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<p><i>Crepidium acuminatum</i> (D. Don) Szlach., commonly known as Jivaka, is an endangered Himalayan orchid, medicinally revered as “Astavarga” in Ayurveda. In order to address taxonomic ambiguities and support conservation efforts, we sequenced and characterized the complete chloroplast genome of this species and compared it with that of related taxa. The plastome was 158,707&#xa0;bp in length, displaying the typical quadripartite structure with 134 genes (87 protein-coding, 39 tRNA, and eight rRNA) and a GC content of 36.9%. Comparative analyses revealed overall structural conservation, but variation in IR/LSC/SSC junctions, SSR profiles, and sequence divergence. Sliding window analysis identified three intraspecific hypervariable regions (<i>trnS–GCU–trnG–UCC, clpP–psbB</i>, and <i>ycf1</i>) and eight interspecific hotspots (<i>matK–trnK</i>, <i>trnS-GCU-trnG-UCC</i>, <i>rpoB–trnC</i>, <i>petG–psaJ</i>, <i>petD–rpoA, ycf1, ndhD–ccsA</i>, and <i>rpl32–ndhF</i>), highlighting their potential as species-specific DNA barcodes and population markers. Codon usage bias and repeat structures provide further genomic signatures relevant to population genetics. Phylogenomic analyses based on 40 chloroplast genomes confirmed the monophyly of <i>Crepidium</i> and resolved the placement of <i>C. acuminatum</i> within Malaxidinae. This is the first report on complete chloroplast genome of this endangered Himalayan orchid.</p>

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Complete chloroplast genome of the endangered Himalayan orchid Crepidium acuminatum: insights into taxonomy, DNA barcoding, and phylogeny

  • 期刊论文

  • 发表日期：

    2026年4月17日

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  • Narender Kumar,
  • Vandana Jaiswal

摘要

Crepidium acuminatum (D. Don) Szlach., commonly known as Jivaka, is an endangered Himalayan orchid, medicinally revered as “Astavarga” in Ayurveda. In order to address taxonomic ambiguities and support conservation efforts, we sequenced and characterized the complete chloroplast genome of this species and compared it with that of related taxa. The plastome was 158,707 bp in length, displaying the typical quadripartite structure with 134 genes (87 protein-coding, 39 tRNA, and eight rRNA) and a GC content of 36.9%. Comparative analyses revealed overall structural conservation, but variation in IR/LSC/SSC junctions, SSR profiles, and sequence divergence. Sliding window analysis identified three intraspecific hypervariable regions (trnS–GCU–trnG–UCC, clpP–psbB, and ycf1) and eight interspecific hotspots (matK–trnK, trnS-GCU-trnG-UCC, rpoB–trnC, petG–psaJ, petD–rpoA, ycf1, ndhD–ccsA, and rpl32–ndhF), highlighting their potential as species-specific DNA barcodes and population markers. Codon usage bias and repeat structures provide further genomic signatures relevant to population genetics. Phylogenomic analyses based on 40 chloroplast genomes confirmed the monophyly of Crepidium and resolved the placement of C. acuminatum within Malaxidinae. This is the first report on complete chloroplast genome of this endangered Himalayan orchid.