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<p><i>Crinum br</i><i>achynema</i> (Amaryllidaceae) is an endemic species of the Western Ghats, India. It has high medicinal value and contains galanthamine (GAL) alkaloid, an anti-Alzheimer drug. The development of molecular markers with high-discrimination ability for <i>C. brachynema</i> is important to make species recognition easier and understand phylogeny and therapeutic values. In this study, we successfully assembled and characterized the complete chloroplast (cp.) genome of <i>C. brachynema</i>, revealing a genome of 158,570 base pairs with a typical tetrad structure. The genome contains 113 unique genes, including 79 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. There were 47 long repeats and 74 simple sequence repeats (SSRs) in the cp. genome that were mostly located in intergenic spacer (IGS). Multiple genome alignments demonstrated a high degree of genomic similarity among seven Amaryllidaceae species with the large single copy (LSC) region exhibiting the most variability. The study identified common hotspot regions, such as <i>rps</i>16-<i>trn</i>Q-UUG, <i>ndh</i>F, <i>rpl</i>32-<i>trn</i>L-UAG, and <i>ycf</i>1 that are shared among Amaryllidaceae species. Phylogenetic analysis revealed a close relationship between <i>C. brachynema</i> and <i>C. asiaticum</i> var. <i>pedunculatum</i>. The outcomes of this study can be applied to epidemiological genetics research enhancing our understanding of cp. genomics. Additionally, this study would&#xa0;serve as a valuable resource for species identification, molecular breeding, and evaluating interspecific diversity within the <i>Crinum</i> genus.</p>

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Comparative Chloroplast Genomics and Phylogeny of Crinum brachynema (Amaryllidaceae): A Narrow Endemic Geophyte of the Western Ghats of India

  • 期刊论文

  • 发表日期：

    2025年2月13日

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  • Asif S. Tamboli,
  • Priya E. Shelke,
  • Rupali N. Chougule,
  • Jin-Suk Youn,
  • Yeon-Sik Choo,
  • Jae Hong Pak,
  • Manoj M. Lekhak

摘要

Crinum brachynema (Amaryllidaceae) is an endemic species of the Western Ghats, India. It has high medicinal value and contains galanthamine (GAL) alkaloid, an anti-Alzheimer drug. The development of molecular markers with high-discrimination ability for C. brachynema is important to make species recognition easier and understand phylogeny and therapeutic values. In this study, we successfully assembled and characterized the complete chloroplast (cp.) genome of C. brachynema, revealing a genome of 158,570 base pairs with a typical tetrad structure. The genome contains 113 unique genes, including 79 protein-coding genes (CDS), 30 tRNA genes, and 4 rRNA genes. There were 47 long repeats and 74 simple sequence repeats (SSRs) in the cp. genome that were mostly located in intergenic spacer (IGS). Multiple genome alignments demonstrated a high degree of genomic similarity among seven Amaryllidaceae species with the large single copy (LSC) region exhibiting the most variability. The study identified common hotspot regions, such as rps16-trnQ-UUG, ndhF, rpl32-trnL-UAG, and ycf1 that are shared among Amaryllidaceae species. Phylogenetic analysis revealed a close relationship between C. brachynema and C. asiaticum var. pedunculatum. The outcomes of this study can be applied to epidemiological genetics research enhancing our understanding of cp. genomics. Additionally, this study would serve as a valuable resource for species identification, molecular breeding, and evaluating interspecific diversity within the Crinum genus.