The Indian Trithuria (Hydatellaceae): complete plastid genome of Trithuria konkanensis, comparative plastome evolution and phylogenomics of the ANA grade angiosperms

Abstract Background Hydatellaceae (Nymphaeales), represented by the single genus Trithuria , is an early-diverging angiosperm lineage within the Amborellales–Nymphaeales–Austrobaileyales (ANA) grade. Trithuria konkanensis is the only species of the genus reported from India; however, its plastid genome remains unexplored. Given its strategic phylogenetic position and importance for elucidating the early evolution and diversification of flowering plants, characterization of the plastid genome of T. konkanensis is essential. Such genomic information will provide valuable insights into plastid genome variation within Hydatellaceae and across ANA grade angiosperms, while also contributing to a better understanding of their phylogenetic relationships. Results The plastid genome of Trithuria konkanensis exhibited a typical quadripartite structure comprising 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The clpP1 gene lacked introns. The plastid genome was 179,088 bp in length, with large single-copy (LSC) and small single-copy (SSC) regions of 68,412 and 6,052 bp, respectively, and an inverted repeat (IR) region of 52,312 bp. A total of 33 protein-coding genes were duplicated within the IR region. Gene-wise nucleotide diversity (π = 0.00000–0.08753) revealed substantial variation across the plastome. The genes clpP1 (0.08753), ndhK (0.07136), rpl32 (0.05338), ccsA (0.05278), ndhF (0.04962), accD (0.04444), and ycf1 (0.03850) exhibited relatively high π values, identifying them as potential molecular markers for phylogenetic and comparative analyses. Among the intergenic spacers, rps12 / ycf1 showed the highest sequence variability, followed by ndhC / atpE , ycf4 / cemA , psbE / petL , ndhF / rpl32 , and rpl32 / ccsA . Phylogenetic analyses based on protein-coding genes, the complete plastome, and nrITS sequences yielded congruent topologies, with T. konkanensis recovered as sister to T. lanterna , while T. filmentosa was recovered as sister to T. inconspicua . Conclusions Among the ANA grade angiosperms, Hydatellaceae possess the largest plastomes (~ 180 kb). This study expands the plastome resources available for Hydatellaceae, providing valuable data for a better understanding of plastome evolution and the evolutionary history of the family. Broader taxon sampling will be essential to determine the extent of plastome diversity and structural variation within Hydatellaceae.