DOI: 10.5061/dryad.nk98sf7xz
title: Data from: Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes

description: Coleoid cephalopods possess numerous complex, species-specific
 morphological and behavioural adaptations, e.g., a uniquely structured
 nervous system that is the largest among the invertebrates. The Hawaiian
 bobtail squid Euprymna scolopes is one of the most established cephalopod
 species. With its recent publication of the chromosomal-scale genome
 assembly and regulatory genomic data, it also emerges as a key model for
 cephalopod gene regulation and evolution. However, the latest genome
 assembly has been lacking a native gene model set. Our manuscript
 describes the generation of new long-read transcriptomic data and,
 combined with a plethora of available transcriptomic datasets, a new
 reference annotation for E. scolopes. 
description: See methods in: Gene modelling and annotation for the Hawaiian
 bobtail squid, <em>Euprymna scolopes, </em>Rogers<em> et
 al.</em> (2023) <em>Scientific Data.</em>
description: See methods in: Gene modelling and annotation for the Hawaiian
 bobtail squid, <em>Euprymna scolopes, </em>Rogers <em>et
 al.</em> (2023) <em>Scientific Data.</em>
description: **Euprymna scolopes gene annotation for V2 genome** This repo contains the
 gene annotation (new BRAKER2 models, combined with some genes from Belcaid
 *et al*. 2019) for the Hawaiian bobtail squid, *Euprymna scolopes* genome
 (Schmidbaur *et al.*, 2022). It is part of the following manuscript, in
 press at *Scientific Data*: Towards a comprehensive gene annotation for
 the Hawaiian bobtail squid, *Euprymna scolopes*. Thea F. Rogers, Gözde
 Yalçın, John Briseno, Nidhi Vijayan, Spencer V. Nyholm, Oleg Simakov.
 **The annotation files are as follows:** eupsc_models_v2.2.gtf #Gene
 annotation GTF eupsc_models_v2.2_cds.fa #Coding sequence file
 eupsc_models_v2.2_prot.fa #Protein sequence file
 eupsc_models_v2.2_interproscan.tsv #Protein annotation
 eupsc_models_v2.2.tags.gtf #Same gene annotation gtf as
 eupsc_models_v2.2.gtf but with explicit exon lines Information on column
 headers for eupsc_models_v2.2.gtf and eupsc_models_v2.2.tags.gtf is as
 follows: 1. **seqname** - name of the chromosome or scaffold; chromosome
 names can be given with or without the 'chr' prefix. **Important
 note**: the seqname must be one used within Ensembl, i.e. a standard
 chromosome name or an Ensembl identifier such as a scaffold ID, without
 any additional content such as species or assembly. See the example GFF
 output below. 2. **source** - name of the program that generated this
 feature, or the data source (database or project name) 3. **feature** -
 feature type name, e.g. Gene, Variation, Similarity 4. **start** - Start
 position* of the feature, with sequence numbering starting at 1. 5.
 **end** - End position* of the feature, with sequence numbering starting
 at 1. 6. **score** - A floating point value. 7. **strand** - defined as +
 (forward) or - (reverse). 8. **frame** - One of '0',
 '1' or '2'. '0' indicates that the first
 base of the feature is the first base of a codon, '1' that the
 second base is the first base of a codon, and so on.. 9. **attribute** - A
 semicolon-separated list of tag-value pairs, providing additional
 information about each feature. Information on column headers for
 eupsc_models_v2.2_interproscan.tsv is as follows: 1. Protein accession
 (e.g. P51587) 2. Sequence MD5 digest (e.g.
 14086411a2cdf1c4cba63020e1622579) 3. Sequence length (e.g. 3418) 4.
 Analysis (e.g. Pfam / PRINTS / Gene3D) 5. Signature accession (e.g.
 PF09103 / G3DSA:2.40.50.140) 6. Signature description (e.g. BRCA2 repeat
 profile) 7. Start location 8. Stop location 9. Score - is the e-value (or
 score) of the match reported by member database method (e.g. 3.1E-52) 10.
 Status - is the status of the match (T: true) 11. Date - is the date of
 the run 12. InterPro annotations - accession (e.g. IPR002093) 13. InterPro
 annotations - description (e.g. BRCA2 repeat) 14. GO annotations with
 their source(s), e.g.
 [GO:0005515(InterPro](go:0005515\(InterPro))|GO:0006302(PANTHER)|GO:0007195(InterPro,PANTHER). This is an optional column; only displayed if the `--goterms` option is switched on 15. Pathways annotations, e.g. REACT_71. This is an optional column; only displayed if the `--pathways` option is switched on **List of commands and scripts used to generate the annotation as well as resources provided to reviewers can be found in GitHub under:**