Comparative plastomes and phylogenetic relationships of Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon from plastomes and ITS.

Abstract

Phylogenomic approaches effectively minimize topological incongruences caused by heterogeneous gene evolutionary rates among lineages. The taxonomic status of Breynia, Glochidion, Synostemon, and Sauropus-whether they should be merged into Phyllanthus or retain their separate generic status-remains controversial. Moreover, these taxonomic revisions lack evidences from phylogenomic evidence. In this study, we assembled the first complete plastid genomes of Breynia disticha, Glochidion eriocarpum, G. hirsutum, G. lanceolarium, Phyllanthus fluitans, Sauropus androgynus, and Synostemon bacciformis to elucidate plastome evolutionary dynamics and resolve phylogenetic relationships among these five genera. The plastomes ranged in size from 152,927 to 157,460 bp, encoding a conserved set of 78 protein-coding genes, 35-36 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes, totaling 117-118 unique genes. Notably, 12 novel tRNA secondary structures were identified, potentially linked to lineage-specific adaptations. Structural variation at the LSC/IRb boundary, driven by IRb expansion-contraction dynamics, resulted in significant gene length and content heterogeneity. Divergence hotspot analyses identified petA-psbJ, rpl22, ndhF-rpl32, and ycf1 as hypervariable loci suitable for DNA barcoding applications. Positive selection signals were detected in five genes (ndhB, rpl33, rps15, ycf2, ycf4), suggesting their critical roles in environmental adaptation. Phylogenomic discordance between plastid and nuclear ribosomal DNA (nrDNA) datasets was pervasive across Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon, likely attributable to historical hybridization or chloroplast capture events. Given that the intergeneric boundaries among Breynia, Glochidion, Phyllanthus s.s., Sauropus, and Synostemon are obscure and that extensive cytonuclear discordance exists, we recommend accepting a broad circumscription of Phyllanthus.