Assembly and characterization of the first mitochondrial genome of Phyllanthaceae: a case study of the ornamental aquatic plant Phyllanthus fluitans.

Phyllanthus fluitans, a member of the Phyllanthaceae, is a unique free-floating aquatic species exhibiting considerable ornamental value. In this study, we assembled the mitochondrial genome of P. fluitans representing the first mitochondrial genome report of the Phyllanthaceae family. The mitogenome comprises two circular chromosomes spanning 230,785 bp (chromosome 1) and 143,421 bp (chromosome 2), collectively harboring 32 protein-coding genes (PCGs), 25 tRNA genes, four rRNA genes, and one pseudogene. Structural analyses identified 118 simple sequence repeats (SSRs), 18 tandem repeats, and 191 dispersed repeats distributed throughout the mitochondrial genome. RNA editing prediction revealed 394 putative editing sites, with notable enrichment in NADH dehydrogenase genes. Critical modifications included start codon conversion in atp6 (ACG → AUG) and stop codon alterations in ccmFc (CGA → UGA) and rpl16 (UAG → UAA). Comparative genomic analyses detected 50 chloroplast-derived DNA fragments, constituting 6.0% of the mitogenome, indicative of historical plastid-to-mitochondrion transfer events. Codon usage bias analysis demonstrated phenylalanine (Phe) as the most frequently encoded amino acid, with selection pressure identified as the predominant driver of codon usage patterns. Phylogenetic reconstruction employing 22 conserved PCGs resolved intra-ordinal relationships among eight Malpighiales families, revealing Phyllanthaceae sister to Salicaceae with robust nodal support. This study advances the utilization of mitochondrial genomes for elucidating phylogenetic relationships within Phyllanthus while providing essential genomic resources for future comparative mitogenomic investigations in Phyllanthaceae. The structural complexity revealed through repeat analyses and RNA editing patterns offers novel insights into plant mitochondrial genome evolution.