Comparative Chloroplast Genome Analysis in High-Yielding Pinus kesiya var. langbianensis

Abstract

Pinus kesiya var. langbianensis, a species endemic to Yunnan, China, accounts for over 90% of Yunnan’s Pinus resin production. However, there is significant variation in resin yield among individuals, and molecular markers for identifying high-yielding individuals have yet to be developed. In this study, a comparative analysis of complete chloroplast genomes of P. kesiya var. langbianensis was conducted to perform a phylogenetic analysis and differentiate high-yielding individuals. Both high-yielding (HY) and low-yielding (LY) trees possess a typical quadripartite structure, with respective genome sizes of 119,812 bp and 119,780 bp. Each chloroplast genome contains 112 genes, including 72 protein-coding genes, 36 tRNAs, and 4 rRNAs. Furthermore, HY and LY trees contain 30 and 34 SSRs, respectively, with mononucleotide repeats being predominant; neither genome exhibited trinucleotide or pentanucleotide repeats. Six highly variable regions were identified: trnI-CAU-psbA, trnH-GUG-trnI-CAU, rpl16, rrn4.5-rrn5, petG-petL, and psaJ. Phylogenetic analysis based on 72 Pinus species revealed that HY and LY trees clustered separately, with the HY tree grouping with P. kesiya and the LY tree with P. yunnanensis. This study provides a theoretical foundation for the molecular identification of high-yield P. kesiya var. langbianensis individuals and enriches the understanding of its phylogenetic relationships.