Comparative plastome analysis of Schweinfurthia papilionacea and Schweinfurthia imbricata clarifying their taxonomic position in Lamiales.

The taxonomic placement of Schweinfurthia has been debated, with traditional classifications placing it in Scrophulariaceae while molecular evidence suggests affinity to Plantaginaceae. We sequenced and analyzed complete chloroplast genomes of Schweinfurthia papilionacea ( 153,238 bp) and S. imbricata (153,206 bp) to resolve this taxonomic uncertainty. Both genomes exhibited typical quadripartite structure with large single-copy regions (LSC: 83,703 - 83,769 bp), small single-copy regions (SSC:  18,087 - 18,089 bp), and inverted repeat regions (IRa/IRb:  25,680 - 25,723 bp each). We identified 132 - 133 unique genes in each species, including  88 protein-coding genes, 36 - 37 tRNA genes, and 4 rRNA genes. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with 42 taxa strongly supported (bootstrap support > 95%, posterior probability > 0.95) the placement of Schweinfurthia within Plantaginaceae, sister to the Antirrhineae tribe. Comparative genomic analysis revealed 98.7% sequence similarity between the two Schweinfurthia species and identified 10 variable sites. Codon usage analysis showed preference for A/T-ending codons (64.2% in S. papilionacea, 64.8% in S. imbricata). These comprehensive chloroplast genomic data provide definitive molecular evidence supporting the transfer of Schweinfurthia from Scrophulariaceae to Plantaginaceae, resolving a long-standing taxonomic controversy.