Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae)
DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) me...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2025-01-01
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| Series: | Plant Diversity |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468265924001677 |
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| author | Yanlei Liu Kai Chen Lihu Wang Xinqiang Yu Chao Xu Zhili Suo Shiliang Zhou Shuo Shi Wenpan Dong |
| author_facet | Yanlei Liu Kai Chen Lihu Wang Xinqiang Yu Chao Xu Zhili Suo Shiliang Zhou Shuo Shi Wenpan Dong |
| author_sort | Yanlei Liu |
| collection | DOAJ |
| description | DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification. |
| format | Article |
| id | doaj-art-5d700ee0a379433ca613ac48cb78aa40 |
| institution | Kabale University |
| issn | 2468-2659 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Plant Diversity |
| spelling | doaj-art-5d700ee0a379433ca613ac48cb78aa402025-02-12T05:31:34ZengKeAi Communications Co., Ltd.Plant Diversity2468-26592025-01-01471115126Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae)Yanlei Liu0Kai Chen1Lihu Wang2Xinqiang Yu3Chao Xu4Zhili Suo5Shiliang Zhou6Shuo Shi7Wenpan Dong8School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, ChinaSchool of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, ChinaSchool of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, ChinaSchool of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, ChinaState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; Corresponding author.College of Life Science, Hebei Normal University, Shijiazhuang 050024, China; Corresponding author.School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China; Corresponding author.DNA barcoding has been extensively used for species identification. However, species identification of mixed samples or degraded DNA is limited by current DNA barcoding methods. In this study, we use plant species in Juglandaceae to evaluate an assembly-free reads accurate identification (AFRAID) method of species identification, a novel approach for precise species identification in plants. Specifically, we determined (1) the accuracy of DNA barcoding approaches in delimiting species in Juglandaceae, (2) the minimum size of chloroplast dataset for species discrimination, and (3) minimum amount of next generation sequencing (NGS) data required for species identification. We found that species identification rates were highest when whole chloroplast genomes were used, followed by taxon-specific DNA barcodes, and then universal DNA barcodes. Species identification of 100% was achieved when chloroplast genome sequence coverage reached 20% and the original sequencing data reached 500,000 reads. AFRAID accurately identified species for all samples tested after 500,000 clean reads, with far less computing time than common approaches. These results provide a new approach to accurately identify species, overcoming limitations of traditional DNA barcodes. Our method, which uses next generation sequencing to generate partial chloroplast genomes, reveals that DNA barcode regions are not necessarily fixed, accelerating the process of species identification.http://www.sciencedirect.com/science/article/pii/S2468265924001677DNA barcodeSpecies identificationRandom DNA barcodeJuglandaceaeAssembly-free |
| spellingShingle | Yanlei Liu Kai Chen Lihu Wang Xinqiang Yu Chao Xu Zhili Suo Shiliang Zhou Shuo Shi Wenpan Dong Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) Plant Diversity DNA barcode Species identification Random DNA barcode Juglandaceae Assembly-free |
| title | Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) |
| title_full | Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) |
| title_fullStr | Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) |
| title_full_unstemmed | Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) |
| title_short | Assembly-free reads accurate identification (AFRAID) approach outperforms other methods of DNA barcoding in the walnut family (Juglandaceae) |
| title_sort | assembly free reads accurate identification afraid approach outperforms other methods of dna barcoding in the walnut family juglandaceae |
| topic | DNA barcode Species identification Random DNA barcode Juglandaceae Assembly-free |
| url | http://www.sciencedirect.com/science/article/pii/S2468265924001677 |
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