Oryza Genome Evolution through a Tetraploid Lens

This repository contains the workflow of analysis relative to the manuscript: Oryza Genome Evolution through a Tetraploid Lens, which explores the consequences of evolution on genome diversification in the Oryza genus.

This work is part of the International Oryza Map Alignment Project (IOMAP).

Usage

This repository includes:

• The scripts used to generate and validate the wild Oryza genome assemblies used in this study;
• The scripts used to generate the Oryza genome-type level pangenomes;
• The relative readme files with detailed description of each step:
  • 1. Genome Assembly
  • 2. K-mer Analysis
  • 3. Pangenome Generation
• The links to the other repositories relative to this work.

Links to the other Repositories

• Microsynteny and phylogenetic analysis of the Oryza nuclear gene clusters:

  • Co-author: Tao Feng [https://github.com/xiaoyezao/Rice-Phylogenomics]

• Phylogenetic analysis of the Oryza chloroplast genomes:

  • Co-author: Nam V. Hoang [https://github.com/nam-hoang/rice_cp_phylo_analysis]

• Expression analysis of homoeologous gene pairs in the tetraploid O. coarctata:

  • Co-author: Gopal Misra [https://github.com/gopal-misra/Oryza_coarctata_expression]

• Genome sequences (fasta files), gene annotations (gff files), and cds and protein sequences (fasta files) of the 11 wild Oryza genomes are available on Gramene Oryza!

  • [https://ftp.gramene.org/oryza/tetraploids/]

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For more details or to request materials, please contact the corresponding authors:

• Alice Fornasiero: alice.fornasiero@kaust.edu.sa
• Andrea Zuccolo: andrea.zuccolo@kaust.edu.sa
• M. Eric Schranz: eric.schranz@wur.nl
• Rod A. Wing: rod.wing@kaust.edu.sa; rwing@arizona.edu

Citation

Fornasiero, A., Feng, T., Al-Bader, N. et al. Oryza genome evolution through a tetraploid lens. Nat Genet (2025). (https://doi.org/10.1038/s41588-025-02183-5)