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Ma KY, Song JJ, Li DP, Wu Y, Wang CH, Liu ZL, Li TT, Ma YJ. Genomic structure analysis and construction of DNA fingerprint for four sheep populations. Animal 2024; 18:101116. [PMID: 38484632 DOI: 10.1016/j.animal.2024.101116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 04/20/2024] Open
Abstract
The Yongdeng Qishan sheep (QS) is a sheep population found locally in China. To gain in-depth knowledge of its population characteristics, three control groups were chosen, comprising the Lanzhou fat-tailed sheep (LFT), TAN sheep (TAN), and Minxian black fur sheep (MBF), inhabiting the nearby environments. This study genotyped a total of 120 individuals from four sheep populations: QS, LFT, TAN, and MBF. Using Specific-Locus Amplified Fragment Sequencing, we conducted genetic diversity, population structure, and selective sweep analysis, and constructed the fingerprint of each population. In total, there were 782 535 single nucleotide polymorphism (SNP) variations identified, with most being situated within regions that are intergenic or intronic. The genetic diversity analysis revealed that the QS population exhibited lower genetic diversity compared to the other three populations. Consistent results were obtained from the principal component, phylogenetic tree, and population structure analysis, indicating significant genetic differences between QS and the other three populations. However, a certain degree of differentiation was observed within the QS population. The linkage disequilibrium (LD) patterns among the four populations showed clear distinctions, with the QS group demonstrating the most rapid LD decline. Kinship analysis supported the findings of population structure, dividing the 90 QS individuals into two subgroups consisting of 23 and 67 individuals. Selective sweep analysis identified a range of genes associated with reproduction, immunity, and adaptation to high-altitude hypoxia. These genes hold potential as candidate genes for marker-assisted selection breeding. Additionally, a total of 86 523 runs of homozygosity (ROHs) were detected, showing non-uniform distribution across chromosomes, with chromosome 1 having the highest coverage percentage and chromosome 26 the lowest. In the high-frequency ROH islands, 79 candidate genes were associated with biological processes such as reproduction and fat digestion and absorption. Furthermore, a DNA fingerprint was constructed for the four populations using 349 highly polymorphic SNPs. In summary, our research delves into the genetic diversity and population structure of QS population. The construction of DNA fingerprint profiles for each population can provide valuable references for the identification of sheep breeds both domestically and internationally.
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Affiliation(s)
- Ke-Yan Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Juan-Juan Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Deng-Pan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Yi Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Chun-Hui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Zi-Long Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - Tao-Tao Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
| | - You-Ji Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China.
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Suchithra KV, Hameed A, Rekha PD, Arun AB. Description and host-range determination of phage PseuPha1, a new species of Pakpunavirus infecting multidrug-resistant clinical strains of Pseudomonas aeruginosa. Virology 2023; 585:222-231. [PMID: 37392714 DOI: 10.1016/j.virol.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/03/2023]
Abstract
A new phage PseuPha1, infecting multiple multi-drug resistant strains of Pseudomonas aeruginosa with strong anti-biofilm activities, was isolated from wastewater in India. PseuPha1 showed optimal multiplicity of infection at 10-3, maintained the infectivity at wide ranges of pH (6-9) and temperature (4-37 ⁰C), and exhibited 50 minutes latent period and a burst size of 200 when tested against P. aeruginosa PAO1. PseuPha1 shared 86.1-89.5% pairwise intergenomic similarity with Pakpunavirus species (n = 11) listed by the International Committee on Taxonomy of Viruses and established distinct phyletic lineages during phylogenetic analyses of phage proteins. While genomic data validated the taxonomic novelty and lytic attributes of PseuPha1, BOX-PCR profiling asserted the genetic heterogeneity of susceptible clinical P. aeruginosa. Our data supported the affiliation of PseuPha1 as a new Pakpunavirus species and provided the first line of evidence for its virulence and infectivity that can be harnessed in wound therapeutics.
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Affiliation(s)
- Kokkarambath Vannadil Suchithra
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India.
| | - Punchappady Devasya Rekha
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India
| | - Ananthapadmanabha Bhagwath Arun
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), University Road, Deralakatte, Mangalore, 575018, India; Yenepoya Institute of Arts, Science, Commerce and Management, Balmatta, Mangalore, 575002, India.
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Li J, Chang X, Huang Q, Liu P, Zhao X, Li F, Wang Y, Chang C. Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China. Front Plant Sci 2023; 14:1080691. [PMID: 36938035 PMCID: PMC10017979 DOI: 10.3389/fpls.2023.1080691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The flower buds of Lonicera japonica Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new L. japonica varieties. METHODS In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China using simplified genome sequencing technology. RESULTS A total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of Lonicera were divided into four subgroups, and the population structure and genetic relationships among existing Lonicera germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 Lonicera varieties. DISCUSSION To our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of Lonicera varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of Lonicera. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.
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Affiliation(s)
- Jianjun Li
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiaopei Chang
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Qian Huang
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Pengfei Liu
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiting Zhao
- Green Medicine Biotechnology Henan Engineering Laboratory, Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, College of Life Science, Henan Normal University, Xinxiang, China
| | - Fengmei Li
- School of Life Science and Basic Medicine, Xinxiang University, Xinxiang, China
| | - Yungang Wang
- Foresty Seeding Service Station of XinXiang, Xinxiang, Henan, China
| | - Cuifang Chang
- State Key Laboratory Cell Differentiation and Regulation, College of Life Science, Henan Normal University, Xinxiang, China
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Buddhachat K, Thongphueak J, Changtor P, Nukool W, Saengthong M, Kamol P, Suyasunanont U, Kosavititkul P, Pradit W, Nganvongpanit K, Chomdej S. Herbal species authentication by melting fingerprint coupled with high resolution melting analysis (MF-HRM). Mol Biol Rep 2023; 50:2421-2433. [PMID: 36592289 DOI: 10.1007/s11033-022-08235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/23/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND Herbal medicines have recently attracted increasing attention for use as food supplements with health benefits; however, species authentication can be difficult due to incomplete morphological characters. Here, a molecular tool was developed for the identification of species in the National List of Essential Medicinal Plants in Thailand. METHODS The identification process used DNA fingerprints including start codon targeted (SCoT) and inter simple sequence repeat (ISSR) polymorphisms, coupled with high resolution melting (HRM), to produce melting fingerprint (MF)-HRM. RESULTS Results indicated that MF-HRM, SCoT-HRM and ISSR-HRM could be used for DNA fingerprints as S34, S36, S9 and S8 of SCoT and UBC873, S25 and UBC841 of ISSR. The melting fingerprints obtained from S34 of SCoT exhibited the best primers for identification of herbal species with 87.5% accuracy and relatively high repeatability. The presence of intraspecific variation in a few species affected the shift of melting fingerprints within species. MF-HRM using S34 showed improved species prediction compared to DNA fingerprints. The concentration of DNA with 10 ng/µl was recommended to perform MF-HRM. MF-HRM enabled species authentication of herbal commercialized products at only 20% resulting from the low quality of DNA isolated, while admixture of multiple product species interfered with the MF process. CONCLUSION Findings suggested that MF-HRM showed promise as a molecular tool for the authentication of species in commercial herbal products with high specificity, moderate repeatability and rapidity without prior sequence information. This information will greatly improve quality control and traceability during the manufacturing process.
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Affiliation(s)
- Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand. .,Center of Excellence in Research for Agricultural Biotechnology, Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok, 65000, Thailand.
| | - Jinnaphat Thongphueak
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Phanupong Changtor
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Wanrachon Nukool
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Maturada Saengthong
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Puntitra Kamol
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Urasri Suyasunanont
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Prasuk Kosavititkul
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Waranee Pradit
- Research Center in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Korakot Nganvongpanit
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai, 50100, Thailand.,Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Siriwadee Chomdej
- Research Center in Bioresources for Agriculture, Industry and Medicine, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Noviana E, Indrayanto G, Rohman A. Advances in Fingerprint Analysis for Standardization and Quality Control of Herbal Medicines. Front Pharmacol 2022; 13:853023. [PMID: 35721184 PMCID: PMC9201489 DOI: 10.3389/fphar.2022.853023] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/26/2022] [Indexed: 01/01/2023] Open
Abstract
Herbal drugs or herbal medicines (HMs) have a long-standing history as natural remedies for preventing and curing diseases. HMs have garnered greater interest during the past decades due to their broad, synergistic actions on the physiological systems and relatively lower incidence of adverse events, compared to synthetic drugs. However, assuring reproducible quality, efficacy, and safety from herbal drugs remains a challenging task. HMs typically consist of many constituents whose presence and quantity may vary among different sources of materials. Fingerprint analysis has emerged as a very useful technique to assess the quality of herbal drug materials and formulations for establishing standardized herbal products. Rather than using a single or two marker(s), fingerprinting techniques take great consideration of the complexity of herbal drugs by evaluating the whole chemical profile and extracting a common pattern to be set as a criterion for assessing the individual material or formulation. In this review, we described and assessed various fingerprinting techniques reported to date, which are applicable to the standardization and quality control of HMs. We also evaluated the application of multivariate data analysis or chemometrics in assisting the analysis of the complex datasets from the determination of HMs. To ensure that these methods yield reliable results, we reviewed the validation status of the methods and provided perspectives on those. Finally, we concluded by highlighting major accomplishments and presenting a gap analysis between the existing techniques and what is needed to continue moving forward.
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Affiliation(s)
- Eka Noviana
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Abdul Rohman
- Departement of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Center of Excellence, Institute for Halal Industry and Systems, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Ramli US, Tahir NI, Rozali NL, Othman A, Muhammad NH, Muhammad SA, Tarmizi AHA, Hashim N, Sambanthamurthi R, Singh R, Manaf MAA, Parveez GKA. Sustainable Palm Oil-The Role of Screening and Advanced Analytical Techniques for Geographical Traceability and Authenticity Verification. Molecules 2020; 25:molecules25122927. [PMID: 32630515 PMCID: PMC7356346 DOI: 10.3390/molecules25122927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/17/2020] [Accepted: 06/21/2020] [Indexed: 12/23/2022] Open
Abstract
Palm oil production from oil palm (Elaeis guineensis Jacq.) is vital for the economy of Malaysia. As of late, sustainable production of palm oil has been a key focus due to demand by consumer groups, and important progress has been made in establishing standards that promote good agricultural practices that minimize impact on the environment. In line with the industrial goal to build a traceable supply chain, several measures have been implemented to ensure that traceability can be monitored. Although the palm oil supply chain can be highly complex, and achieving full traceability is not an easy task, the industry has to be proactive in developing improved systems that support the existing methods, which rely on recorded information in the supply chain. The Malaysian Palm Oil Board (MPOB) as the custodian of the palm oil industry in Malaysia has taken the initiative to assess and develop technologies that can ensure authenticity and traceability of palm oil in the major supply chains from the point of harvesting all the way to key downstream applications. This review describes the underlying framework related to palm oil geographical traceability using various state-of-the-art analytical techniques, which are also being explored to address adulteration in the global palm oil supply chain.
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Affiliation(s)
- Umi Salamah Ramli
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
- Correspondence: ; Tel.: +60-3-8769-4495
| | - Noor Idayu Tahir
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Nurul Liyana Rozali
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Abrizah Othman
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Nor Hayati Muhammad
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Syahidah Akmal Muhammad
- School of Industrial Technology/Analytical Biochemistry Research Centre, Universiti Sains Malaysia, USM, George Town 11800, Penang, Malaysia;
| | - Azmil Haizam Ahmad Tarmizi
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Norfadilah Hashim
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Rajinder Singh
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Mohamad Arif Abd Manaf
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia; (N.I.T.); (N.L.R.); (A.O.); (N.H.M.); (A.H.A.T.); (N.H.); (R.S.); (R.S.); (M.A.A.M.); (G.K.A.P.)
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Figueiredo Rocha VC, de Souza-Filho AF, Ikuta CY, Hildebrand E Grisi Filho JH, de Azevedo Issa M, Coelho Mota PMP, de Juan Ferré L, Rodríguez LD, Martínez BR, Heinemann MB, Ferreira Neto JS. High discrimination of Mycobacterium bovis isolates in Brazilian herds by spoligotyping. Prev Vet Med 2020; 179:104976. [PMID: 32361639 DOI: 10.1016/j.prevetmed.2020.104976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/21/2020] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Bovine tuberculosis is an infectious disease caused by Mycobacterium bovis (M. bovis), that leads to economic losses in infected herds and it is also considered an important zoonosis. The molecular typing methods of M. bovis isolates are fundamental for the bovine tuberculosis surveillance system, and spoligotyping is the standard genotyping technique for this species. Thus, the aim of the present study is to analyze the spatial and cluster distribution of M. bovis strains from several regions of Brazil through molecular typing. Spoligotyping technique was applied on 422 isolates identified as M. bovis, and Ripley's K function was used to perform the spatial and cluster analysis of each identified profile. Forty-three (43) different profiles were identified and spoligotype SB0121 was the most frequent and showed a uniform pattern in the spatial distribution while spoligotypes SB0295, SB1380 and SB1050 formed clusters. In addition, three novel spoligotype profiles (SB2361, SB2362, SB2364) were identified in different herds. In this perspective, it is believed that molecular identification and typing can significantly improve the performance of surveillance systems for bovine tuberculosis in Brazil.
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Affiliation(s)
| | | | - Cassia Yumi Ikuta
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, São Paulo, Brazil
| | | | - Marina de Azevedo Issa
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - Pedro Moacyr Pinto Coelho Mota
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - Lúcia de Juan Ferré
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
| | | | - Beatriz Romero Martínez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Madrid, Spain
| | - Marcos Bryan Heinemann
- Universidade de São Paulo, Faculdade de Medicina Veterinária e Zootecnia, São Paulo, Brazil.
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Jiang B, Zhao Y, Yi H, Huo Y, Wu H, Ren J, Ge J, Zhao J, Wang F. PIDS: A User-Friendly Plant DNA Fingerprint Database Management System. Genes (Basel) 2020; 11:E373. [PMID: 32235513 DOI: 10.3390/genes11040373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/27/2020] [Accepted: 03/29/2020] [Indexed: 11/23/2022] Open
Abstract
The high variability and somatic stability of DNA fingerprints can be used to identify individuals, which is of great value in plant breeding. DNA fingerprint databases are essential and important tools for plant molecular research because they provide powerful technical and information support for crop breeding, variety quality control, variety right protection, and molecular marker-assisted breeding. Building a DNA fingerprint database involves the production of large amounts of heterogeneous data for which storage, analysis, and retrieval are time and resource consuming. To process the large amounts of data generated by laboratories and conduct quality control, a database management system is urgently needed to track samples and analyze data. We developed the plant international DNA-fingerprinting system (PIDS) using an open source web server and free software that has automatic collection, storage, and efficient management functions based on merging and comparison algorithms to handle massive microsatellite DNA fingerprint data. PIDS also can perform genetic analyses. This system can match a corresponding capillary electrophoresis image on each primer locus as fingerprint data to upload to the server. PIDS provides free customization and extension of back-end functions to meet the requirements of different laboratories. This system can be a significant tool for plant breeders and can be applied in forensic science for human fingerprint identification, as well as in virus and microorganism research.
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Yang J, Zhang J, Han R, Zhang F, Mao A, Luo J, Dong B, Liu H, Tang H, Zhang J, Wen C. Target SSR-Seq: A Novel SSR Genotyping Technology Associate With Perfect SSRs in Genetic Analysis of Cucumber Varieties. Front Plant Sci 2019; 10:531. [PMID: 31105728 PMCID: PMC6492046 DOI: 10.3389/fpls.2019.00531] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/05/2019] [Indexed: 05/03/2023]
Abstract
Simple sequence repeats (SSR) - also known as microsatellites - have been used extensively in genetic analysis, fine mapping, quantitative trait locus (QTL) mapping, as well as marker-assisted selection (MAS) breeding and other techniques. Despite a plethora of studies reporting that perfect SSRs with stable motifs and flanking sequences are more efficient for genetic research, the lack of a high throughput technology for SSR genotyping has limited their use as genetic targets in many crops. In this study, we developed a technology called Target SSR-seq that combined the multiplexed amplification of perfect SSRs with high throughput sequencing. This method can genotype plenty of SSR loci in hundreds of samples with highly accurate results, due to the substantial coverage afforded by high throughput sequencing. We also detected 844 perfect SSRs based on 182 resequencing datasets in cucumber, of which 91 SSRs were selected for Target SSR-seq. Finally, 122 SSRs, including 31 SSRs for varieties identification, were used to genotype 382 key cucumber varieties readily available in Chinese markets using our Target SSR-seq method. Libraries of PCR products were constructed and then sequenced on the Illumina HiSeq X Ten platform. Bioinformatics analysis revealed that 111 filtered SSRs were accurately genotyped with an average coverage of 1289× at an extremely low cost; furthermore, 398 alleles were observed in 382 cucumber cultivars. Genetic analysis identified four populations: northern China type, southern China type, European type, and Xishuangbanna type. Moreover, we acquired a set of 16 core SSRs for the identification of 382 cucumber varieties, of which 42 were isolated as backbone cucumber varieties. This study demonstrated that Target SSR-seq is a novel and efficient method for genetic research.
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Affiliation(s)
- Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Ruixi Han
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Feng Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Aijun Mao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Bobo Dong
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hui Liu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Hao Tang
- Development Center of Science and Technology, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- *Correspondence: Changlong Wen,
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Chideroli RT, Gonçalves DD, Suphoronski SA, Alfieri AF, Alfieri AA, de Oliveira AG, de Freitas JC, Pereira UDP. Culture Strategies for Isolation of Fastidious Leptospira Serovar Hardjo and Molecular Differentiation of Genotypes Hardjobovis and Hardjoprajitno. Front Microbiol 2017; 8:2155. [PMID: 29163438 PMCID: PMC5673650 DOI: 10.3389/fmicb.2017.02155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/20/2017] [Indexed: 11/13/2022] Open
Abstract
The Leptospira serovar Hedjo belongs to the serogroup sejroe and this serovar is the most prevalent in bovine herds worldwide. The sejroe serogroup is the most frequently detected by serology in Brazilian cattle herds suggesting that it is due serovar Hardjo. In the molecular classification, this serovar has two genotypes: Hardjobovis and Hardjoprajitno. This serovar is as considered as fastidious pathogens, and their isolation is one of the bottlenecks in leptospirosis laboratories. In addition, its molecular characterization using genomic approaches is oftentimes not simple and time-consuming. This study describes a method for isolating the two genotypes of serovar Hardjo using culture medium formulations and suggests a get-at-able molecular characterization. Ten cows naturally infected which were seropositive were selected from small dairy farms, and their urine was collected for bacterial isolation. We evaluated three modifications of liquid Leptospira medium culture supplemented with sodium pyruvate, superoxide dismutase enzyme and fetal bovine serum, and the isolates were characterized by molecular techniques. After isolation and adaptation in standard culture medium, the strains were subcultured for 1 week in the three modified culture media for morphologic evaluation using electronic microscopy. Strains were molecularly identified by multilocus variable-number tandem-repeat analysis (MLVA), partial sequencing and phylogenic analyses of gene sec Y. Combining the liquid culture medium formulations allowed growth of the Leptospira serovar Hardjo in three tubes. Two isolates were identified as genotype Hardjobovis, and the other as genotype Hardjoprajitno. Morphologically, compared with control media, cells in the medium supplemented with the superoxide dismutase enzyme were more elongated and showed many cells in division. The cells in the medium supplemented with fetal bovine serum were fewer and lost their spirochete morphology. This indicated that the additional supplementation with fetal bovine serum assisted in the initial growth and maintenance of the viable leptospires and the superoxide dismutase enzyme allowed them to adapt to the medium. These culture strategies allowed for the isolation and convenient molecular characterization of two genotypes of serovar Hardjo, creating new insight into the seroepidemiology of leptospirosis and its specific genotypes. It also provides new information for the immunoprophylaxis of bovine leptospirosis.
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Affiliation(s)
- Roberta T. Chideroli
- Department of Veterinary Preventive Medicine, State University of Londrina, Londrina, Brazil
| | - Daniela D. Gonçalves
- Department of Veterinary Preventive Medicine and Public Health, Paranaense University, Umuarama, Brazil
| | - Suelen A. Suphoronski
- Department of Veterinary Preventive Medicine, State University of Londrina, Londrina, Brazil
| | - Alice F. Alfieri
- National Institute of Science and Technology for Dairy Production Chain (INCT - LEITE), Universidade Estadual de Londrina, Londrina, Brazil
| | - Amauri A. Alfieri
- National Institute of Science and Technology for Dairy Production Chain (INCT - LEITE), Universidade Estadual de Londrina, Londrina, Brazil
| | - Admilton G. de Oliveira
- Laboratory of Microbial Biotechnology, Department of Microbiology, State University of Londrina, Londrina, Brazil
| | - Julio C. de Freitas
- Department of Veterinary Preventive Medicine, State University of Londrina, Londrina, Brazil
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Nagib S, Glaeser SP, Eisenberg T, Sammra O, Lämmler C, Kämpfer P, Schauerte N, Geiger C, Kaim U, Prenger-Berninghoff E, Becker A, Abdulmawjood A. Fatal infection in three Grey Slender Lorises (Loris lydekkerianus nordicus) caused by clonally related Trueperella pyogenes. BMC Vet Res 2017; 13:273. [PMID: 28851356 PMCID: PMC5576266 DOI: 10.1186/s12917-017-1171-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background Trueperella pyogenes is a worldwide known bacterium causing mastitis, abortion and various other pyogenic infections in domestic animals like ruminants and pigs. In this study we represent the first case report of three unusual fatal infections of Grey Slender Lorises caused by Trueperella pyogenes. Meanwhile, this study represents the first in-depth description of the multilocus sequence analysis (MLSA) on T. pyogenes species. Case presentation Three Trueperella pyogenes were isolated from three different Grey Slender Lorises, which died within a period of two years at Frankfurt Zoo (Frankfurt am Main - Germany). The three Grey Slender Loris cases were suffering from severe sepsis and died from its complication. During the bacteriological investigation of the three cases, the T. pyogenes were isolated from different organisms in each case. The epidemiological relationship between the three isolates could be shown by four genomic DNA fingerprint methods (ERIC-PCR, BOX-PCR, (GTG)5-PCR, and RAPD-PCR) and by multilocus sequence analysis (MLSA) investigating four different housekeeping genes (fusA-tuf-metG-gyrA). Conclusion In this study, we clearly showed by means of using three different rep-PCRs, by RAPD-PCR and by MLSA that the genomic fingerprinting of the investigated three T. pyogenes have the same clonal origin and are genetically identical. These results suggest that the same isolate contaminated the animal’s facility and subsequently caused cross infection between the three different Grey Slender Lorises. To the best of our knowledge, this is the first epidemiological approach concentrating on T. pyogenes using MLSA.
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Affiliation(s)
- Samy Nagib
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Tobias Eisenberg
- Landesbetrieb Hessisches Landeslabor, Schubertstraße. 60, D-35392, Gießen, Germany
| | - Osama Sammra
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Christoph Lämmler
- Institut für Pharmakologie und Toxikologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, D-35392, Gießen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26-32, D-35392, Gießen, Germany
| | - Nicole Schauerte
- Zoologischer Garten Frankfurt am Main, Bernhard-Grzimek-Allee 1, D-60316, Frankfurt, Germany
| | - Christina Geiger
- Zoologischer Garten Frankfurt am Main, Bernhard-Grzimek-Allee 1, D-60316, Frankfurt, Germany
| | - Ute Kaim
- Landesbetrieb Hessisches Landeslabor, Schubertstraße. 60, D-35392, Gießen, Germany
| | - Ellen Prenger-Berninghoff
- Institut für Hygiene und Infektionskrankheiten der Tiere, Justus-Liebig-Universität Gießen, Frankfurter Straße. 85-91, D-35392, Gießen, Germany
| | - André Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173, Hannover, Germany
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173, Hannover, Germany.
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Ganogpichayagrai A, Rungsihirunrat K, Palanuvej C, Ruangrungsi N. Characterization of Mangifera indica cultivars in Thailand based on macroscopic, microscopic, and genetic characters. J Adv Pharm Technol Res 2016; 7:127-133. [PMID: 27833891 PMCID: PMC5052938 DOI: 10.4103/2231-4040.191419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Thai mango cultivars are classified into six groups plus one miscellaneous group according to germplasm database for mango. Characterization is important for conservation and the development of Thai mango cultivars. This study investigated macroscopic, microscopic leaf characteristics, and genetic relationship among 17 cultivars selected from six groups of mango in Thailand. Selected mango samples were obtained from three different locations in Thailand (n = 57). They were observed for their leaf and fruit macroscopic characteristics. Leaf measurement for the stomatal number, veinlet termination number, and palisade ratio was evaluated under a microscope attached with digital camera. DNA fingerprint was performed using CTAB extraction of DNA and inter-simple sequence repeat (ISSR) amplification. Forty-five primers were screened; then, seven primers that amplified the reproducible band patterns were selected to amplified and generate dendrogram by Unweighted Pair-Group Method with Arithmetic Average. These selected 17 Thai mango cultivars had individually macroscopic characteristics based on fruits and leaves. For microscopic characteristics, the stomatal number, veinlet termination number, and palisade ratio were slightly differentiable. For genetic identification, 78 bands of 190-2660 bps were amplified, of which 82.05% were polymorphic. The genetic relationship among these cultivars was demonstrated and categorized into two main clusters. It was shown that ISSR markers could be useful for Thai mango cultivar identification.
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Affiliation(s)
- Aunyachulee Ganogpichayagrai
- Public Health Sciences Programme, College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kanchana Rungsihirunrat
- Public Health Sciences Programme, College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanida Palanuvej
- Public Health Sciences Programme, College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nijsiri Ruangrungsi
- Public Health Sciences Programme, College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand
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