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Rayo E, Ulrich GF, Zemp N, Greeff M, Schuenemann VJ, Widmer A, Fischer MC. Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens. Sci Rep 2024; 14:12875. [PMID: 38834639 DOI: 10.1038/s41598-024-63587-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, Melitaea diamina, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.
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Affiliation(s)
- Enrique Rayo
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
- Institut Für Veterinärpathologie, University of Zurich, Zurich, Switzerland
| | - Gabriel F Ulrich
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Niklaus Zemp
- Genetic Diversity Centre (GDC), ETH Zurich, Zurich, Switzerland
| | - Michael Greeff
- Institute of Agricultural Sciences (IAS), ETH Zurich, Zurich, Switzerland
| | - Verena J Schuenemann
- Department of Environmental Sciences (DUW), University of Basel, Basel, Switzerland
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Alex Widmer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland
| | - Martin C Fischer
- Institute of Integrative Biology (IBZ), ETH Zurich, Zurich, Switzerland.
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Marín DV, Castillo DK, López-Lavalle LAB, Chalarca JR, Pérez CR. An optimized high-quality DNA isolation protocol for spodoptera frugiperda J. E. smith (Lepidoptera: Noctuidae). MethodsX 2021; 8:101255. [PMID: 34434778 PMCID: PMC8374285 DOI: 10.1016/j.mex.2021.101255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/28/2021] [Indexed: 11/27/2022] Open
Abstract
An optimized high-quality DNA isolation protocol was developed using body segment tissue from the Fall Armyworm (Spodoptera frugiperda), that will allow documenting genetic variability based on biotypes, facilitating studies on the appearance, distribution and population dynamics of the fall armyworm at the molecular level. The resulting protocol is an easy-to-use, timesaving method that can rapidly achieve high quality, high-yielding total genomic DNA, using chemicals and everyday consumables available in a molecular laboratory. This new method of DNA extraction avoids the contamination of polysaccharides, salts, phenols, proteins and other cellular by-products that can interfere with subsequent reactions. DNA purity estimates reveal A260: A280 ratios greater than 1.9, which were evidenced by quality test on agarose gel, observing complete integrity and high purity of the resulting samples, and yielded 30–99 µg/g of total DNA. Therefore, the quality of the DNA produced from this extraction is suitable for subsequent molecular applications: (i) next generation whole genome sequencing, (ii) conventional polymerase chain reaction for genotyping, (iii) barcodes and (iv) gene cloning. In addition, to become an anticipating diagnostic tool for invasive lepidopteran larval stages:The resulting protocol is an easy-to-use time-saving method. This new extraction method prevents contamination from polysaccharides, salts, phenols, proteins, and other cellular sub-products. DNA purity estimations reveal A260:A280 ratios above 1.9.
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Affiliation(s)
- Diana Victoria Marín
- Universidad Nacional de Colombia, Sede Palmira, Palmira, Valle del Cauca, Colombia.,The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Diana Katherine Castillo
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Luis Augusto Becerra López-Lavalle
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
| | - Jairo Rodríguez Chalarca
- The Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira km 17, Valle del Cauca, Colombia
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Zhao L, Hu Y, Liu W, Wu H, Xiao J, Zhang C, Zhang H, Zhang X, Liu J, Lu X, Zheng W. Identification of camel species in food products by a polymerase chain reaction-lateral flow immunoassay. Food Chem 2020; 319:126538. [PMID: 32146291 DOI: 10.1016/j.foodchem.2020.126538] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 10/25/2019] [Accepted: 03/01/2020] [Indexed: 01/08/2023]
Abstract
With an increased demand for camel meat, camel meat-related food products are susceptible to food fraud. To effectively authenticate camel-containing foods, a novel analytical technique based on polymerase chain reaction (PCR)-lateral flow immunoassay (LFI) was developed. The camel-specific PCR primers were designed to target at the mitochondrial COI gene. Both of the in silico and in vitro tests confirmed that the PCR-LFI was specific. A limit of detection of 0.1% w/w of camel meat in beef was achieved for both the raw and cooked (i.e. boiling and deep frying) meat samples. This novel method was used to authenticate 20 processed camel-meat products purchased from local grocery stores in China and online. Two products purchased online were identified as containing no camel meat. Overall, this novel PCR-LFI method is ideal for governmental laboratories to rapidly authenticate camel-meat containing food products.
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Affiliation(s)
- Liangjuan Zhao
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China; Tianjin Customs District, Tianjin 300387, China
| | - Yaxi Hu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Wei Liu
- Tianjin Customs District, Tianjin 300387, China
| | - Hong Wu
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Jing Xiao
- China National Center for Food Safety Risk Assessment, Beijing 100022, China
| | - Can Zhang
- Center for Disease Prevention and Control of Chinese PLA, Beijing 100071, China
| | | | - Xia Zhang
- Tianjin Customs District, Tianjin 300387, China
| | - Jinyu Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC V6T1Z4, Canada.
| | - Wenjie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China.
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Wang Z, Song M, Li Y, Chen S, Ma H. Differential color development and response to light deprivation of fig (Ficus carica L.) syconia peel and female flower tissues: transcriptome elucidation. BMC PLANT BIOLOGY 2019; 19:217. [PMID: 31122203 PMCID: PMC6533723 DOI: 10.1186/s12870-019-1816-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/30/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Color directly affects fruit quality and consumer preference. In fig syconia, the female flower tissue is contained in a receptacle. Anthocyanin pigmentation of this tissue and the peel differs temporally and spatially. A transcriptome study was carried out to elucidate key genes and transcription factors regulating differences in fig coloring. RESULTS Anthocyanins in the female flower tissue were identified mainly as pelargonidin-3-glucoside and cyanidin-3-rutinoside; in the peel, the major anthocyanins were cyanidin 3-O-glucoside and cyanidin-3-rutinoside. Anthocyanin content was significantly higher in the female flower tissue vs. peel before fig ripening, whereas at ripening, the anthocyanin content in the peel was 5.39 times higher than that in the female flower tissue. Light-deprivation treatment strongly inhibited peel, but not female flower tissue, anthocyanin pigmentation. RNA-Seq revealed 522 differentially expressed genes (recruited with criteria log2 ≥ 2 and P < 0.05) at fig ripening, with 50 upregulated and 472 downregulated genes in the female flower tissue. Light deprivation upregulated 1180 and downregulated 856 genes in the peel, and upregulated 909 and downregulated 817 genes in the female flower tissue. KEGG enrichment revealed significantly changed expression in the phenylpropanoid-biosynthesis and flavonoid-biosynthesis pathways in the peel, but not in the female flower tissue, with significant repression of FcCHS, FcCHI, FcF3H, FcF3'H, FcDFR and FcUFGT transcripts. Light deprivation led to differential expression of 71 and 80 transcription factor genes in the peel and female flower tissue, respectively. Yeast one-hybrid screen revealed that FcHY5 and FcMYB114 bind the promoter regions of FcCHS and FcDFR, respectively in the flavonoid-biosynthesis pathway. CONCLUSIONS Phenylpropanoid- and flavonoid-biosynthesis pathways were differentially expressed spatially and temporally in the peel and female flower tissue of fig syconia; pathway expression in the peel was strongly regulated by light signal. Differentially expressed transcription factors were recruited as candidates to screen important expression regulators in the light-dependent and light-independent anthocyanin-synthesis pathway. Our study lays the groundwork for further elucidation of crucial players in fig pigmentation.
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Affiliation(s)
- Ziran Wang
- College of Horticulture, China Agricultural University, Beijing, People’s Republic of China
| | - Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, People’s Republic of China
| | - Yunze Li
- College of Horticulture, China Agricultural University, Beijing, People’s Republic of China
| | - Shangwu Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, People’s Republic of China
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Liu Q, Liu L, Zhang M, Zhang Q, Wang Q, Ding X, Shao L, Zhou Z, Wang S. A Simple and Efficient Method of Extracting DNA from Aged Bones and Teeth. J Forensic Sci 2017; 63:824-828. [PMID: 29240980 DOI: 10.1111/1556-4029.13603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 04/27/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
DNA is often difficult to extract from old bones and teeth due to low levels of DNA and high levels of degradation. This study established a simple yet efficient method for extracting DNA from 20 aged bones and teeth (approximately 60 years old). Based on the concentration and STR typing results, the new method of DNA extraction (OM) developed in this study was compared with the PrepFiler™ BTA Forensic DNA Extraction Kit (BM). The total amount of DNA extracted using the OM method was not significantly different from that extracted using the commercial kit (p > 0.05). However, the number of STR loci detected was significantly higher in the samples processed using the OM method than using the BM method (p < 0.05). This study aimed to establish a DNA extraction method for aged bones and teeth to improve the detection rate of STR typing and reduce costs compared to the BM technique.
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Affiliation(s)
- Qiqi Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liyan Liu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Minli Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qingzhen Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Qiong Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Xiaoran Ding
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Liting Shao
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Zhe Zhou
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
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