Allotetraploid Cyprinid Fish Genomes for Subgenome Dominance Analysis

Anjum Shahzad provides processed data and Python scripts for a genomics study on subgenome dominance in allotetraploid cyprinid fish. The repository includes scripts for data cleaning, gene mapping, phylogenetic tree generation, and dominance analysis. The dataset was last updated on May 3, 2026, and is shared under a CC-BY-4.0 license.

Use Cases

• Analyzing A:B subgenome expression ratios across different cyprinid species based on the described analysis scripts.
• Reproducing phylogenetic trees and figures from the associated research paper using the provided processed data.
• Studying the impact of domestication and cave adaptation on subgenome dominance patterns in fish genomes.
• Mapping genes to specific subgenomes (A or B) in common carp and related species using the described mapping methodology.

Strengths

• Includes custom Python scripts for full reproducibility of analyses and figures.
• Data is shared under a permissive CC-BY-4.0 license, facilitating reuse.
• Processed data files are provided, reducing initial data cleaning overhead for specific analyses.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• The description indicates raw input files must be provided by the user from external sources like Ensembl.

Provenance

Source

figshare, author Anjum Shahzad.

Collection Method

Processed data from genome assemblies of cyprinid fish species, likely from Ensembl.

Freshness

Last updated 2026-05-03 15:19:42; freshness should be verified.