دورية أكاديمية
Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes.
| العنوان: | Different reference genomes determine different results: Comparing SNP calling in RAD-seq of Engelhardia roxburghiana using different reference genomes. |
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| المؤلفون: | Huang PH; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China; Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China; University of Chinese Academy of Sciences, Beijing 100049, China., Wang TR; Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China., Li M; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China., Fang OY; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China., Su RP; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China., Meng HH; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar. Electronic address: menghonghu@xtbg.ac.cn., Song YG; Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China. Electronic address: ygsong@cemps.ac.cn., Li J; Plant Phylogenetics and Conservation Group, Center for Integrative Conservation & Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China. Electronic address: jieli@xtbg.ac.cn. |
| المصدر: | Plant science : an international journal of experimental plant biology [Plant Sci] 2024 Jul; Vol. 344, pp. 112109. Date of Electronic Publication: 2024 May 03. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Elsevier Ireland Country of Publication: Ireland NLM ID: 9882015 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-2259 (Electronic) Linking ISSN: 01689452 NLM ISO Abbreviation: Plant Sci Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: <2010>- : Shannon, Co. Clare : Elsevier Ireland Original Publication: Shannon [Clare] : Elsevier Scientific Publishers Ireland Ltd., c1985- |
| مواضيع طبية MeSH: | Polymorphism, Single Nucleotide* , Genome, Plant* , High-Throughput Nucleotide Sequencing*/methods, Sequence Analysis, DNA/methods |
| مستخلص: | Advances in next-generation sequencing (NGS) have significantly reduced the cost and improved the efficiency of obtaining single nucleotide polymorphism (SNP) markers, particularly through restriction site-associated DNA sequencing (RAD-seq). Meanwhile, the progression in whole genome sequencing has led to the utilization of an increasing number of reference genomes in SNP calling processes. This study utilized RAD-seq data from 242 individuals of Engelhardia roxburghiana, a tropical tree of the walnut family (Juglandaceae), with SNP calling conducted using the STACKS pipeline. We aimed to compare both reference-based approaches, namely, employing a closely related species as the reference genome versus the species itself as the reference genome, to evaluate their respective merits and limitations. Our findings indicate a substantial discrepancy in the number of obtained SNPs between using a closely related species as opposed to the species itself as reference genomes, the former yielded approximately an order of magnitude fewer SNPs compared to the latter. While the missing rate of individuals and sites of the final SNPs obtained in the two scenarios showed no significant difference. The results showed that using the reference genome of the species itself tends to be prioritized in RAD-seq studies. However, if this is unavailable, considering closely related genomes is feasible due to their wide applicability and low missing rate as alternatives. This study contributes to enrich the understanding of the impact of SNP acquisition when utilizing different reference genomes. Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have influenced the work reported in this paper. (Copyright © 2024 Elsevier B.V. All rights reserved.) |
| فهرسة مساهمة: | Keywords: RAD-seq; Reference-based approach; SNP calling; STACKS |
| تواريخ الأحداث: | Date Created: 20240504 Date Completed: 20240519 Latest Revision: 20240519 |
| رمز التحديث: | 20240520 |
| DOI: | 10.1016/j.plantsci.2024.112109 |
| PMID: | 38704094 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1873-2259 |
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| DOI: | 10.1016/j.plantsci.2024.112109 |