', 'Prot_pos_v2', 'Gene_ID2', 'PFAM_start', 'PFAM_end', 'PFAM']. The first three columns correspond to the positions of edited amino acids. The remaining columns are the overlap with the PFAM table.
Edit_prot_pos_TMHMM_intersect.bed	bedtools intersect output from Edited aminoacids and TMHMMv.2 transmembrane annotation. Columns = ['GeneID', 'Prot_pos', 'Prot_pos_v2', 'Gene_ID2', 'TMHMM_start', 'TMHMM_end', 'Location']. Note: The duplicate Prot_pos variable corresponds to the position of edited amino acid on the protein. The term 'Location' refers to the location of the amino acid with respect to the TMHMM annotation (outside, inside, or TMhelix protein segments)
Edited_vs_Non_edited_DpalHbl.gt.tab	Genotypes of D. opalescens and H. bleekeri at sites where Doryteuthis pealeii is 'Adenosine' on coding regions. Genotypes derive from high-confidence genomic calls obtained from genomic shotgun sequence reads against the reference D. pealeii genome.
Dpealeiiv2.gene_exons.filt_Chr.gff3	GFF3 file of filtered exons
DpealeiiV2.filtered.annot.txt	Gene description file of filtered genes
featureCount.tophat.M.primary.ignoreDup.filtered_tpm.txt	TPM expression table obtained using tophat

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.

mRNA editing analysis of Doryteuthis pealeii

Data files

Abstract

Methods

Usage notes