New genome assemblies for Poeciliidae: A foundation for adaptation studies

Multiple lineages in the family Poeciliidae have independently adapted to hydrogen-sulfide-rich springs. The independent colonizations of such springs mean that there are naturally replicated lineages that provide a powerful model for studying adaptation and convergent evolution. However, there are limited genomic resources for many genera and species across Poeciliidae. Here, we present six high-quality, chromosome-level, annotated genome assemblies for Poecilia and Gambusia populations, five of which are the first for the species or ecotype, and the remaining assembly improved the current reference genome contiguity by more than 100-fold. We compare repeat content and model historical changes in effective population size using these new assemblies., , # Data from: New genome assemblies for Poeciliidae: A foundation for adaptation studies

**Dataset DOI:** [https://doi.org/10.5061/dryad.bg79cnpnh](https://doi.org/10.5061/dryad.bg79cnpnh)

**Description of the Data and File Structure**

This dataset includes genome assemblies, annotation files, and predicted coding and protein sequences for several species in the family *Poeciliidae*. These resources serve as a foundation for comparative and adaptive genomics studies across sulfidic and nonsulfidic populations.

Each genome was assembled and annotated using the BRAKER2 pipeline, producing gene predictions in both GTF (contig-level) and GFF (scaffold-level) formats. Scaffold-level annotations were generated with **Liftoff** using the corresponding contig-level annotations. Predicted coding sequences and translated amino acid sequences are also included. In addition, Kraken2-filtered FASTA files contain the final assemblies after contaminant removal.

**Files and Descriptions**

| **File..., , **Changes after Oct 16, 2025:** 

Added the renamed GFF files to align with NCBI scaffold names