Bipartite mitogenome of Fargesia angustissima reveals repeat-mediated structural dynamics, inter-organellar DNA transfers, and phylogenetic discordance

BACKGROUND: As an endemic bamboo and a critical dietary staple for the endangered giant panda, Fargesia angustissima T. P. Yi is integral to the ecological stability of Western Sichuan's forest ecosystems. Nevertheless, the absence of a complete mitogenome has constrained investigations into its complex genomic architecture, evolutionary history, and the genetic basis underlying the montane adaptation. RESULTS: Using a hybrid sequencing strategy (BGI short reads and PacBio HiFi long reads), we de novo assembled and characterized the bipartite mitogenome of F. angustissima (429,279 bp, 44.18% GC content). The mitogenome encodes a conserved repertoire of 37 unique protein-coding genes (PCGs), exhibiting a pronounced A/U-ending codon bias driven by directional mutation pressure. Long-read mapping validated that a 7,368 bp palindromic repeat (R1) maintained major bipartite isomers (45.45% recombinant frequency), while 39 tetrameric Simple Sequence Repeats (SSRs) and 298 dispersed repeat pairs mediate localized structural variations. To counteract sequence-level mutational drift, 488 C-to-U RNA-editing sites impose strict functional stringency. These modifications predominantly convert hydrophilic Ser/Pro to hydrophobic Leu (42.0%) to ensure the proper membrane integration of respiratory complexes, while also generating obligate stop codons in atp6, atp9, and ccmFC. Moreover, we identified 27 plastid-derived sequences (MTPTs) spanning 20.151 kb, demonstrating an asymmetric intracellular DNA migration pattern; the plastid Large Single Copy (LSC) region (e.g., MTPT27) serves as an evolutionary hotspot for sequence transfer, contrasting with the structural conservatism of the Inverted Repeat (IR) regions (MTPT1, MTPT11, and MTPT12). Despite high sequence identity (> 99.8%) across the Bambusoideae, synteny analyses revealed extensive structural rearrangements. Subsequent phylogenetic reconstruction uncovered significant inter-organellar topological conflicts, providing genomic evidence for historical reticulate evolution and incomplete lineage sorting (ILS) during the rapid diversification of the Fargesia genus. CONCLUSIONS: The F. angustissima mitogenome exemplifies a paradigm of structural plasticity, post-transcriptional constraint, and phylogenetic discordance. By overcoming the low nucleotide diversity barrier inherent to temperate bamboos, a structurally and functionally derived marker framework was established. The genomic reference and the associated candidate loci provide a molecular blueprint for non-destructive population genetics and data-driven conservation within giant panda habitats.