Data from: Reference-guided chromosome-scale genome assembly with insights on population genomics of the Atlantic Goliath grouper (Epinephelus itajara), Islas Del Rosario, Colombia
Data files
Sep 14, 2026 version files 371.48 MB
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E_itajara_cdna.fa
43.28 MB
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E_itajara_cds.fa
43.28 MB
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E_itajara_exonDensity.txt
343.86 KB
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E_itajara_geneDensity.txt
346.86 KB
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E_itajara_proteins.fa
16.65 MB
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E_itajara_ragtag.scaffold.E_lanceolatus_np2_correc_MT_maker.gff3.gz
256.92 MB
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E_itajara_stats.txt
2.06 KB
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ragtag.scaffold.correc.np2.E_lanceolatus_MT.fasta.mod.EDTA.TElib.fa
10.65 MB
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README.md
6.80 KB
Abstract
This dataset contains supplementary genomic resources associated with the chromosome-level genome assembly and annotation of the Atlantic goliath grouper, Epinephelus itajara. The files include annotated coding DNA sequences (CDS), cDNA sequences, predicted protein sequences, GFF3 genome annotation files, a custom transposable element (TE) library, and genome-wide density tracks for genes and exons generated during genome annotation and comparative genomics analyses. In addition, the dataset includes annotation summary statistics describing gene length, transcript length, CDS length, protein length, exon counts, and transcript-per-gene distributions derived from the final genome annotation.
The dataset complements the raw sequencing reads and assembled genome publicly available through NCBI GenBank under accession GCA_055440715.1 and SRA accessions SRR36198771–SRR36198789. These additional files provide reusable genomic resources for comparative genomics, genome annotation, evolutionary analyses, population genomics, and conservation genetics studies involving groupers and other teleost fishes.
No ethical or legal restrictions apply to the reuse of these data. The dataset is intended to facilitate reproducibility and future comparative analyses involving Epinephelus itajara and related species.
Dataset DOI: 10.5061/dryad.xgxd254wt
Description of the data and file structure
This dataset was generated as part of a whole-genome sequencing and comparative genomics study of the Atlantic goliath grouper, Epinephelus itajara, aimed at developing the first chromosome-level reference genome for the species. The project included genome assembly, transposable element annotation, genome annotation, comparative genomics analyses with other species from the genus Epinephelus, and population genomics analyses of captive individuals from the Colombian Caribbean.
The files deposited in this repository correspond to annotation-derived genomic resources generated from the final assembled genome, including CDS, cDNA, protein sequences, GFF3 annotation files, transposable element libraries, genome density tracks, and annotation summary statistics. These resources were produced to facilitate reproducibility and future studies in comparative genomics, conservation genetics, evolutionary biology, and aquaculture research involving groupers and related teleost fishes.
Files and variables
File: E_itajara_exonDensity.txt
Description: Tab-delimited file containing exon density estimates across the Epinephelus itajara genome in fixed genomic windows generated from the final GFF3 annotation. Values were produced using the TranscriptomeAnalyzer function of NGSEP v5.0.0.
Variables
- chr01: Chromosome or scaffold identifier
- 1: Start position of genomic window (bp)
- 100000: End position of genomic window (bp)
- 0: Number of exon events detected within the 100 Kbp window
- 0: Total number of exon bases within the 100 Kbp window
Missing values are not expected in this file.
File: E_itajara_cdna.fa
Description: FASTA file containing predicted cDNA sequences derived from the final genome annotation generated with MAKER v3.01.04. Sequence headers correspond to transcript identifiers from the GFF3 annotation.
File: E_itajara_geneDensity.txt
Description: Tab-delimited file containing gene density estimates across the genome in fixed genomic windows generated from the final annotation using NGSEP v5.0.0.
Variables
- chr01: Chromosome or scaffold identifier
- 1: Start position of genomic window (bp)
- 100000: End position of genomic window (bp)
- 0: Number of gene events detected within the 100 Kbp window
- 0: Total number of gene bases within the 100 Kbp window
Missing values are not expected in this file.
File: E_itajara_cds.fa
Description: FASTA file containing predicted coding DNA sequences (CDS) extracted from the final genome annotation. Sequence identifiers correspond to annotated transcript models.
File: E_itajara_stats.txt
Description:
Summary statistics generated from the final genome annotation using the TranscriptomeAnalyzer function of NGSEP v5.0.0. The file contains histogram distributions and descriptive statistics for gene length, transcript length, CDS length, protein length, exon number, and transcripts per gene derived from the final genome annotation of Epinephelus itajara.
Variables
For histogram sections:
- First column — Lower bound of the interval/range
- Second column — Number of genes, transcripts, CDS regions, proteins, or exons within the corresponding interval
Units
- Gene, transcript, CDS, and protein lengths are reported in base pairs (bp), except protein length, which is reported in amino acids (aa).
- Number of exons and transcripts per gene are unitless counts.
Missing values are not expected in this file.
File: E_itajara_proteins.fa
Description: FASTA file containing predicted protein sequences translated from annotated coding regions generated during genome annotation.
File: ragtag.scaffold.correc.np2.E_lanceolatus_MT.fasta.mod.EDTA.TElib.fa
Description: Custom transposable element (TE) library generated using EDTA v2.2.1 from the final assembled genome of Epinephelus itajara. The library was used for repeat masking and TE annotation analyses.
File: E_itajara_ragtag.scaffold.E_lanceolatus_np2_correc_MT_maker.gff3.gz
Description: Genome annotation file in GFF3 format generated using MAKER v3.01.04. The file contains genomic coordinates and structural annotations for genes, transcripts, exons, CDS regions, and other annotated genomic features.
Code/software
The genomic resources included in this dataset can be viewed and analyzed using standard bioinformatics software and text-processing tools compatible with FASTA, GFF3, TXT, and compressed GZIP formats.
Software used to generate and process the files
- MAKER v3.01.04 — used for genome annotation and generation of GFF3.
- RepeatMasker v4.1.7-p1 — used for repeat masking prior to genome annotation.
- EDTA v2.2.1 — used to generate the custom transposable element (TE) library included in this dataset.
- NGSEP v5.0.0 — specifically the TranscriptomeAnalyzer function, used to generate CDS, cDNA, protein FASTA files, annotation statistics, and genomic density files.
Workflow overview
The genome assembly of Epinephelus itajara was first repeat-masked using RepeatMasker with a custom TE library generated by EDTA. Genome annotation was subsequently performed using MAKER v3.01.04 to generate the final GFF3 annotation. Annotation-derived sequence files (CDS, cDNA, and proteins), genomic density tracks, and annotation summary statistics were subsequently generated using the TranscriptomeAnalyzer function implemented in NGSEP v5.0.0 with default parameters.
Access information
Other publicly accessible locations of the data:
Raw sequencing reads, genome assembly, BioSample records, and associated metadata are publicly available through the National Center for Biotechnology Information databases under the following accessions:
- BioProject: PRJNA1338326
- Genome assembly: GCA_055440715.1
- SRA accessions: SRR36198771–SRR36198789
- BioSample records associated with the BioProject are available through NCBI BioSample. (SAMN52585810–SAMN52585826 and SAMN52403715)
Data was derived from the following sources:
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This dataset was derived from the chromosome-level genome assembly and annotation of Epinephelus itajara generated in this study. Raw sequencing reads and primary genome assembly files were obtained from the associated NCBI BioProject and processed using MAKER v3.01.04, EDTA v2.2.1, RepeatMasker v4.1.7-p1, and NGSEP v5.0.0.
All NCBI data are publicly accessible under the NCBI data usage policies.
Genome annotation was performed using MAKER v3.01.04 [1] following repeat masking with RepeatMasker v4.1.7-p1 [2] and a custom transposable element (TE) library generated using EDTA v2.2.1 [3-12]. Additional methodological details regarding genome annotation, repeat masking, and TE annotation are provided in the associated primary research article.
Annotation-derived statistics and sequence resources were generated using the TranscriptomeAnalyzer function implemented in NGSEP v5.0.0 [13-16] with default parameters, from the final genome assembly and GFF3 annotation files. This included extraction of CDS, cDNA, and protein FASTA files, as well as summary statistics describing gene length, transcript length, exon number, CDS length, protein length, and transcript-per-gene distributions. Gene and exon density tracks were additionally generated for downstream genomic visualization and comparative genomics analyses.
Bibliography:
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