DOI: 10.5061/dryad.mpg4f4r6w
title: Data for: Highly contiguous genome assembly of Drosophila prolongata – a model for evolution of sexual dimorphism and male-specific innovations

description: 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-coding. The assembly includes 98.5% of Diptera BUSCO
 genes, including 93.8% present as a single copy. Despite some likely
 regional duplications, the completeness of this genome suggests that it
 can be readily used for gene expression, GWAS, and other genomic analyses.
description: # 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 sequences and gene annotations. The `Final_Versions/prolongata/` subdirectory has all files related to *D. prolongata*: The deduplicated assembly sequences `prolongataSaPa_WGS-DeDup.fa` and corresponding annotation `prolongataSaPa_WGS-DeDup.gff`; for scaffolds removed as duplicate (*i.e.* alternate haplotigs) the sequences `prolongataSaPa_WGS-RemovedDups.fa` and corresponding annotation `prolongataSaPa_WGS-RemovedDups.gff`. The `Final_Versions/carrolli/` subdirectory has the gene annotation file `carrolli_GCA_018152295.1.gff` for the publicly available D. carrolli assembly version GCA_018152295.1. #### Intermediate Versions of Assembly and Annotation The `Dovetail/` directory has files, data, and reports provided by Dovetail Genomics in producing the HiRise assembly. The `HiC_HiCRise_MLkUi/ `subdirectory includes information on the HiC scaffolding process and includes the final Dovetail assembly `drosophila_prolongata_29Dec2017_MLkUi.fasta.gz` and the bam file for mapped HiC reads. The `PBassembly/` subdirectory contains information and data from the PacBio sequencing and Falcon assembly process, including the `p_ctg.fasta.gz` primary assembly and `a_ctg.fasta.gz` associated haplotig scaffold sequences. The `gff_combine/` directory has the intermediate genome annotation files which were combined to produce the annotations available in `Final_Versions/`. They split first by species (subdirectories `carrolli/` and `prolongata/`), then by program used to generate the annotation (subdirectories `liftoff/` and `maker/`). These intermediate annotations were combined using a pipeline detailed in the [annotation_tools](https://github.com/dluecke/annotation_tools) github repo. #### Assessing Assembly and Annotations The `busco/` directory has all results from standard BUSCO analyses; runs labeled "genome" are for assemblies, runs for "transcripts" are against transcript sequences extracted from the assembly using the relevant genome annotation. Included are analyses of focal species *D. prolongata* and *D. carrolli*, and of reference species *D. melanogaster* and *D. rhopaloa*. Results from *D. prolongata* after removal of duplicate scaffolds are labeled "dedup". The `mummer/species_alignments/` subdirectory has primary results (delta files) from mummer alignments against reference species and tsv files used for alignment plotting, split into `melanogaster/` and `rhopaloa/` subdirectories. The value for the c parameter used (seed alignment length) is included in file names. delta files were converted into tsv files and plotted in R with a pipeline detailed in the [annotation_tools](https://github.com/dluecke/annotation_tools) github repo. #### Identification of Duplicate Scaffolds/Regions The BUSCO-based pipeline to identify and remove duplicate scaffolds using the BUSCO results file `busco/prolongata_genome_01/run_diptera_odb10/full_table.tsv` is detailed in the [annotation_tools](https://github.com/dluecke/annotation_tools) github repo. The `mummer/confirm_duplicates/` subdirectory has delta results file for mummer alignments between removed duplicate scaffolds and retained scaffolds with corresponding duplicate sequence, along with tsv files used for alignment plotting as detailed in the [annotation_tools](https://github.com/dluecke/annotation_tools) github repo. The `blast/` directory has files used in the reciprocal BLAST-based tagging of candidate duplicate genes in the *D. prolongata* assembly, including results for all-against-all BLAST searches of gene region sequences from the *D. prolongata* and *D. rhopaloa* annotations, along with the gene region sequences from both species assemblies which were used as queries and references. The `AllVsAll/` and `AllVsRhop/` subdirectories have results for *D. prolongata* sequences queried against *D. prolongata* sequences and against *D. rhopaloa* sequences respectively. The pipeline to extract gene region sequences and process BLAST results is detailed in the [annotation_tools](https://github.com/dluecke/annotation_tools) github repo. ## Sharing/Access information This is a section for linking to other ways to access the data, and for linking to sources the data is derived from, if any. Links to other publicly accessible locations of the assembly, and RNA-seq data used for MAKER annotation runs, can be found here: * [https://www.ncbi.nlm.nih.gov/bioproject/1057277](https://www.ncbi.nlm.nih.gov/bioproject/1057277) The assembly was produced in collaboration with Dovetail genomics: * [https://cantatabio.com/dovetail-genomics/](https://cantatabio.com/dovetail-genomics/) ## Code/Software Custom scripts used for these analysis is available in this public GitHub repository: * [https://github.com/dluecke/annotation_tools](https://github.com/dluecke/annotation_tools)