Genebank genomics allows greatly improved taxonomic correction for Capsicum spp. accessions using a novel automated classification method

Abstract

To maximise the benefit of exploiting genebank resources, accurate and complete taxonomic assignments are imperative. The rise of genebank genomics allows genetic methods to be used for this task, but these need to be largely automated since the number of samples dealt with is too great for efficient manual recategorisation, but no clearly optimal method has yet arisen. A recent landmark genebank genomic study sequenced over 10,000 accessions of peppers (Capsicum spp.), for which the exploitation of genebank material is of huge commercial, cultural, and scientific importance. This study resulted in precisely the type of dataset that will, in coming decades, be likely be produced for hundreds of plant taxa. The long-appreciated difficulties of pepper taxonomy are evident from the many obvious misclassifications noted in this and other studies, providing a perfect opportunity to simultaneously advance methods development in the area, to correct many genebank taxonomic assignments of pepper accessions, and to provide insights into pepper taxonomy in general. This paper aims to achieve these goals using an approach that combines several ideas from standard classification algorithms to create a highly flexible and customisable classifier that performs favourably when compared with key alternative methods. The various characteristics of different methods are discussed, and possible sensible alterations to pepper taxonomy based on the results are proposed for discussion by the community.