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<p>Morphology-based taxonomy was extensively used to distinguish <i>Dryopteris</i> species. However, resolving species complex is still problematic using existing methods. The current study employed DNA barcoding to validate the effectiveness of plastid DNA barcode markers, specifically using the coding regions <i>rbcL</i>, <i>mat</i>K, <i>psbA,</i> and <i>atpB</i> loci, among the 12 <i>Dryopteris</i> species to resolve the complexity. Computational approaches were used to annotate, analyse, and calculate the DNA sequence composition of each DNA marker using different parameters. The results indicated that the nucleotide variability was high in <i>matK</i> and <i>atpB</i> which increases the resolving power among <i>Dryopteris</i> species. The <i>psbA</i> and <i>rbcL</i> markers showed low differentiation and were not suitable for distinguishing species. The phylogenetic tree was constructed using the maximum-likelihood method to understand the genetic relationship among the 12 <i>Dryopteris</i> species. The gene tree constructed using <i>matK</i> and <i>atpB</i> DNA barcodes resolved all the 12 species, such as <i>D. championii, D. crassirhizoma, D. decipiens, D. deparioides, D. filix-mas, D. fragrans, D. fulgens, D. gaoligongensis, D. goeringiana, D. podophylla, D. sieboldii, D. sinonepalensis, D. sparsa,</i> and <i>D. yoroii</i>. In contrast, the <i>psb</i>A and <i>rbcL</i> locus demonstrated less efficacy in differentiating the species. The resolving power was significantly enhanced when using the <i>matK</i> and <i>atpB</i> markers making it a more suitable DNA barcode for assessing genetic relatedness <i>Dryopteris</i> at the species level. This comprehensive study provides the valuable insights on selection of appropriate DNA barcode loci for species authentication and understanding the phylogenetic relationships within theDryopteridaceae.</p>

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In-silico validation of plastid DNA barcodes to delineate the wood ferns Dryopteris (Adanson, 1763)

  • 期刊论文

  • 发表日期：

    2025年7月7日

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  • Krishnamoorthy Devanathan,
  • Stalin Nithaniyal,
  • Raju Balaji

摘要

Morphology-based taxonomy was extensively used to distinguish Dryopteris species. However, resolving species complex is still problematic using existing methods. The current study employed DNA barcoding to validate the effectiveness of plastid DNA barcode markers, specifically using the coding regions rbcL, matK, psbA, and atpB loci, among the 12 Dryopteris species to resolve the complexity. Computational approaches were used to annotate, analyse, and calculate the DNA sequence composition of each DNA marker using different parameters. The results indicated that the nucleotide variability was high in matK and atpB which increases the resolving power among Dryopteris species. The psbA and rbcL markers showed low differentiation and were not suitable for distinguishing species. The phylogenetic tree was constructed using the maximum-likelihood method to understand the genetic relationship among the 12 Dryopteris species. The gene tree constructed using matK and atpB DNA barcodes resolved all the 12 species, such as D. championii, D. crassirhizoma, D. decipiens, D. deparioides, D. filix-mas, D. fragrans, D. fulgens, D. gaoligongensis, D. goeringiana, D. podophylla, D. sieboldii, D. sinonepalensis, D. sparsa, and D. yoroii. In contrast, the psbA and rbcL locus demonstrated less efficacy in differentiating the species. The resolving power was significantly enhanced when using the matK and atpB markers making it a more suitable DNA barcode for assessing genetic relatedness Dryopteris at the species level. This comprehensive study provides the valuable insights on selection of appropriate DNA barcode loci for species authentication and understanding the phylogenetic relationships within theDryopteridaceae.