Sahin Ezgi Cabuk, Aydin Yildiz, Uncuoglu Ahu Altinkut
Department of Biology, Faculty of Science, Marmara University, Istanbul, Türkiye.
Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul, Türkiye.
Mol Biol Rep. 2025 Jun 12;52(1):584. doi: 10.1007/s11033-025-10602-3.
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.
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.
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.
秋水仙属植物属于秋水仙科，在全球具有重要的经济和药用价值。然而，准确鉴定该属内的许多物种具有挑战性。为了克服这一障碍，我们开展了一项研究，涉及来自土耳其不同地点的155个基因型，通过比较DNA条形码（具体使用matK、rbcL、trnH - psbA叶绿体DNA（cp - DNA）条形码区域）区分秋水仙属物种的有效性来进行评估。
经过PCR扩增和序列分析后，进行了多序列比对。检测到终止密码子并对序列进行了清理。进行了保守区域鉴定和GC含量分析。分析了物种鉴别情况（最佳匹配、最佳近匹配、所有物种条形码功能）。使用威尔科克森秩和检验来评估物种内和物种间遗传变异的差异。结果表明，trnH - psbA成为物种分化最有效的位点，与matK和rbcL相比，其种内距离（平均值：3.915）和种间距离（最大值：1.844）显著更高。matK显示出中等的鉴定成功率，而rbcL的表现最差。trnH - psbA在“最佳匹配”和“最佳近匹配”类别中表现出色；rbcL的错误鉴定率最高。
本研究强调了DNA条形码，特别是trnH - psbA位点，在区分秋水仙属物种方面的重要性。该位点显示出比matK和rbcL位点显著更高的遗传距离，突出了其在物种鉴定中的有效性。这些见解对于理解秋水仙属物种的遗传多样性以及加强未来分类学和保护工作的资源至关重要。
