The Complete Chloroplast Genome of Ficus gasparriniana var. laceratifolia Reveals Discordance Between Morphology-Based Classification and Plastid Phylogeny

Background/Objectives: Ficus gasparriniana var. laceratifolia (H. Lév. & Vaniot) Corner is treated as a variety of F. gasparriniana and placed in Ficus subg. Ficus on morphological grounds, but complete plastome evidence for its plastid phylogenetic placement has been lacking. We assembled and analyzed its chloroplast genome to evaluate this morphology-based placement using plastid genomic evidence and to expand genomic resources for the genus. Methods: The plastome was assembled from paired-end reads using GetOrganelle and subsequently annotated. We characterized its genome architecture, simple sequence repeats (SSRs), codon-usage bias, inverted repeat (IR) junctions, and nucleotide diversity after standardizing sequence start positions and small single-copy (SSC) region orientation. Plastid phylogenetic relationships were inferred from four single-IR datasets: whole-plastome, coding, non-coding, and partitioned. Results: The 160,476-bp plastome exhibited the typical quadripartite structure and contained 110 unique genes. Its repeat composition and preference for A/U-ending codons were consistent with an AT-rich plastome, and 61 SSRs and five candidate variable regions represented potential marker resources for future Ficus studies. In all four phylogenetic datasets, F. gasparriniana var. laceratifolia was consistently grouped with F. pumila with maximum ultrafast bootstrap support (UFBoot = 100), conflicting with its morphology-based classification. Approximately unbiased (AU) tests rejected the sampled morphology-based constraint in every dataset, indicating that this morphology–plastid discordance was robust to dataset choice. Conclusions: This plastome provides a valuable genomic resource and reveals robust discordance between morphology-based classification and plastid phylogenetic placement. These findings provide a foundation for future nuclear-genomic and population-level tests of the alternative evolutionary scenarios underlying this discordance.