AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids
AlloSHP combines the strategies of simultaneous mapping against multiple reference genomes and syntenic alignment of these genomes to call SHPs, using as input data a single VCF file and the reference genomes of the known or closest extant diploid progenitor species. This novel approach provides a valuable tool for the evolutionary study of allopolyploid species, both at the interspecific and intraspecific levels, allowing the simultaneous analysis of a large number of accessions and avoiding the complex process of assembling polyploid genomes.
Authors
- Pilar Catalán (ORCID: https://orcid.org/0000-0001-7793-5259)
- Rubén Sancho (ORCID: https://orcid.org/0000-0002-4845-4242)
- John P. Vogel (ORCID: https://orcid.org/0000-0003-1786-2689)
- Bruno Contreras‐Moreira (ORCID: https://orcid.org/0000-0002-5462-907X)
Institutions
- Consejo Superior de Investigaciones Científicas (ES)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- Universidad de Zaragoza (ES)
- Fundación Biofísica Bizkaia (ES)
- Estación Experimental de Aula Dei (ES)
Publication Details
- Journal
- Plant Methods
- Published
- 2025-10-24
- DOI
- https://doi.org/10.1186/s13007-025-01458-6
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- U.S. Department of Energy
- Joint Genome Institute
- Ministerio de Ciencia e Innovación
- Universidad de Zaragoza
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo
- Office of Science
- Consejo Superior de Investigaciones Científicas