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

## TL;DR

This paper reports the complete chloroplast genome of a critically endangered tree species, offering insights into its evolution and aiding conservation efforts.

## Contribution

The study provides the first complete chloroplast genome of Lithocarpus yongfuensis and identifies a potential DNA barcode for species identification.

## Key findings

- The cp genome is 161,258 bp long with a typical quadripartite structure and 131 annotated genes.
- Phylogenetic analysis places L. yongfuensis in the Southeast China clade, closely related to three other Lithocarpus species.
- The rps16–trnK‐UUU intergenic spacer is identified as a potential DNA barcode for L. yongfuensis.

## Abstract

This study aims to delineate the chloroplast (cp) genome of the critically endangered Lithocarpus yongfuensis (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 Lithocarpus. 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 (rpoC2 and matK) showing evidence of positive selection. The rps16–trnK‐UUU intergenic spacer was identified as a potential DNA barcode for distinguishing L. yongfuensis. Phylogenetic analysis based on complete cp genomes placed L. yongfuensis within the Southeast China clade, closely allied to
L. crassifolius
, L. litseifolius, and
L. brevicaudatus
. These findings provide essential genomic resources for conservation genetics and offer insights into the adaptive evolution of this rare species.

We assembled and annotated the complete chloroplast genome of L. yongfuensis. The genome structure, gene content, and phylogenetic relationships were analyzed, providing new insights into the species' evolutionary history. These findings offer valuable genomic resources for future studies on taxonomy, conservation, and molecular breeding of L. yongfuensis.