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Exploring intra- and intergenomic variation in haplotype-resolved pangenomes.
Eef M Jonkheer1,2, Dick de Ridder1, Theo A J van der Lee2
1Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands.
Plant Biotechnology Journal
|January 5, 2025
Summary
Researchers developed PanTools, a novel software package for analyzing plant pangenomes. This tool enhances the exploration of complex, phased genomes, particularly polyploids, revealing significant genetic diversity and aiding in the detection of genomic variations.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Haplotype-resolved (phased) genome assemblies are increasingly prevalent in plant genomics due to advances in sequencing.
- Existing computational tools struggle to effectively analyze these phased genomes, especially for polyploid species.
Purpose of the Study:
- To introduce PanTools, a novel software package designed for analyzing phased genome assemblies.
- To enhance the exploration of intra- and intergenomic variation within plant pangenomes, including polyploids.
Main Methods:
- Developed a pangenome approach by updating the graph representation and adding functionalities to PanTools.
- Incorporated features to assess synteny, gene retention, repeat profiling, and mutation rates (synonymous and nonsynonymous).
- Constructed and analyzed pangenomes for potato (diploid and tetraploid) and apple (diploid) species.
Main Results:
- PanTools successfully analyzed diploid and tetraploid potato and diploid apple pangenomes.
- High intra- and intergenomic allelic diversity was observed, including gene presence/absence, SNPs, indels, and structural variants.
- New functionalities proved effective in identifying introgressions and potential misassemblies in phased genomes.
Conclusions:
- PanTools provides essential capabilities for exploring complex phased plant genomes, particularly polyploids.
- The software facilitates the discovery of genetic diversity and aids in quality control of genome assemblies.
- PanTools is publicly available, supporting further research in plant genomics.
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