Chloroplast genome characterization of Adenophora taquetii and comparative analysis with related Adenophora species

Abstract

Background: Adenophora taquetii is an endemic species of Jeju Island, Republic of Korea, and has medicinal and ornamental value. However, genomic resources for this species, particularly the chloroplast genome data, remain limited. Objective: We sequenced, assembled, and characterized the complete chloroplast genome of A. taquetii and compared it with those of other Adenophora species. Methods: Whole-genome sequencing data were generated using an Illumina HiSeq platform. Raw reads were preprocessed using Trimmomatic, mapped with BWA-MEM, and used for chloroplast genome assembly with NOVOPlasty, Fast-Plast, and GetOrganelle. Genome annotation was performed using GeSeq, comparative analysis was conducted using mVISTA in LAGAN mode, simple sequence repeats (SSRs) were identified using MISA, single-nucleotide polymorphism (SNP) matrices were generated using SAMtools, and phylogenetic analysis was performed using maximum likelihood and Bayesian inference based on aligned complete chloroplast genome sequences. Results: The chloroplast genome of A. taquetii was 161,772 bp long and exhibited the typical quadripartite structure of angiosperm chloroplast genomes, comprising a large single-copy (LSC) region (113,770 bp), a small single-copy (SSC) region (27,738 bp), and two inverted repeat (IR) regions (10,132 bp each). Comparative analysis revealed substantial variation in chloroplast genome size among related species, ranging from 157,851 bp in A. stricta to 218,673 bp in A. verticillata. In total, 143 genes were annotated in A. taquetii, including 96 protein-coding, 38 tRNA, and 9 rRNA genes. In addition, 25 SSRs and 1,161 SNPs were identified, and phylogenetic analysis supported a close relationship between A. taquetii and A. stricta. Conclusion: The complete chloroplast genome of A. taquetii provides a useful genomic resource for comparative chloroplast genomics, species identification, and phylogenetic studies within the genus Adenophora.