Making the most out of it: shallow genome-skimming possibilities for the systematics of prickly lineages of Solanum (Solanaceae)

Abstract

PremiseGenome skimming (GS) is a cost-effective approach for plant phylogenomics, but its ability to recover informative datasets from different genomic compartments, particularly genome-wide SNPs, remains poorly explored in Solanum. MethodsWe evaluated shallow GS for phylogenetic inference in South American prickly Solanum lineages by recovering plastid, mitochondrial, and nuclear datasets, including coding regions and genome-wide SNPs. Phylogenies were inferred using maximum-likelihood and coalescent approaches under different SNP filtering strategies. ResultsGS successfully recovered complete plastomes, organellar coding regions, and large SNP datasets, but failed to consistently assemble mitochondrial genomes or recover low-copy nuclear genes. SNP-based analyses, especially from the nuclear genome, produced stable, well-supported phylogenies that were largely congruent across inference methods. In contrast, coding-region datasets, particularly from the mitochondrial genome, showed greater topological discordance, revealing cytonuclear conflict. DiscussionOur results demonstrate that shallow GS is an effective strategy for generating informative SNP datasets for phylogenetic inference in Solanum, despite limitations in recovering complete mitochondrial genomes and low-copy nuclear loci. SNP-based analyses substantially expand the phylogenetic potential of GS, providing a practical and cost-effective alternative for systematic studies.