DOI: 10.5061/dryad.x0k6djj09
title: Annotation of the novel humpback whale (<em>Megaptera novaeangliae</em>) reference genome

description: We present a comprehensive annotation of the humpback whale (Megaptera
 novaeangliae) genome, representing the most complete and biologically
 coherent gene-model resource available to date for this species.
 Leveraging R (v2025.05.1+513) within a fully reproducible analysis
 pipeline, we evaluated 1,308,486 genomic features—including 21,833
 protein-coding genes and 386,765 annotated exons. The structural features
 of our annotation are consistent with mammalian expectations (median gene
 length ≈ 4.3 kb; intron lengths peaking in the 1–10 kb range) and show
 coding‐sequence integrity (99.7 % of transcripts are in-frame). Gene loci
 are distributed non‐uniformly across scaffolds, with densities ranging
 from ~7 to ~15 genes per megabase, covering ~25–30 % of the assembled
 genome sequence. We further identified ~2,000 multi‐copy gene families and
 numerous tandem duplication clusters (2–12 members). These results
 demonstrate that the M. novaeangliae genome is both structurally complete
 and functionally rich, providing a robust foundation for future
 comparative, physiological, and conservation‐genomics investigations.
description: # README: Genome Annotation and Structural Validation of the Humpback
 Whale (*Megaptera novaeangliae*) ## 1. General Information * **Submission
 Title:** Genome annotation and structural validation of the humpback whale
 *Megaptera novaeangliae* * **Contact Information:** Maria-Vittoria G.
 Carminati
 ([m.carminati@deepbiotech.com](mailto:m.carminati@deepbiotech.com)) *
 **Dataset Overview:** This dataset contains the primary Gene Transfer
 Format (GTF) annotation and derived validation files for the *Megaptera
 novaeangliae* genome. These files provide the evidence for the quality and
 structure of 21,833 protein-coding genes and 386,765 exons. --- ## 2.
 Terminology and Units for New Users * **Base pair (bp):** The fundamental
 unit of DNA length. All genomic coordinates and lengths in this dataset
 are in bp. * **Megabase (Mb):** One million base pairs. * **Scaffold /
 seqnames:** Unique identifiers for the DNA sequence fragments in the
 genome assembly. * **Isoform / Transcript:** Alternative versions of mRNA
 produced from a single gene. * **Intergenic Space:** The DNA sequence
 located between two adjacent genes. * **Coding Sequence (CDS):** The
 portion of a gene that codes for protein translation. --- ## 3. Primary
 Data Record: Megaptera_novaeangliae_annotated.gtf * **Description:** The
 primary structural annotation file describing the location of genes and
 exons. * **Format:** Tab-separated (GTF 2.2). * **Variables (Columns):**
 1. **seqname:** Name of the genomic scaffold. 2. **source:** Prediction
 software (BRAKER3). 3. **feature:** Element type (`gene`, `transcript`,
 `exon`, `CDS`, `start_codon`, `stop_codon`). 4. **start / end:** 1-based
 coordinates in **bp**. 5. **score:** Confidence value (represented as
 "." if not applicable). 6. **strand:** Orientation on the DNA
 (`+` or `-`). 7. **frame:** Reading frame (`0`, `1`, `2`, or `.`). 8.
 **attribute:** Semicolon-separated tags including `gene_id`,
 `transcript_id`, and `gene_name`. --- ## 4. Derived Tabular Data (CSV and
 TXT) ### 00_summary.txt Summary of total gene and transcript counts. ###
 01_multicopy_gene_families.csv * `gene_name`: (String) Standardized name
 of the gene family. * `n`: (Integer) Total count of gene copies
 identified. ### 02_transcripts_per_gene_derived.csv * `gene_id`: (String)
 Unique gene identifier. * `n_tx`: (Integer) Number of isoforms per gene.
 ### 03_exons_per_transcript.csv * `transcript_id`: (String) Unique
 transcript identifier. * `n_exons`: (Integer) Total exons in the
 transcript. ### 04_genes_per_seq_all.csv * `seqnames`: (String) Scaffold
 name. * `n_genes`: (Integer) Total genes on the scaffold. ###
 05_gene_density_per_seq.csv * `seqnames`: (String) Scaffold name. *
 `approx_len`: (Integer) Length of scaffold in **bp**. * `n_genes`:
 (Integer) Total gene count. * `gene_density_perMb`: (Float) Density
 expressed as (n_genes / approx_len * 1,000,000). ###
 06_intergenic_distances_primary.csv * `gene_id`: (String) Gene ID (or `NA`
 for scaffold start regions). * `seqnames`: (String) Scaffold name. *
 `start` / `end`: (Integer) Coordinates in **bp**. * `intergenic`:
 (Integer) Distance to the preceding gene in **bp**. ###
 07_gene_density_1Mb_windows.csv * `seqnames`: (String) Scaffold name. *
 `bin`: (Integer) The starting coordinate of the 1,000,000 bp window. *
 `genes_per_Mb`: (Integer) Gene count within that specific window. ###
 08_tandem_duplication_clusters.csv * `gene_name`: (String) Name of the
 duplicated gene family. * `cluster`: (Integer) Numerical ID of the
 cluster. * `size`: (Integer) Number of genes in the cluster. * `span_bp`:
 (Integer) Total genomic length covered by the cluster in **bp**. ###
 09_qc_cds_mod3.txt Technical report verifying that Coding Sequence (CDS)
 lengths are multiples of 3. ### exon_lengths.csv / intron_lengths.csv *
 `exon_len` / `intron_len`: (Integer) Length of the individual feature in
 **bp**. ### overlapping_gene_pairs.csv * `geneA` / `geneB`: (String)
 Overlapping Gene IDs. * `pair_type`: (Category) `same-strand` or
 `opposite-strand`. ### genes_near_scaffold_edges.csv * `dist_to_end`:
 (Integer) Distance to the nearest scaffold end in **bp**. * `near_edge`:
 (Boolean) `TRUE` if the gene is at the edge; `FALSE` otherwise. --- ## 5.
 Visualizations (Figures) The following PNG files provide visual validation
 of the metrics described in the tabular files: *
 **Fig_ContigEdge_Genes_Clean.png**: Distribution of genes relative to
 scaffold ends. * **Fig_ExonLength_Log.png**: Log-transformed distribution
 of exon lengths. * **Fig_ExonLength_p995.png**: Distribution of exon
 lengths (99.5th percentile). * **Fig_Exons_per_Transcript_Clean.png**:
 Frequency of exons per transcript model. *
 **Fig_Gene_Density_per_Seq_Primary_Clean.png**: Global gene density per
 scaffold. * **Fig_GeneDensity_1Mb_Faceted_Clean.png**: Faceted view of
 gene density across windows. * **Fig_GeneLength_ByTop10Seq.png**: Gene
 length comparisons across the 10 largest scaffolds. *
 **Fig_GeneLength_Distribution_p995.png**: Global distribution of gene
 lengths. * **Fig_GeneOverlaps_Clean.png**: Visualization of overlapping
 gene models. * **Fig_Genes_per_Seq_Top50.png**: Gene counts for the 50
 largest scaffolds. * **Fig_Intergenic_Dist_p995.png**: Distribution of
 distances between adjacent genes. * **Fig_IntronLength_Log.png**:
 Log-scaled distribution of intron lengths. *
 **Fig_IntronLength_p995.png**: Distribution of intron lengths (99.5th
 percentile). * **Fig_Isoform_Classes.png**: Classification of transcript
 isoforms. * **Fig_Lorenz_Genes_Clean.png**: Lorenz curve showing the
 distribution of genes across scaffolds. *
 **Fig_Multicopy_Top25_Lollipop.png**: Top 25 most frequent multicopy gene
 families. * **Fig_RankSize_GeneCounts_Clean.png**: Rank-size distribution
 of gene counts per scaffold. * **Fig_Transcripts_per_Gene_Clipped.png**:
 Count of transcripts per gene (clipped to show distribution). --- ## 6.
 Code/Software **Software Needed to View Data:** * **Tabular Data:** Text
 editors or **LibreOffice Calc**. * **Annotation (.gtf):** **Integrative
 Genomics Viewer (IGV)** or **JBrowse 2**. **Software Used for Analysis:**
 * **BRAKER3 (v3.0.8):** Prediction pipeline using RNA-seq (SRR28920143,
 SRR8388975, SRR2183423) and OrthoDB v12. * **R (v2025.05.1+513):** Data
 processing, statistical analysis, and figure generation. * **R Packages:**
 `tidyverse` (`dplyr`, `ggplot2`), `GenomicRanges`. **Workflow:** BRAKER3
 generated the primary GTF. R was then used to parse the GTF, calculate
 structural statistics (lengths, densities, distances), and generate the
 validation figures listed above.