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. 2025 Oct 24;21(1):134.
doi: 10.1186/s13007-025-01458-6.

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

R Sancho  1   2 , P Catalán  3   4 , J P Vogel  5 , B Contreras-Moreira  6   7
Affiliations

AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids

R Sancho et al. Plant Methods. .

Abstract

Background: The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformatics tools and protocols have been developed to study polyploid genomes, but sometimes require the assembly of their genomes, or at least the genes, limiting their use.

Results: We have developed AlloSHP, a command-line tool for detecting and extracting single homeologous polymorphisms (SHPs) from the subgenomes of allopolyploid species. This tool integrates three main algorithms, WGA, VCF2ALIGNMENT and VCF2SYNTENY, and allows the detection of SHPs for the study of diploid-polyploid complexes with available diploid progenitor genomes, without assembling and annotating the genomes of the allopolyploids under study. AlloSHP has been validated on three diploid-polyploid plant complexes, Brachypodium, Brassica, and Triticum-Aegilops, and a set of synthetic hybrid yeasts and their progenitors of the genus Saccharomyces. The results and congruent phylogenies obtained from the four datasets demonstrate the potential of AlloSHP for the evolutionary analysis of allopolyploids with a wide range of ploidy and genome sizes.

Conclusions: 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.

Keywords: Allopolyploids; Homeologous chromosomes; Single homeologous polymorphisms-SHPs; Subgenome; Synteny.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Simplified illustration of the main pipeline processes. A Alignment of syntenic regions between reference genomes A (chromosomes A1-A5) and B (chromosomes B1-B10) using CGaln (left) and displayed in a riparian plot (right). B Mapping of reads against the concatenated reference genomes A and B. Reads from allopolyploid samples (sample 1 and sample 2) are represented by arrows (forward and reverse). Red and blue colors indicate reads mapped against genome A or B, respectively. C Multiple sequence alignment of Single Homeologous Polymorphisms (SHPs). Each letter corresponds to an SHP mapped against the reference genomes A or B. Each sample (Allotetraploid 1 and 2, and Diploid (species A) and Diploid (species B)) has as many draft subgenomes as reference genomes used in the mapping. Artifactual subgenomes are those derived from unspecific mappings and are defined by setting a %SHP threshold using cross-validation against the non-self mappings of diploid samples. These are then eliminated downstream
Fig. 2
Fig. 2
Flowchart of the main tasks and deliverables of the AlloSHP pipeline. The gray squares indicate the three main algorithms (WGA (A), VCF2ALIGNMENT (B), and VCF2SYNTENY (C)) that make up the pipeline. The white squares indicate the input files required for each algorithm and the resulting output files. The dashed boxes indicate the two configuration files needed for the VCF2ALIGNMENT and VCF2SYNTENY algorithms
Fig. 3
Fig. 3
Phylograms inferred using the SHPs alignment from the four diploid-polyploid complex datasets [A Brachypodium distachyon complex, B Brassica complex, C Triticum-Aegilops complex, and D Saccharomyces haploids and synthetic hybrids] used for the pipeline validation. Numbers indicate branches with SH-aLRT/UltraFast Bootstrap supports (BS) < 80/95; the remaining branches have 100/100 values
See this image and copyright information in PMC

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