Poecilia picta female genome assembly files
Data files
Sep 27, 2023 version files 866.71 MB
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PO1787_Poecilia_picta.protein.fasta
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PO1787_Poecilia_picta.transcript.fasta
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Poecilia_picta_annotation_report.pdf
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Poecilia_picta_female_genome_annotation.gff
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Poecilia_picta_female_genome.fasta
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Poecilia_picta_scaffolding_report.pdf
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README.md
Mar 11, 2024 version files 876.25 MB
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PO1787_Poecilia_picta.protein.fasta
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PO1787_Poecilia_picta.transcript.fasta
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Poecilia_picta_annotation_report.pdf
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Poecilia_picta_female_genome_annotation.gff3
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Poecilia_picta_female_genome.fasta
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Poecilia_picta_scaffolding_report.pdf
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README.md
Abstract
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.
README: Poecilia picta female genome assembly files
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/) under accessions PRJNA862953, PRJNA884377 and PRJNA884372.