Anatomy and the chloroplast genome of Bischofia plants reveal important phylogenetic relationship and the genetic diversity in phyllanthaceae.

Plants of the genus Bischofia (Phyllanthaceae) possess significant ornamental and cultural value and are widely used in urban landscaping. However, their morphological similarities make accurate species identification challenging. Although chloroplast genome sequences have become a crucial source of phylogenetic information for plant classification, the chloroplast genomes of Bischofia had not been deciphered within a comparative framework. In this study, we described key leaf anatomical traits and sequenced, assembled, and annotated the complete chloroplast genomes of Bischofia javanica and B. polycarpa to clarify their taxonomic boundaries. Anatomical investigation revealed significant divergence in leaf thickness, palisade mesophyll structure, and vascular traits. Both assembled chloroplast genomes displayed a typical circular quadripartite structure, with lengths of 162,495 bp and 162,228 bp, respectively. The B. javanica chloroplast genome contains 83 protein-coding genes, 8 rRNA genes, and 37 tRNA genes, while B. polycarpa contains 84 protein-coding genes, 8 rRNA genes, and 38 tRNA genes. Notably, the rpoC2 gene was present in B. polycarpa but absent in B. javanica-a condition validated by PCR using multiple individuals and primer sets and unique within Phyllanthaceae. Codon usage was biased toward A/U endings. Genome comparison revealed high nucleotide diversity in rpl22, ycf1, matK, clpP, and ndhF, suggesting their potential as DNA barcodes. Phylogenetic analysis confirmed a close relationship between the two Bischofia species and placed Bischofia, Baccaurea, and Antidesma in a distinct clade within Phyllanthaceae. This study provides the first integrated anatomical and chloroplast genomic resources for Bischofia. The complete chloroplast genomes, along with identified highly variable regions and the unique absence of rpoC2 in B. javanica, offer valuable tools for species identification, phylogenetic reconstruction, and understanding genome evolution in Phyllanthaceae.