Data for: Highly contiguous genome assembly of Drosophila prolongata – a model for evolution of sexual dimorphism and male-specific innovations

Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2Mb) genome assembly of 220Mb. The repetitive content of the genome is 24.6%, the plurality of which are LTR retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-c..., , , # Data for: Highly Contiguous Genome Assembly of Drosophila prolongata - a Model for Evolution of Sexual Dimorphism and Male-specific Innovations

[https://doi.org/10.5061/dryad.mpg4f4r6w](https://doi.org/10.5061/dryad.mpg4f4r6w)

Genome annotations for *D. prolongata* and *D. carrolli*, described in *D. prolongata* genome report (Luecke *et al* 2024).

Fasta files with scaffolds identified as duplicate sequence and removed from intermediate *D. prolongata* assembly.

All versions of *D. prolongata* genome assembly: Final version described in paper and submitted to NCBI, Dovetail HiRise assembly including duplicate scaffolds, and Dovetail Falcon assembly before HiC scaffolding.

Supporting data provided by Dovetail Genomics alongside completed HiRise assembly.

Full results and intermediate files for BLAST, BUSCO, and mummer analyses.

## Description of the data and file structure

#### Final Versions of Assembly and Annotation

The `Final_Versions/` directory has all Final Version sequ...