The nuclear and mitochondrial genomes of the lined rockskipper, Istiblennius lineatus (Teleostei: Blenniidae)

Structural annotation of the nuclear genome assembly for Istiblennius lineatus. GFF and protein fasta files. Structural annotation followed a Snakemake pipeline originally used for fish genome annotation (Oriowo et al. (2025); https://github.com/YanisChrys/phoxinus_annotation). Briefly, repetitive elements were identified de novo with RepeatModeler v.2.0.1 and repetitive DNA was masked with RepeatMasker version v.4.1.0 (Smit et al. 2013) using the repeat library previously identified via RepeatModeler and using rmblastn v.2.10.0 (Flynn et al. 2020) as a search engine. The masked genome assembly was used for structural annotation of proteins using direct RNA-seq evidence and homology to known fish proteins using BRAKER v.3.0.7 (Gabriel et al. 2024 Feb 29). RNA-seq alignment maps were generated by mapping the newly generated RNA-seq data onto the masked genome using STAR v.2.7.10 (Dobin et al. 2013). The protein database consisted of annotated proteins from 13 fish species: Acanthochromis polyacanthus (NCBI Acc. No. GCF_021347895.1), Cyprinodon variegatus (GCF_000732505.1), Danio rerio (GCF_000002035.6), Gouania willdenowi (GCF_900634775.1), Lepisosteus oculatus (GCF_000242695.1), Mugil cephalus (GCF_022458985.1), Oreochromis niloticus (GCF_001858045.2), Oryzias latipes (GCF_000313675.1), Salarias fasciatus (GCF_902148845.1), Stegastes partitus (GCF_000690725.1), and Xiphophorus maculatus (GCF_002775205.1) downloaded from NCBI, Salaria pavo downloaded from Figshare (https://doi.org/10.6084/m9.figshare.26854312), and Ophioblennius macclurei downloaded from ENA (Kulikov et al. 2026; PRJEB95139).