mRNA editing analysis of Doryteuthis pealeii
Creators
- 1. University of California Berkeley
- 2. Marine Biological Laboratory
- 3. University of California, Berkeley
- 4. University of Vienna
- 5. Hiroshima University
- 6. University of Chicago
- 7. HudsonAlpha Institute for Biotechnology
Description
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.
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.
| 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.
Funding provided by: Austrian Science Fund
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002428
Award Number: P30686-B29
Funding provided by: NSF
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100008982
Award Number: IOS-1354898
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: 5UL1TR002389-02
Funding provided by: National Institutes of Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000002
Award Number: UL1 TR000430
Funding provided by: Grass Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100001654
Award Number:
Funding provided by: Marine Biological Laboratory
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100006049
Award Number: Hibbitt Early Career Fellowship
Funding provided by: Marine Biological Laboratory
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100006049
Award Number: Whitman Fellowship
Funding provided by: Chan-Zuckerberg BioHub*
Crossref Funder Registry ID:
Award Number:
Files
DpealeiiV2.filtered.annot.txt
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