Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes

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. , See methods in: Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes, Rogers et al. (2023) Scientific Data., See methods in: Gene modelling and annotation for the Hawaiian bobtail squid, Euprymna scolopes, Rogers et al. (2023) Scientific Data., **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...