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Background <p><i>Adenophora taquetii</i> 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.</p> Objective <p>We sequenced, assembled, and characterized the complete chloroplast genome of <i>A. taquetii</i> and compared it with those of other <i>Adenophora</i> species.</p> Methods <p>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.</p> Results <p>The chloroplast genome of <i>A. taquetii</i> was 161,772&#xa0;bp long and exhibited the typical quadripartite structure of angiosperm chloroplast genomes, comprising a large single-copy (LSC) region (113,770&#xa0;bp), a small single-copy (SSC) region (27,738&#xa0;bp), and two inverted repeat (IR) regions (10,132&#xa0;bp each). Comparative analysis revealed substantial variation in chloroplast genome size among related species, ranging from 157,851&#xa0;bp in <i>A. stricta</i> to 218,673&#xa0;bp in <i>A. verticillata</i>. In total, 143 genes were annotated in <i>A. taquetii</i>, 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 <i>A. taquetii</i> and <i>A. stricta</i>.</p> Conclusion <p>The complete chloroplast genome of <i>A. taquetii</i> provides a useful genomic resource for comparative chloroplast genomics, species identification, and phylogenetic studies within the genus <i>Adenophora</i>.</p>

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

  • 期刊论文

  • 发表日期：

    2026年6月15日

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  • Song-I Han,
  • Sheikh Mansoor,
  • Jiwon Kim,
  • Nur Azizah Arryanie Binti Morshidi,
  • Jae-Hoon Kim,
  • Kyung-Hwan Boo

摘要

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.