Structural Characteristics, Comparative Analyses, and Conservation Significance of the Complete Chloroplast Genome of the Critically Endangered <i>Lithocarpus yongfuensis</i> (Fagaceae)

This study aims to delineate the chloroplast (cp) genome of the critically endangered <i>Lithocarpus yongfuensis</i> (Fagaceae), with fewer than 10 wild individuals known. Genomic information for this species is scarce, hindering conservation strategies. We sequenced, assembled, and annotated its complete cp genome, analyzed its structure, and conducted comparative and phylogenetic analyses within the genus <i>Lithocarpus</i>. The cp genome is 161,258 bp in length, exhibiting a typical quadripartite structure and containing 131 annotated genes (86 protein-coding, 8 rRNA, and 37 tRNA genes). Comparative analysis revealed a conserved genomic architecture across the genus, with two protein-coding genes (<i>rpoC2</i> and <i>matK)</i> showing evidence of positive selection. The <i>rps16-trnK-UUU</i> intergenic spacer was identified as a potential DNA barcode for distinguishing <i>L. yongfuensis</i>. Phylogenetic analysis based on complete cp genomes placed <i>L. yongfuensis</i> within the Southeast China clade, closely allied to <i>L. crassifolius</i>, <i>L. litseifolius</i>, and <i>L. brevicaudatus</i>. These findings provide essential genomic resources for conservation genetics and offer insights into the adaptive evolution of this rare species.