Journal Article

Phylogenetic analysis of Asiatic species in the tropical genus Beilschmiedia (Lauraceae)

Xin, Peiyao, Zhu, Wen, Ma, Jurong, Tan, Yunhong, Song, Yu

2025

Overview

The tropial genus Beilschmiedia , comprising over 250 species worldwide, includes approximately 40 species distributed in the northern tropical forests of Asia. However, the phylogenetic relationships among these Asiatic Beilschmiedia species remain incompletely understood. In this study, we sequenced and assembled complete chloroplast genomes from six Asiatic Beilschmiedia species, including five from China and one from Indonesia. The genomes range in size from 158,275 to 158,620 bp and exhibit a typical quadripartite structure, similar to other basal Lauraceae species. We identified 116 to 122 simple sequence repeats (SSRs) and 19 to 28 dispersed repeats within the genomes. The relative synonymous codon usage (RSCU) of 79 protein-coding genes exhibited minimal variation. Notably, the boundary genes rpl23 and ycf1 displayed varying degrees of expansion and contraction, along with incomplete replication phenomena. Using a sliding window approach, we constructed a coalescent tree with ASTRAL software to analyze the phylogenetic relationships. The resulting main topology was highly consistent with the Maximum Likelihood (ML) and Bayesian inference (BI) analyses, clearly dividing the Asiatic core Beilschmiedia into two distinct groups: Group A and Group B. Group A showed an extremely low nucleotide diversity (π) value of 0.00063, while Group B exhibited 2.79-fold higher diversity. The highly variable regions trnS - trnG and rpl32 - trnL are proposed as molecular markers for distinguishing between Groups A and B. Furthermore, we identified seven additional highly variable regions: ndhF , ndhF - rpl32 , rpl2 , rpl2 - trnH , rpl32 , rps15 - ycf1 , and ycf1 . These regions may serve as potential molecular markers for the Asiatic Beilschmiedia species. These findings provide new insights into the phylogenetic relationships among Asiatic Beilschmiedia species, highlighting the potential of specific molecular markers in future research.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Bayesian analysis / Beilschmiedia / Beilschmiediineae / Biogeography / Biomedical and Life Sciences / Candidate barcode / Chloroplast genome / Chloroplasts / Codon / Comparative genomics / Diseases and pests / DNA sequencing / Genes / Genetic aspects / Genome, Chloroplast / Genomes / Growth / Lauraceae / Lauraceae - classification / Lauraceae - genetics / Laurel / Life Sciences / Microarrays / Microbial Genetics and Genomics / Microsatellite Repeats / Nucleotide sequencing / Nucleotides / Phylogenetic relationship / Phylogenetics / Phylogeny / Plant Genetics and Genomics / Proteins / Proteomics / Simple sequence repeats / Species / Statistical inference / Topology / Transfer RNA / Tropical forests