Comparison of four DNA barcoding loci to distinguish between some Apiaceae family species

Abdelaziz et al. Beni-Suef Univ J Basic Appl Sci https://doi.org/10.1186/s43088-023-00457-7 (2024) 13:12 Beni-Suef University Journal of Basic and Applied Sciences Open Access RESEARCH Comparison of four DNA barcoding loci to distinguish between some Apiaceae family species Shaimaa A. Abdelaziz1, Khaled A. M. Khaled2 , Rania A. A. Younis1, Magdy A. Al‑Kordy3, Fotouh M. El‑Domyati1 and Mona M. Moghazee1*    Abstract Background The Apiaceae family is among the most significant plant families because it contains both beneficial and poisonous plants. Due to their morphological similarity, these harmless and lethal species are frequently con‑ founded. Cumin, fennel, and anise are the most prevalent members of the family Apiaceae in Egypt. Members of this family are routinely used as medical surrogates, so it is crucial that they are correctly identified and distinguished. DNA barcoding is a molecular technique used for identifying species and reconstructing phylogenetic trees. Results Six plants from this family were chosen for this study due to their medicinal importance, and four DNA bar‑ coding loci (rbcL, matK, trnH-psaA, and ITS) were used to identify them. The amplicons were sequenced, and the com‑ parative analysis was conducted between the sequences evaluated and the most significant Blast results. The DNA rbcL, trnH-psaA, and ITS barcodes exhibited similar amplicons among the six species of Apiaceae, while the trnH-psaA barcode exhibited different amplicons among the Apiaceae. Maximum likelihood approach was used to calculate the genetic distance between the sex species of Apiaceae. The most significant findings were that the one from four DNA barcoding was able to distinguish between distinct species and confirm their evolutionary belonging to this family. Conclusions The current study concludes that trnH-psbA and ITS DNA identifiers can be used to accurately identify, differentiate, and record Apiaceae species, while the rbcl DNA barcode appears to have fallen short of its intended purpose. So, the data that come from DNA barcodes could be used for the biodiversity assessment and the similarities between hazardous and commercial plants to resolve some of these deficiencies. Keywords Apiaceae family, DNA barcoding markers (rbcL, matK, trnH-psbA and ITS), Phylogenetics *Correspondence: Mona M. Moghazee 1 Genetic Department, Faculty of Agriculture, Ain Shams University, Hadayek Shoubra, P.O. Box 68, Cairo 11241, Egypt 2 Genetics Department, Faculty of Agriculture, Beni-Suef University, Beni Suef 62513, Egypt 3 Genetics and Cytology Department, Biotechnology Research Institute, National Research Centre, El Dokki, Giza, Egypt 1 Background To keep the world’s healthcare system running, we need medicinal plants. Herbal remedies have been shown to cure a wide range of illnesses and disorders, sometimes with fewer side effects and at a lower cost than pharmaceutical options [26]. It is estimated that there are between 3600 and 3751 different species of plants in the Apiaceae family [24]. Many important phytochemicals, including phenolic compounds and flavonoids, are found in the Apiaceae family. Flavonoids’ antiviral, anticancer, antioxidant, and anti-inflammatory characteristics are © The Author(s) 2023. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Abdelaziz et al. Beni-Suef Univ J Basic Appl Sci (2024) 13:12 only a few of their many positive health effects. In addition, they shield the heart and the brain from damage. Variations in the effects of flavonoids on certain cellular activities have been reported [29] but more research is needed. Essential oils, extracted from various species in this family, have approximately 760 different chemical classes with substantial therapeutic potential. Coriander seed oil has a high concentration of petroselinic acid. The European Commission approved its sale as a novel food additive in 2014 [20] in accordance with Regulation (EC) No 258/97 of the European Parliament and Council. This family has a lot of plants, for example, Parsley (Petroselinum crispum L.), anise (Pimpinella anisum), coriander (Coriandrum sativum), cumin (Cuminum cyminum L.), dill (Anethum graveolens Mill.), fennel (Foeniculum vulgare Mill.), and caraway (Carum carvi L.) [10]. The presence of volatile chemicals is a telltale sign of these plants, which have long been thought to have somewhat negative medicinal effects on the body and mind. However, there are some dangerous members of the Apiaceae family. Hemlock water-dropwort (Oenanthe crocata L.), fool’s parsley (Aethusa cynapium L.), poison hemlock (Conium maculatum L.), and water hemlock (Cicuta virosa L.) are some of the most well-known examples of these plants. Toxic species are sometimes mistaken for fragrant food species because of their similar chemical makeup and structure [21]. Traditional approaches to biodiversity assessment are time-consuming and rely on taxonomic data, which is becoming scarcer. Recent advances like molecular methods are useful tools for identifying certain clonal variations, and establishing genetic stability [1, 2, 11–14, 23]. As reported by [6], DNA barcoding may one day offer a faster and more accurate alternative to traditional methods of estimating species diversity that rely on expert field identification personnel. DNA barcoding has had a significant favorable effect on biodiversity identification and categorization [17]. DNA barcodes have two main uses: (1) to determine the species of an unidentified material and (2) to help researchers discover new species by screening thousands of copies of a small number of reference genes. The chloroplast genome, which includes all the DNA sequences in a single plastid, has more information than any singlelocus marker for identifying and classifying plant species. DNA barcodes that make use of chloroplast genomes actively to distinguish between plant species are an important area of research and development [30]. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) has proposed using ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and maturase K (matK), both located in the plastid genome, as (...truncated)