DOI: 10.5061/dryad.5qfttdzcf
title: Poecilia picta female genome assembly files

description: Sex chromosome dosage compensation is a model to understand the
 coordinated evolution of transcription, however, the advanced age of the
 sex chromosomes in model systems makes it difficult to study how the
 complex regulatory mechanisms underlying chromosome-wide dosage
 compensation can evolve. The sex chromosomes of Poecilia picta have
 undergone recent and rapid divergence, resulting in widespread gene loss
 on the male Y, coupled with complete X Chromosome dosage compensation, the
 first case reported in a fish. The recent de novo origin of dosage
 compensation presents a unique opportunity to understand the genetic and
 evolutionary basis of coordinated chromosomal gene regulation. By
 combining a new chromosome-level assembly of P. picta with whole-genome
 bisulfite sequencing and RNA-seq data, we determine that the Yin Yang 1
 (YY1) DNA-binding motif is associated with male-specific hypomethylated
 regions on the X, but not the autosomes. These YY1 motifs are the result
 of a recent and rapid repetitive element expansion on the P. picta X
 Chromosome, which is absent in closely related species that lack dosage
 compensation. Taken together, our results present compelling support that
 a disruptive wave of repetitive element insertions carrying YY1 motifs
 resulted in the remodeling of the X Chromosome epigenomic landscape and
 the rapid de novo origin of a dosage compensation system.
description: # Poecilia picta female genome assembly files
 [https://doi.org/10.5061/dryad.5qfttdzcf](https://doi.org/10.5061/dryad.5qfttdzcf) **Poecilia_picta_female_genome.fasta** Genome assembly .fasta file for the female *Poecilia picta* genome assembly. The assembled genome containing 23 chromosomes, unassembled scaffolds, and the mitochondrial genome. Chromosomes are named based on synteny with the *Poecilia reticulata* female genome assembly. **Poecilia_picta_female_genome_annotation.gff3** The accompanying gene annotation file for the Poecilia_picta_female_genome in .gff format. Annotations were generated by the Dovetail genomics annotation pipeline aided by RNA-seq data from muscle, head, liver, testis, and ovary tissue. NOTE: a previous version of this file ending in .gff contained multiple annotation errors. These errors have been corrected in the updated .gff3 annotation file. **PO1787_Poecilia_picta.transcript.fasta** Gene CDS sequences in .fasta format. **PO1787_Poecilia_picta.protein.fasta** Gene peptide sequences in .fasta format. **Poecilia_picta_scaffolding_report.pdf** Scaffolding report from the Dovetail genomes genome HiRise assembly. **Poecilia_picta_annotation_report.pdf** Annotation report from the Dovetail genomics annotation pipeline. ## Description of the data and file structure Genome assembly and annotation was completed by Dovetail genomics. The assembled genome .fasta file can also be found at the NCBI genome database (BioProject PRJNA862953). Please note that the annotation, transcript, and peptide files provided here are from the Dovetail annotation and may differ from those generated by the NCBI annotation pipeline. ## Sharing/Access information All sequencing data associated with the genome assembly and annotation can be found at the NCBI BioProject database ([https://www.ncbi.nlm.nih.gov/bioproject/](https://www.ncbi.nlm.nih.gov/bioproject/)) under accessions PRJNA862953, PRJNA884377 and PRJNA884372.