Computational Pangenomics: Software Tools and Applications in Plants and Agriculture

Improvements in DNA sequencing, assembly algorithms, and computing infrastructure have resulted in the proliferation of multiple reference quality genomes within individual species. These pangenomes are a more comprehensive representation of the conservation and variation of sequence within a species and promise to be a powerful tool for identifying critical genes and regulatory regions that define the species. It also allows detection of diverse genomic regions that are important for adaptation, improving our ability to monitor, conserve, and shape genetic diversity in the face of changing climates.

While the pangenome paradigm is already being widely used for the analysis of human and microbial genomes, the approach has seen less adoption in plants due to the size and complexity of plant genomes. The development of new bioinformatics software and the effective application of existing software to plant pangenomes could have significant implications for plant genomics and agriculture, which may be critical to global food security and combating climate change.

The focus of this Research Topic is the presentation of new bioinformatics tools and computational approaches for the analysis of pangenomics data, with applications to plants and agriculture. Subtopics may include:

* Showing the efficacy of novel algorithms for computational pangenomics
* Presenting new software tools for computational pangenome analysis
* Novel research in plants enabled by pangenomic techniques
* Association studies that connect pangenomes to phenotypes
* Surveys of existing software tools and protocols for pangenome analysis in plants
* Identifying unmet needs in the plant pangenome space