Cost-Effective Approaches to Elucidate Intergeneric Relationships of Plants: Utilizing Multiple Conserved Nuclear Genes and Whole Chloroplast Genomes

The chloroplast (cp) genome sequence, which is a widely used and affordable tool, is utilized for plant classification. However, its effectiveness remains unclear. This study contrasts the phylogenetics derived from whole cp genome sequences with those obtained using Read2Tree, another cost-efficient method capable of extracting multiple conserved nuclear gene sequences. To explore this topic, we focused on the Aurantioideae subfamily, which includes Citrus and its relatives, where phylogenetic trees based on nuclear DNA from high-throughput sequencing are available. In intergeneric relationships, phylogenetic trees generated with Read2Tree were consistent with previous high-precision nuclear DNA-based trees but differed from those generated using whole cp genome sequences. Thus, even in plants in which past polyploidization or hybridization between distantly related species had not been previously assumed, the two phylogenetic trees did not coincide. Both techniques present unique pros and cons, leaving it unclear which technique is superior for understanding a plant's evolutionary history. However, integrating both approaches is more useful for effectively classifying plants than it is for understanding the unified evolutionary history based on phylogenetics. We propose that integrating these two cost-effective methods by utilizing the same raw sequencing data is a mainstream approach in DNA-based plant classification. ### Competing Interest Statement The authors have declared no competing interest.