Machine learning approaches to identify core and dispensable genes in pangenomes

A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequencing the genomes of many individuals. Here we aim to leverage the previously characterized core and dispensable gene content for two grass species ( Brachypodium distachyon and Oryza sativa ) to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops which often lack the adequate genomic resources.