DOI: 10.5061/dryad.bg79cnpnh
title: Data from: New genome assemblies for Poeciliidae: A foundation for adaptation studies

description: 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.
description: # 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 pattern** | **Description** | | :------------------------ | :-------------------------------------------------------------------------------------------------------------------------- | | `*.fa` | Filtered contig-level assemblies after removal of contaminants using Kraken2 | | `*.aa` | Predicted amino acid (protein) sequences generated by BRAKER | | `*.codingseq` | Predicted coding sequences (CDS) generated by BRAKER | | `*.gtf` | Gene annotations (GTF format) of predicted protein-coding genes from the BRAKER pipeline applied to contig-level assemblies | | `*scaffold.braker.gff` | Gene annotations (GFF3 format) of predicted genes lifted to scaffold-level assemblies using Liftoff | | `*ncbi.anno.polished.gff` | Gene annotations (GFF3 format) of liftover refseq genes renamed to align with NCBI assembly scaffold names | 
 
 **Included Files** #### *Poecilia mexicana* (nonsulfidic and sulfidic) *
 `Pmex_NS_kraken_filtered.fa` * `Pmex_NS_braker.aa` *
 `Pmex_NS_braker.codingseq` * `Pmex_NS_braker.gtf` *
 `Pmex_NS.ragtag.scaffold.braker.gff` *
 `Pmex_NS.ragtag.scaffold.liftoff.ncbi.anno.polished.gff` *
 `Pmex_S_kraken_filtered.fa` * `Pmex_S_braker.aa` *
 `Pmex_S_braker.codingseq` * `Pmex_S_braker.gtf` *
 `Pmex_S.ragtag.scaffold.braker.gff` *
 `Pmex_S.ragtag.scaffold.liftoff.ncbi.anno.polished.gff` #### *Poecilia
 sulphuraria* * `Psulph_kraken_filtered.fa` * `Psulph_braker.aa` *
 `Psulph_braker.codingseq` * `Psulph_braker.gtf` *
 `Psulph.ragtag.scaffold.braker.gff` *
 `Psulph.ragtag.scaffold.liftoff.ncbi.anno.polished.gff`  #### *Gambusia
 eurystoma* * `Geury_kraken_filtered.fa` * `Geury.aa` * `Geury.codingseq` *
 `Geury.gtf` * `Geury.ragtag.scaffold.braker.gff` ### *Gambusia sexradiata*
 (sulfidic and nonsulfidic) * `Gsex_S_kraken_filtered.fa` * `Gsex_S.aa` *
 `Gsex_S.codingseq` * `Gsex_S.gtf` * `Gsex_S.ragtag.scaffold.braker.gff` *
 `Gsex_NS_kraken_filtered.fa` * `Gsex_NS.aa` * `Gsex_NS.codingseq` *
 `Gsex_NS.gtf` * `Gsex_NS.ragtag.scaffold.braker.gff`