Scholarlink

Background <p>The genus <i>Colchicum</i>, belonging to the family Colchicaceae, holds significant economic and medicinal value globally. However, precise identification of many species within this genus is challenging. In order to address this obstacle, we carried out a study involving 155 genotypes from various locations in Türkiye to assess the effectiveness of DNA barcoding, specifically utilizing the <i>matK</i>, <i>rbcL</i>, <i>trnH-psbA</i> chloroplast DNA (cp-DNA) barcode regions, by comparing their effectiveness in distinguishing <i>Colchicum</i> species.</p> Methods and results <p>Following PCR amplification and sequence analysis, multiple sequence alignment was conducted. Stop codons were detected and sequences were cleaned. Conserved region identification, and GC content analysis were carried out. Species discrimination was analysed (best match, best close-match, all species barcodes functions). The Wilcoxon Ranked Sum test was used to assess differences in genetic variation within and between species. As a result, <i>trnH-psbA</i> emerged as the most effective locus for species differentiation, with significantly higher intra-specific (mean: 3.915) and inter-specific distances (maximum: 1.844) compared to <i>matK</i> and <i>rbcL</i>. <i>matK</i> displayed moderate identification success rates, while <i>rbcL</i> had the lowest performance. <i>trnH-psbA</i> excelled in the ‘best match’ and ‘best close match’ categories; <i>rbcL</i> recorded the highest incorrect identification rates.</p> Conclusion <p>This study highlights the importance of DNA barcoding, specifically the <i>trnH-psbA</i> locus, in distinguishing <i>Colchicum</i> species. The locus shows significantly higher genetic distances than the <i>matK</i> and <i>rbcL</i> loci, underscoring its effectiveness for species identification. These insights are crucial for comprehending the genetic diversity of <i>Colchicum</i> species and enhancing resources for future taxonomy and conservation efforts.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Assessing the accuracy of cp-DNA barcodes in Colchicum species identification

  • 期刊论文

  • 发表日期：

    2025年6月12日

查看全文
  • Ezgi Cabuk Sahin,
  • Yildiz Aydin,
  • Ahu Altinkut Uncuoglu

摘要

Background

The genus Colchicum, belonging to the family Colchicaceae, holds significant economic and medicinal value globally. However, precise identification of many species within this genus is challenging. In order to address this obstacle, we carried out a study involving 155 genotypes from various locations in Türkiye to assess the effectiveness of DNA barcoding, specifically utilizing the matK, rbcL, trnH-psbA chloroplast DNA (cp-DNA) barcode regions, by comparing their effectiveness in distinguishing Colchicum species.

Methods and results

Following PCR amplification and sequence analysis, multiple sequence alignment was conducted. Stop codons were detected and sequences were cleaned. Conserved region identification, and GC content analysis were carried out. Species discrimination was analysed (best match, best close-match, all species barcodes functions). The Wilcoxon Ranked Sum test was used to assess differences in genetic variation within and between species. As a result, trnH-psbA emerged as the most effective locus for species differentiation, with significantly higher intra-specific (mean: 3.915) and inter-specific distances (maximum: 1.844) compared to matK and rbcL. matK displayed moderate identification success rates, while rbcL had the lowest performance. trnH-psbA excelled in the ‘best match’ and ‘best close match’ categories; rbcL recorded the highest incorrect identification rates.

Conclusion

This study highlights the importance of DNA barcoding, specifically the trnH-psbA locus, in distinguishing Colchicum species. The locus shows significantly higher genetic distances than the matK and rbcL loci, underscoring its effectiveness for species identification. These insights are crucial for comprehending the genetic diversity of Colchicum species and enhancing resources for future taxonomy and conservation efforts.