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...延长果蝇（Drosophila prolongata）隶属于黑腹果蝇类群（melanogaster species group）与rhopaloa亚群（rhopaloa subgroup），原生分布于东南亚亚热带高地。该物种具有一系列新近演化形成的雄性特异性形态、生理与行为特征，这些特征使其与近缘物种形成显著区分，使其成为研究性二态性演化、检验性选择理论的优质模型。此前该物种缺乏基因组相关资源，这阻碍了对其性别特异性发育与行为的分子机制解析。为解决这一问题，我们利用长读长测序（long-read sequencing）与Hi-C支架挂载（Hi-C scaffolding）技术组装了延长果蝇的基因组，最终获得了总长度220Mb、高度完整且连续的基因组组装结果（支架N50为2.2Mb）。该基因组的重复序列含量为24.6%，其中占比最高的类群为LTR反转录转座子（LTR retrotransposons），占重复序列总量的33.2%。基于RNA测序（RNA-seq）数据与近缘物种同源性的基因组注释共预测得到19330个基因，其中16170个为蛋白编码基因…… ### 关联数据：《延长果蝇（Drosophila prolongata）高连续性基因组组装——性二态性与雄性特异性创新演化的研究模型》 DOI: https://doi.org/10.5061/dryad.mpg4f4r6w 延长果蝇（D. prolongata）与卡罗尔果蝇（D. carrolli）的基因组注释信息详见该延长果蝇基因组研究报告（Luecke等，2024）。 包含经鉴定为重复序列的支架序列（scaffold）、且已从延长果蝇中间组装结果中移除的FASTA文件。 延长果蝇基因组组装的所有版本：论文中描述并提交至NCBI的最终版本、包含重复支架序列的Dovetail HiRise组装版本，以及Hi-C支架挂载前的Dovetail Falcon组装版本。 由Dovetail Genomics公司提供的配套HiRise组装支持数据。 BLAST、BUSCO与mummer分析的完整结果及中间文件。 ## 数据与文件结构说明 #### 组装与注释的最终版本 `Final_Versions/` 目录包含所有最终版本序列……