Data and code from: Independent origin of genomic imprinting in placental fish
Data files
Sep 30, 2026 version files 84.13 MB
-
01-RNAseq_alignment_using_STAR.sh
1.97 KB
-
02-RNAseq_alignment_using_TopHat.sh
1.61 KB
-
03-RNAseq_SNPcalling_lineA_lineB.sh
4.57 KB
-
04-samtools_SNP_allelic_counts.pl
4.58 KB
-
05-DEG_analysis.R
2.53 KB
-
06-single_cell_RNAseq.R
6.92 KB
-
07-visualization_Figure1.R
12.69 KB
-
08-visualization_Figure2.R
4.72 KB
-
09-visualization_Figure3.R
2.40 KB
-
DataS1.csv
25.16 MB
-
DataS2.csv
36.23 MB
-
DataS3.csv
21.26 MB
-
DataS4.csv
43.20 KB
-
DataS5.csv
355.07 KB
-
DataS6.csv
1.02 MB
-
DataS7.csv
12.18 KB
-
README.md
9.02 KB
Abstract
Genomic imprinting results in biased expression of one parental allele. Such non-Mendelian expression occurs in angiosperms and placental mammals, which share an active paternal genome during maternal offspring provisioning. It is hypothesized that imprinting modulates conflict between maternal control of resource allocation and paternal control of resource acquisition. If true, then imprinting should evolve in any organism that evolves a placenta. Here, we demonstrate genomic imprinting in a placental poeciliid fish, Poeciliopsis prolifica. Using transcriptomes from reciprocal crosses between two inbred strains, we identified 84 protein-coding genes with robust evidence of imprinting in the P. prolifica placenta. These include the teleost ortholog of the mammalian imprinted gene, grb10, and a pair of adjacent genes, dpp4 and gcga, with opposing effects on glucose metabolism that are oppositely imprinted in a fashion that potentially resolves parental conflict. Significantly elevated allelic DNA methylation on the promoters of two focal imprinted genes suggests epigenetic mechanisms of imprinting similar to those in mammals. We also discovered the convergent recruitment of a gene network associated with nutrient transport in mammals. This is the first demonstration of genomic imprinting in a non-mammalian vertebrate and supports the potential role of imprinting in resolving parental conflict.
Dataset DOI: 10.5061/dryad.ns1rn8q8r
Description of the data and file structure
This repository contains the files necessary to replicate the analyses presented in the manuscript "Independent origin of genomic imprinting in placental fish.”. It includes 4 custom scripts that should be run in Linux to generate SNP information, 5 R scripts for differentially experssion analysis, single-cell RNA-seq analysis and figure visualization, and 7 csv files containing detailed SNP information from the placental, embryonic, and maternal follicle samples of Poeciliopsis prolifica, the differentially expressed genes (DEGs) identified between the placenta and embryo of Poeciliopsis prolifica, as well as the orthologs used for evolutionary rate correlation analysis and the enriched pathways among the top 5 dpp4 evolutionary rate correlation (ERC) partners.
01-RNAseq_alignment_using_STAR.sh
This file contains the script used for RNAseq data alignment of placental, embryonic, and maternal follicle samples using STAR (version 2.7.5), including genome index generation and sequence read alignment.
02-RNAseq_alignment_using_TopHat.sh
This file contains the script used for RNAseq data alignment of placental, embryonic, and maternal follicle samples using TopHat.
03-RNAseq_SNPcalling_lineA_lineB.sh
This file contains the script used to generate the VCF file containing variant information for each sample.
04-samtools_SNP_allelic_counts.pl
This file is used to parse the VCF file and generate the more readable table including ‘chr’, ‘position’, ‘called_allele’, ‘ref_allele’, ’alter_allele’, ‘coverage’, ‘ref_count’, ‘alter_count’, ‘ref_count2’, ‘alter_count2’, ‘indel_count’, ‘other_count’.
05-DEG_analysis.R
This file is used to identify the differentially expressed genes between the placental and embryonic samples of Poeciliopsis prolifica.
06-single_cell_RNAseq.R
This file is used to process the single-cell RNA-seq data from two independent human placenta studies. It includes scripts for filtering, annotating and classifying cell types, as well as localizing the expression of specific genes.
07-visualization_Figure1.R/ 08-visualization_Figure2.R/ 09-visualization_Figure3.R
These files are used to visualize the SNP distribution in each sample, the SNP alternative allele expression ratio in two reciprocal crosses, and the degree of bias for statistically supported protein-coding imprinted genes in the placenta.
- DataS1.csv. Single-nucleotide polymorphisms (SNPs) and allelic expression counts in the placental samples of Poeciliopsis prolifica.
This file contains the SNP information and allelic expression counts in the placental samples of Poeciliopsis Prolifica. The description of each column is provided below:
- SNP_ID: The unique identifier assigned to each SNP.
- Scaffold: The scaffold on which the SNP is located.
- Position: The exact genomic position of the SNP on the scaffold.
- Strand: The strand of the gene harboring the SNP.
- Ref_allele: The allele present in the reference genome.
- Alt_allele: The alternative allele at the SNP position.
- Gene_ID: The gene harboring the SNP.
- Annotation: The predicted effect of the SNP on gene function.
*_ref_count: The number of reference allele-containing reads in the RNA-seq data.
*_alt_count: The number of alternative allele-containing reads in the RNA-seq data.
- DataS2.csv. Single-nucleotide polymorphisms (SNPs) and allelic expression counts in the embryo samples of Poeciliopsis prolifica.
This file contains the SNP information and allelic expression counts in the embryonic samples of Poeciliopsis Prolifica. The description of each column is provided below:
- SNP_ID: The unique identifier assigned to each SNP.
- Scaffold: The genomic scaffold on which the SNP is located.
- Position: The exact genomic position of the SNP on the scaffold.
- Strand: The strand of the gene harboring the SNP.
- Ref_allele: The allele present in the reference genome.
- Alt_allele: The alternative allele at the SNP position.
- Gene_ID: The gene harboring the SNP.
- Annotation: The predicted effect of the SNP on gene function.
*_ref_count: The number of reference allele-containing reads in the RNA-seq data.
*_alt_count: The number of alternative allele-containing reads in the RNA-seq data.
- DataS3.csv. Single-nucleotide polymorphisms (SNPs) and allelic expression counts in the maternal follicle samples of Poeciliopsis prolifica.
This file contains the SNP information and allelic expression counts in the maternal follicle samples of Poeciliopsis Prolifica. The description of each column is provided below:
- SNP_ID: The unique identifier assigned to each SNP.
- Scaffold: The genomic scaffold on which the SNP is located.
- Position: The exact genomic position of the SNP on the scaffold.
- Strand: The strand of the gene harboring the SNP.
- Ref_allele: The allele present in the reference genome.
- Alt_allele: The alternative allele at the SNP position.
- Gene_ID: The gene harboring the SNP.
- Annotation: The predicted effect of the SNP on gene function.
*_ref_count: The number of reference allele-containing reads in the RNA-seq data.
*_alt_count: The number of alternative allele-containing reads in the RNA-seq data.
- DataS4.csv. Paternally and maternally expressed candidate imprinted genes in the placenta of Poeciliopsis prolifica.
This file contains the information of identified paternally or maternally biased imprinted genes. The description of each column is provided below:
- Gene_Name: The name of the imprinted genes.
- Gene_ID: The NCBI Gene ID.
- Imprinting_Status: The parental origin of the preferentially expressed allele.
Note: Notes on each identified imprinted gene. Genes containing at least two independent SNPs were considered candidate imprinted genes. Genes with at least two independent significant SNPs (adjusted p < 0.05) were classified as high-confidence imprinted genes.
- DataS5.csv. Significantly differentially expressed genes (DEGs) identified between the placenta and embryo of Poeciliopsis prolifica.
This file contains the list of differentially expressed genes identified between the placenta and embryo of Poeciliopsis prolifica. The description of each column is provided below:
- Gene_ID: The NCBI Gene ID.
- Gene_Name: The name of the imprinted genes.
- log(fold change): The log transformed fold change in gene expression between the placental and embryonic samples.
- logCPM: The log transformed counts per million.
- P-Value: The P value from the statistical test for differential gene expression.
- FDR: False discovery rate. The adjusted P-value calculated using the Benjamini-Hochberg (BH) method.
- DataS6.csv. A list of shared orthologous genes between Poeciliopsis prolifica and humans used as the background set used in the evolutionary rate correlation (ERC) analysis.
This file contains 10056 shared orthologous genes between Poeciliopsis Prolifica and humans used as the background set used in the evolutionary rate correlation (ERC) analysis. The description of each column is provided below:
- Gene_Name: The name of each ortholog.
- P. prolifica_GeneID: The gene ID of corresponding gene in our P. prolifica assembly.
- P. prolifica_NCBI_GeneID: The NCBI gene ID of corresponding gene in the NCBI P. prolifica annotation.
- P. prolifica_Scaffold: The scaffold on which the gene is located in P. prolifica genome.
- P. prolifica_Start: The start position of the gene in the P. prolifica genome.
- P. prolifica_End: The end position of the gene in the P. prolifica genome
- P. prolifica_Strand: The strand on which the gene is located in the P. prolifica genome.
- Human_GeneID: The gene ID of corresponding gene in the human genome.
- Human_start: The start position of the gene in the human genome.
- Human_end: The end position of the gene in the human genome.
- Human_Strand: The strand on which the gene is located in the human genome.
- DataS7.csv. Significantly enriched pathways among the top 5 dpp4 evolutionary rate correlation (ERC) partners.
This file contains the pathways significantly enriched by the top 5 dpp4 evolutionary rate correlation (ERC) partners. The description of each column is provided below:
- Top5_Protein: The top five DPP4 evolutionary rate correlation (ERC) partners, including ANPEP, CLRN3, FLVCR2, GSK3A, MFSD4A.
- GO_ID: The Gene Ontology term identified.
- Ontology: The GO ontology category: Biological Process (BP), Molecular Function (MF), or Cellular Component (CC).
- Description: The description of the GO term.
- P.adjust: The adjusted P value for GO enrichment analysis, calculated using the Benjamini-Hochberg (BH) method.