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de Carvalho JA, Monteiro RC, Hagen F, de Camargo ZP, Rodrigues AM. Trends in Molecular Diagnostics and Genotyping Tools Applied for Emerging Sporothrix Species. J Fungi (Basel) 2022; 8:jof8080809. [PMID: 36012797 PMCID: PMC9409836 DOI: 10.3390/jof8080809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/23/2022] Open
Abstract
Sporotrichosis is the most important subcutaneous mycosis that affects humans and animals worldwide. The mycosis is caused after a traumatic inoculation of fungal propagules into the host and may follow an animal or environmental transmission route. The main culprits of sporotrichosis are thermodimorphic Sporothrix species embedded in a clinical clade, including S. brasiliensis, S. schenckii, S. globosa, and S. luriei. Although sporotrichosis occurs worldwide, the etiological agents are not evenly distributed, as exemplified by ongoing outbreaks in Brazil and China, caused by S. brasiliensis and S. globosa, respectively. The gold standard for diagnosing sporotrichosis has been the isolation of the fungus in vitro. However, with the advance in molecular techniques, molecular assays have complemented and gradually replaced the classical mycological tests to quickly and accurately detect and/or differentiate molecular siblings in Sporothrix. Nearly all techniques available for molecular diagnosis of sporotrichosis involve PCR amplification, which is currently moving towards detecting Sporothrix DNA directly from clinical samples in multiplex qPCR assays. From an epidemiological perspective, genotyping is key to tracing back sources of Sporothrix infections, detecting diversity in outbreak areas, and thus uncovering finer-scale epidemiological patterns. Over the past decades, molecular epidemiological studies have provided essential information to policymakers regarding outbreak management. From high-to-low throughput genotyping methods, MLSA, AFLP, SSR, RAPD, PCR-RFLP, and WGS are available to assess the transmission dynamics and sporotrichosis expansion. This review discusses the trends in the molecular diagnosis of sporotrichosis, genotyping techniques applied in molecular epidemiological studies, and perspectives for the near future.
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Affiliation(s)
- Jamile Ambrósio de Carvalho
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ruan Campos Monteiro
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
| | - Ferry Hagen
- Department of Medical Mycology, Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands;
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Zoilo Pires de Camargo
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil; (J.A.d.C.); (R.C.M.); (Z.P.d.C.)
- Department of Medicine, Discipline of Infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo 04023062, Brazil
- Correspondence: ; Tel.: +55-1155764551 (ext. 1540)
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Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
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de Carvalho JA, Hagen F, Fisher MC, de Camargo ZP, Rodrigues AM. Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species. PLoS Negl Trop Dis 2020; 14:e0008330. [PMID: 32609739 PMCID: PMC7329091 DOI: 10.1371/journal.pntd.0008330] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/27/2020] [Indexed: 11/19/2022] Open
Abstract
Sporotrichosis is a chronic subcutaneous mycosis caused by Sporothrix species, of which the main aetiological agents are S. brasiliensis, S. schenckii, and S. globosa. Infection occurs after a traumatic inoculation of Sporothrix propagules in mammals' skin and can follow either a classic route through traumatic inoculation by plant debris (e.g., S. schenckii and S. globosa) or an alternative route through zoonotic transmission from animals (e.g., S. brasiliensis). Epizootics followed by a zoonotic route occur in Brazil, with Rio de Janeiro as the epicenter of a recent cat-transmitted epidemic. DNA-based markers are needed to explore the epidemiology of these Sporothrix expansions using molecular methods. This paper reports the use of amplified-fragment-length polymorphisms (AFLP) to assess the degree of intraspecific variability among Sporothrix species. We used whole-genome sequences from Sporothrix species to generate 2,304 virtual AFLP fingerprints. In silico screening highlighted 6 primer pair combinations to be tested in vitro. The protocol was used to genotype 27 medically relevant Sporothrix. Based on the overall scored AFLP markers (97-137 fragments), the values of polymorphism information content (PIC = 0.2552-0.3113), marker index (MI = 0.002-0.0039), effective multiplex ratio (E = 17.8519-35.2222), resolving power (Rp = 33.6296-63.1852), discriminating power (D = 0.9291-0.9662), expected heterozygosity (H = 0.3003-0.3857), and mean heterozygosity (Havp = 0.0001) demonstrated the utility of these primer combinations for discriminating Sporothrix. AFLP markers revealed cryptic diversity in species previously thought to be the most prevalent clonal type, such as S. brasiliensis, responsible for cat-transmitted sporotrichosis, and S. globosa responsible for large sapronosis outbreaks in Asia. Three combinations (#3 EcoRI-FAM-GA/MseI-TT, #5 EcoRI-FAM-GA/MseI-AG, and #6 EcoRI-FAM-TA/MseI-AA) provide the best diversity indices and lowest error rates. These methods make it easier to track routes of disease transmission during epizooties and zoonosis, and our DNA fingerprint assay can be further transferred between laboratories to give insights into the ecology and evolution of pathogenic Sporothrix species and to inform management and mitigation strategies to tackle the advance of sporotrichosis.
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Affiliation(s)
- Jamile Ambrósio de Carvalho
- Departament of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Ferry Hagen
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
- Laboratory of Medical Mycology, Jining No. 1 People's Hospital, Jining, Shandong, Peoples Republic of China
| | - Matthew C. Fisher
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Zoilo Pires de Camargo
- Departament of Medicine, Discipline of infectious Diseases, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Anderson Messias Rodrigues
- Laboratory of Emerging Fungal Pathogens, Department of Microbiology, Immunology, and Parasitology, Discipline of Cellular Biology, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
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Saldanha LL, Allard PM, Afzan A, de Melo FPDSR, Marcourt L, Queiroz EF, Vilegas W, Furlan CM, Dokkedal AL, Wolfender JL. Metabolomics of Myrcia bella Populations in Brazilian Savanna Reveals Strong Influence of Environmental Factors on Its Specialized Metabolism. Molecules 2020; 25:molecules25122954. [PMID: 32604974 PMCID: PMC7356273 DOI: 10.3390/molecules25122954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
Environmental conditions influence specialized plant metabolism. However, many studies aiming to understand these modulations have been conducted with model plants and/or under controlled conditions, thus not reflecting the complex interaction between plants and environment. To fully grasp these interactions, we investigated the specialized metabolism and genetic diversity of a native plant in its natural environment. We chose Myrcia bella due to its medicinal interest and occurrence in Brazilian savanna regions with diverse climate and soil conditions. An LC-HRMS-based metabolomics approach was applied to analyze 271 samples harvested across seven regions during the dry and rainy season. Genetic diversity was assessed in a subset of 40 samples using amplified fragment length polymorphism. Meteorological factors including rainfall, temperature, radiation, humidity, and soil nutrient and mineral composition were recorded in each region and correlated with chemical variation through multivariate analysis (MVDA). Marker compounds were selected using a statistically informed molecular network and annotated by dereplication against an in silico database of natural products. The integrated results evidenced different chemotypes, with variation in flavonoid and tannin content mainly linked to soil conditions. Different levels of genetic diversity and distance of populations were found to be correlated with the identified chemotypes. These observations and the proposed analytical workflow contribute to the global understanding of the impact of abiotic factors and genotype on the accumulation of given metabolites and, therefore, could be valuable to guide further medicinal exploration of native species.
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Affiliation(s)
- Luiz Leonardo Saldanha
- Faculty of Sciences, São Paulo State University (UNESP), CEP 17033-360, Bauru, São Paulo, Brazil; (F.P.d.S.R.d.M.); (A.L.D.)
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
- Correspondence: (L.L.S.); (J.-L.W.); Tel.: +55-19-3526-4194 (L.L.S.); +41-22-379-3385 (J.-L.W.)
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
| | - Adlin Afzan
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
| | | | - Laurence Marcourt
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
| | - Emerson Ferreira Queiroz
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
| | - Wagner Vilegas
- Institute of Biosciences, São Paulo State University (UNESP), CEP 11330-900, São Vicente, São Paulo, Brazil;
| | - Cláudia Maria Furlan
- Institute of Biosciences, University of São Paulo, CEP 05508-090, São Paulo, São Paulo, Brazil;
| | - Anne Lígia Dokkedal
- Faculty of Sciences, São Paulo State University (UNESP), CEP 17033-360, Bauru, São Paulo, Brazil; (F.P.d.S.R.d.M.); (A.L.D.)
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva (IPSWS), CH-1211 Geneva 4, Switzerland; (P.-M.A.); (A.A.); (L.M.); (E.F.Q.)
- Correspondence: (L.L.S.); (J.-L.W.); Tel.: +55-19-3526-4194 (L.L.S.); +41-22-379-3385 (J.-L.W.)
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Jarocki P, Komoń-Janczara E, Glibowska A, Dworniczak M, Pytka M, Korzeniowska-Kowal A, Wzorek A, Kordowska-Wiater M. Molecular Routes to Specific Identification of the Lactobacillus Casei Group at the Species, Subspecies and Strain Level. Int J Mol Sci 2020; 21:ijms21082694. [PMID: 32294944 PMCID: PMC7216162 DOI: 10.3390/ijms21082694] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/05/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Lactobacillus includes, among others, Lactobacillus casei, Lactobacillus paracasei and Lactobacillus rhamnosus, species that are collectively referred to as the Lactobacillus casei group. Many studies have shown that strains belonging to this group may decrease lactose intolerance, the effects of inflammatory bowel disease, diarrhea, constipation, food allergies and even colon cancer. Moreover, evidences exists of positive effects of these bacteria on mucosal immunity and blood cholesterol level. Because of their beneficial influence on human health, many of them are used as food additives and probiotic pharmaceuticals. It should be stressed that health-promoting properties are not attributed at the species level, but to specific strains. Therefore, procedures are necessary to allow specific identification at each phylogenetic level-genus, species and strain. In this paper we present a practical overview of molecular methods for the identification and differentiation of L. casei bacteria. The research included 30 bacterial strains belonging to three species: L.casei, L. paracasei and L. rhamnosus. Among the tested procedures were genus- and species-specific PCR, multiplex-PCR, Real-Time HRM analysis, RFLP-PCR, rep-PCR, RAPD-PCR, AFLP-PCR, and proteomic methods such as MALDI-TOF MS typing and SDS-PAGE fingerprinting. The obtained results showed that multiplex-PCR and MALDI-TOF MS turned out to be the most useful methods to identify the tested bacteria at the species level. At the strain level, the AFLP-PCR method showed the highest discriminatory power. We hope that the presented results will allow for the easy selection of an appropriate procedure, depending on the experiment conducted and the equipment capabilities of any given laboratory.
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Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
- Correspondence: (P.J.); (M.K.-W.); Tel.: +48-81462-3351 (P.J.)
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Agnieszka Glibowska
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Michał Dworniczak
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Monika Pytka
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
| | - Agnieszka Korzeniowska-Kowal
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (A.K.-K.); (A.W.)
| | - Anna Wzorek
- Polish Collection of Microorganisms (PCM), Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw, Poland; (A.K.-K.); (A.W.)
| | - Monika Kordowska-Wiater
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland; (E.K.-J.); (A.G.); (M.D.); (M.P.)
- Correspondence: (P.J.); (M.K.-W.); Tel.: +48-81462-3351 (P.J.)
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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El-Demerdash ESS, Elsherbeny EA, Salama YAM, Ahmed MZ. Genetic diversity analysis of some Egyptian Origanum and Thymus species using AFLP markers. J Genet Eng Biotechnol 2019; 17:13. [PMID: 31814081 PMCID: PMC6900380 DOI: 10.1186/s43141-019-0012-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/04/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the present investigation, two genera of family Labiatae (genus Origanum and genus Thymus including their available species in Egypt) were analyzed genetically on DNA level using amplified fragment length polymorphism (AFLP) markers. Four selective primer combinations (E-AGC/M-CAA, E-AGC/M-CAC, E-AGG/M-CTC, and E-ACC/M-CAT) were used to detect genetic variations (polymorphisms) within and between the studied plant species of each genus and with their cultivated relatives. RESULTS A total of 193 amplified fragments were obtained overall primer combinations with a disparity in the number of bands for each primer combination. The primer combination E-AGG/M-CTC exhibited a large number of amplicons (67) compared to the other primers with polymorphism percentage 69%. The polymorphism information content (PIC) was calculated for the four primer combinations showing a very high values ranging between 0.98 and 0.99. On the other hand, Thymus species (Thymus vulgaris, Thymus capitatus L., and Thymus decassatus Benth.) exhibited a total number of 171 amplicons for all primer combinations with an average of 42 bands. The primer combination E-AGG/M-CTC produced the largest number of bands (62 bands) with polymorphism percentage 35%, even though the primer combination AGC/M-CAA was more efficient to give high polymorphisms within Thymus species where it resulted in a total of 35 bands with polymorphism percentage 63%. The PIC values were calculated ranging from 0.96 to 0.99. CONCLUSION One can conclude that AFLP technique was informative and efficient technique to give a good coverage of Origanum and Thymus genomes. Furthermore, it was helpful to elucidate the genetic variations and phylogenetic relationships within the studied species as a basis for further studies on these genera and related species.
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Affiliation(s)
- El-Shaimaa Saad El-Demerdash
- Genetic Resources Department, Desert Research Center (DRC), 1 Mathaf El-Matarya Street, El-Matarya B.O.P 11753 Elmatarya, Cairo, Egypt.
| | - Esraa Attia Elsherbeny
- Genetic Resources Department, Desert Research Center (DRC), 1 Mathaf El-Matarya Street, El-Matarya B.O.P 11753 Elmatarya, Cairo, Egypt
| | - Yasser Abdelhakim Mohamed Salama
- Genetic Resources Department, Desert Research Center (DRC), 1 Mathaf El-Matarya Street, El-Matarya B.O.P 11753 Elmatarya, Cairo, Egypt
| | - Mohamed Zoelfakar Ahmed
- Genetic Resources Department, Desert Research Center (DRC), 1 Mathaf El-Matarya Street, El-Matarya B.O.P 11753 Elmatarya, Cairo, Egypt
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Li J, Zeng Z, Wang Y, Liang D, Zhang P. Sequence capture using AFLP-generated baits: A cost-effective method for high-throughput phylogenetic and phylogeographic analysis. Ecol Evol 2019; 9:5925-5937. [PMID: 31161009 PMCID: PMC6540676 DOI: 10.1002/ece3.5176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/06/2019] [Accepted: 03/29/2019] [Indexed: 12/30/2022] Open
Abstract
Target sequence capture is an efficient technique to enrich specific genomic regions for high-throughput sequencing in ecological and evolutionary studies. In recent years, many sequence capture approaches have been proposed, but most of them rely on commercial synthetic baits which make the experiment expensive. Here, we present a novel sequence capture approach called AFLP-based genome sequence capture (AFLP Capture). This method uses the AFLP (amplified fragment length polymorphism) technique to generate homemade capture baits without the need for prior genome information, thus is applicable to any organisms. In this approach, biotinylated AFLP fragments representing a random fraction of the genome are used as baits to capture the homologous fragments from genomic shotgun sequencing libraries. In a trial study, by using AFLP Capture, we successfully obtained 511 orthologous loci (>700,000 bp in total length) from 11 Odorrana species and more than 100,000 single nucleotide polymorphisms (SNPs) in four analyzed individuals of an Odorrana species. This result shows that our method can be used to address questions of various evolutionary depths (from interspecies level to intraspecies level). We also discuss the flexibility in bait preparation and how the sequencing data are analyzed. In summary, AFLP Capture is a rapid and flexible tool and can significantly reduce the experimental cost for phylogenetic studies that require analyzing genome-scale data (hundreds or thousands of loci).
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Affiliation(s)
- Jia‐Xuan Li
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Zhao‐Chi Zeng
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Ying‐Yong Wang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Dan Liang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Peng Zhang
- State Key Laboratory of Biocontrol, College of Ecology and Evolution, School of Life SciencesSun Yat‐Sen UniversityGuangzhouChina
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9
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Garrido-Cardenas JA, Mesa-Valle C, Manzano-Agugliaro F. Trends in plant research using molecular markers. PLANTA 2018; 247:543-557. [PMID: 29243155 DOI: 10.1007/s00425-017-2829-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 05/21/2023]
Abstract
A deep bibliometric analysis has been carried out, obtaining valuable parameters that facilitate the understanding around the research in plant using molecular markers. The evolution of the improvement in the field of agronomy is fundamental for its adaptation to the new exigencies that the current world context raises. In addition, within these improvements, this article focuses on those related to the biotechnology sector. More specifically, the use of DNA markers that allow the researcher to know the set of genes associated with a particular quantitative trait or QTL. The use of molecular markers is widely extended, including: restriction fragment length polymorphism, random-amplified polymorphic DNA, amplified fragment length polymorphism, microsatellites, and single-nucleotide polymorphisms. In addition to classical methodology, new approaches based on the next generation sequencing are proving to be fundamental. In this article, a historical review of the molecular markers traditionally used in plants, since its birth and how the new molecular tools facilitate the work of plant breeders is carried out. The evolution of the most studied cultures from the point of view of molecular markers is also reviewed and other parameters whose prior knowledge can facilitate the approach of researchers to this field of research are analyzed. The bibliometric analysis of molecular markers in plants shows that top five countries in this research are: US, China, India, France, and Germany, and from 2013, this research is led by China. On the other hand, the basic research using Arabidopsis is deeper in France and Germany, while other countries focused its efforts in their main crops as the US for wheat or maize, while China and India for wheat and rice.
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Fan Y, Zhang C, Wu W, He W, Zhang L, Ma X. Analysis of Genetic Diversity and Structure Pattern of Indigofera Pseudotinctoria in Karst Habitats of the Wushan Mountains Using AFLP Markers. Molecules 2017; 22:molecules22101734. [PMID: 29035322 PMCID: PMC6151804 DOI: 10.3390/molecules22101734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 11/16/2022] Open
Abstract
Indigofera pseudotinctoria Mats is an agronomically and economically important perennial legume shrub with a high forage yield, protein content and strong adaptability, which is subject to natural habitat fragmentation and serious human disturbance. Until now, our knowledge of the genetic relationships and intraspecific genetic diversity for its wild collections is still poor, especially at small spatial scales. Here amplified fragment length polymorphism (AFLP) technology was employed for analysis of genetic diversity, differentiation, and structure of 364 genotypes of I. pseudotinctoria from 15 natural locations in Wushan Montain, a highly structured mountain with typical karst landforms in Southwest China. We also tested whether eco-climate factors has affected genetic structure by correlating genetic diversity with habitat features. A total of 515 distinctly scoreable bands were generated, and 324 of them were polymorphic. The polymorphic information content (PIC) ranged from 0.694 to 0.890 with an average of 0.789 per primer pair. On species level, Nei’s gene diversity (Hj), the Bayesian genetic diversity index (HB) and the Shannon information index (I) were 0.2465, 0.2363 and 0.3772, respectively. The high differentiation among all sampling sites was detected (FST = 0.2217, GST = 0.1746, G’ST = 0.2060, θB = 0.1844), and instead, gene flow among accessions (Nm = 1.1819) was restricted. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. The population genetic structure resolved by the UPGMA tree, principal coordinate analysis, and Bayesian-based cluster analyses irrefutably grouped all accessions into two distinct clusters, i.e., lowland and highland groups. This structure pattern may indicate joint effects by the neutral evolution and natural selection. Restricted Nm was observed across all accessions, and genetic barriers were detected between adjacent accessions due to specifically geographical landform.
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Affiliation(s)
- Yan Fan
- Chongqing Academy of Animal Husbandry, Chongqing 400039, China.
| | - Chenglin Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wendan Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wei He
- Chongqing Academy of Animal Husbandry, Chongqing 400039, China.
| | - Li Zhang
- Chongqing Academy of Animal Husbandry, Chongqing 400039, China.
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
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TfoI produced by Tepidimonas fonticaldi PL17, a moderate thermophilic bacterium, is an isoschizomer of MseI. Extremophiles 2017; 21:523-535. [DOI: 10.1007/s00792-017-0922-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/27/2017] [Indexed: 10/19/2022]
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12
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Amaradasa BS, Everhart SE. Effects of Sublethal Fungicides on Mutation Rates and Genomic Variation in Fungal Plant Pathogen, Sclerotinia sclerotiorum. PLoS One 2016; 11:e0168079. [PMID: 27959950 PMCID: PMC5154572 DOI: 10.1371/journal.pone.0168079] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/26/2016] [Indexed: 11/24/2022] Open
Abstract
Pathogen exposure to sublethal doses of fungicides may result in mutations that may represent an important and largely overlooked mechanism of introducing new genetic variation into strictly clonal populations, including acquisition of fungicide resistance. We tested this hypothesis using the clonal plant pathogen, Sclerotinia sclerotiorum. Nine susceptible isolates were exposed independently to five commercial fungicides with different modes of action: boscalid (respiration inhibitor), iprodione (unclear mode of action), thiophanate methyl (inhibition of microtubulin synthesis) and azoxystrobin and pyraclostrobin (quinone outside inhibitors). Mycelium of each isolate was inoculated onto a fungicide gradient and sub-cultured from the 50–100% inhibition zone for 12 generations and experiment repeated. Mutational changes were assessed for all isolates at six neutral microsatellite (SSR) loci and for a subset of isolates using amplified fragment length polymorphisms (AFLPs). SSR analysis showed 12 of 85 fungicide-exposed isolates had a total of 127 stepwise mutations with 42 insertions and 85 deletions. Most stepwise deletions were in iprodione- and azoxystrobin-exposed isolates (n = 40/85 each). Estimated mutation rates were 1.7 to 60-fold higher for mutated loci compared to that expected under neutral conditions. AFLP genotyping of 33 isolates (16 non-exposed control and 17 fungicide exposed) generated 602 polymorphic alleles. Cluster analysis with principal coordinate analysis (PCoA) and discriminant analysis of principal components (DAPC) identified fungicide-exposed isolates as a distinct group from non-exposed control isolates (PhiPT = 0.15, P = 0.001). Dendrograms based on neighbor-joining also supported allelic variation associated with fungicide-exposure. Fungicide sensitivity of isolates measured throughout both experiments did not show consistent trends. For example, eight isolates exposed to boscalid had higher EC50 values at the end of the experiment, and when repeated, only one isolate had higher EC50 while most isolates showed no difference. Results of this support the hypothesis that sublethal fungicide stress increases mutation rates in a largely clonal plant pathogen under in vitro conditions. Collectively, this work will aid our understanding how non-lethal fungicide exposure may affect genomic variation, which may be an important mechanism of novel trait emergence, adaptation, and evolution for clonal organisms.
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Affiliation(s)
- B. Sajeewa Amaradasa
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Sydney E. Everhart
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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Arias M, Hernandez M, Remondegui N, Huvenaars K, van Dijk P, Ritter E. First genetic linkage map of Taraxacum koksaghyz Rodin based on AFLP, SSR, COS and EST-SSR markers. Sci Rep 2016; 6:31031. [PMID: 27488242 PMCID: PMC4973268 DOI: 10.1038/srep31031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/11/2016] [Indexed: 11/09/2022] Open
Abstract
Taraxacum koksaghyz Rodin (TKS) has been studied in many occasions as a possible alternative source for natural rubber production of good quality and for inulin production. Some tire companies are already testing TKS tire prototypes. There are also many investigations on the production of bio-fuels from inulin and inulin applications for health improvement and in the food industry. A limited amount of genomic resources exist for TKS and particularly no genetic linkage map is available in this species. We have constructed the first TKS genetic linkage map based on AFLP, COS, SSR and EST-SSR markers. The integrated linkage map with eight linkage groups (LG), representing the eight chromosomes of Russian dandelion, has 185 individual AFLP markers from parent 1, 188 individual AFLP markers from parent 2, 75 common AFLP markers and 6 COS, 1 SSR and 63 EST-SSR loci. Blasting the EST-SSR sequences against known sequences from lettuce allowed a partial alignment of our TKS map with a lettuce map. Blast searches against plant gene databases revealed some homologies with useful genes for downstream applications in the future.
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Affiliation(s)
- Marina Arias
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Monica Hernandez
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Naroa Remondegui
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
| | - Koen Huvenaars
- KeyGene, Agro Business Park 90, Wageningen, 6708 PW, The Netherlands
| | - Peter van Dijk
- KeyGene, Agro Business Park 90, Wageningen, 6708 PW, The Netherlands
| | - Enrique Ritter
- Neiker Tecnalia (Granja Modelo de Arkaute), Ctra. N1-Km 355, Arcaute (Alava) CP: 01192, Spain
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14
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Kelleher P, Murphy J, Mahony J, van Sinderen D. Next-generation sequencing as an approach to dairy starter selection. DAIRY SCIENCE & TECHNOLOGY 2015; 95:545-568. [PMID: 26798445 PMCID: PMC4712225 DOI: 10.1007/s13594-015-0227-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/25/2015] [Accepted: 04/02/2015] [Indexed: 02/06/2023]
Abstract
Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
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Affiliation(s)
- Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork, Cork, Ireland
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Abstract
Leishmania is an infectious protozoan parasite related to African and American trypanosomes. All Leishmania species that are pathogenic to humans can cause dermal disease. When one is confronted with cutaneous leishmaniasis, identification of the causative species is relevant in both clinical and epidemiological studies, case management, and control. This review gives an overview of the currently existing and most used assays for species discrimination, with a critical appraisal of the limitations of each technique. The consensus taxonomy for the genus is outlined, including debatable species designations. Finally, a numerical literature analysis is presented that describes which methods are most used in various countries and regions in the world, and for which purposes.
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Affiliation(s)
- Gert Van der Auwera
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium Antwerp University, Department of Biomedical Sciences, Antwerp, Belgium
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16
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Genetic Diversity and Phylogenetic Relationship Analysis between Red Jungle Fowl and Domestic Chicken using AFLP Markers. J Poult Sci 2015. [DOI: 10.2141/jpsa.0140145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Bahador A, Taheri M, Pourakbari B, Hashemizadeh Z, Rostami H, Mansoori N, Raoofian R. Emergence of Rifampicin, Tigecycline, and Colistin-ResistantAcinetobacter baumanniiin Iran; Spreading of MDR Strains of Novel International Clone Variants. Microb Drug Resist 2013; 19:397-406. [DOI: 10.1089/mdr.2012.0233] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Abbas Bahador
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Diagnostic Laboratory Sciences and Technology Research Center, Faculty of Paramedical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Babak Pourakbari
- Pediatrics Infectious Disease Research Center, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Hashemizadeh
- Department of Microbiology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Rostami
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Noormohamad Mansoori
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Raoofian
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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18
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Towards a transferable and cost-effective plant AFLP protocol. PLoS One 2013; 8:e61704. [PMID: 23613908 PMCID: PMC3628351 DOI: 10.1371/journal.pone.0061704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 03/15/2013] [Indexed: 11/30/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae), Pennisetum setaceum and Poa annua (Poaceae), Lantana camara (Verbenaceae), Bassia diffusa (Chenopodiaceae), Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae)). Highly polymorphic and reproducible genotypic fingerprints (between 37–144 polymorphic loci per species tested) were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.
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Vanstechelman I, Sabbe K, Vyverman W, Vanormelingen P, Vuylsteke M. Linkage mapping identifies the sex determining region as a single locus in the Pennate diatom Seminavis robusta. PLoS One 2013; 8:e60132. [PMID: 23527302 PMCID: PMC3603935 DOI: 10.1371/journal.pone.0060132] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
The pennate diatom Seminavis robusta, characterized by an archetypical diatom life cycle including a heterothallic mating system, is emerging as a model system for studying the molecular regulation of the diatom cell and life cycle. One of its main advantages compared with other diatom model systems is that sexual crosses can be made routinely, offering unprecedented possibilities for forward genetics. To date, nothing is known about the genetic basis of sex determination in diatoms. Here, we report on the construction of mating type-specific linkage maps for S. robusta, and use them to identify a single locus sex determination system in this diatom. We identified 13 mating type plus and 15 mating type minus linkage groups obtained from the analysis of 463 AFLP markers segregating in a full-sib family, covering 963.7 and 972.2 cM, respectively. Five linkage group pairs could be identified as putative homologues. The mating type phenotype mapped as a monogenic trait, disclosing the mating type plus as the heterogametic sex. This study provides the first evidence for a genetic sex determining mechanism in a diatom.
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Affiliation(s)
- Ives Vanstechelman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Koen Sabbe
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Pieter Vanormelingen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
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20
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De Vos S, Bossier P, Van Stappen G, Vercauteren I, Sorgeloos P, Vuylsteke M. A first AFLP-based genetic linkage map for brine shrimp Artemia franciscana and its application in mapping the sex locus. PLoS One 2013; 8:e57585. [PMID: 23469207 PMCID: PMC3587612 DOI: 10.1371/journal.pone.0057585] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/22/2013] [Indexed: 12/26/2022] Open
Abstract
We report on the construction of sex-specific linkage maps, the identification of sex-linked markers and the genome size estimation for the brine shrimp Artemia franciscana. Overall, from the analysis of 433 AFLP markers segregating in a 112 full-sib family we identified 21 male and 22 female linkage groups (2n = 42), covering 1,041 and 1,313 cM respectively. Fifteen putatively homologous linkage groups, including the sex linkage groups, were identified between the female and male linkage map. Eight sex-linked AFLP marker alleles were inherited from the female parent, supporting the hypothesis of a WZ-ZZ sex-determining system. The haploid Artemia genome size was estimated to 0.93 Gb by flow cytometry. The produced Artemia linkage maps provide the basis for further fine mapping and exploring of the sex-determining region and are a possible marker resource for mapping genomic loci underlying phenotypic differences among Artemia species.
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Affiliation(s)
- Stephanie De Vos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Peter Bossier
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Gilbert Van Stappen
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Ilse Vercauteren
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Patrick Sorgeloos
- Laboratory of Aquaculture, Artemia Reference Center (ARC), Department of Animal Production, Ghent University, Gent, Belgium
| | - Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Gent, Belgium
- Department of Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- * E-mail:
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Nakatsuka T, Yamada E, Saito M, Hikage T, Ushiku Y, Nishihara M. Construction of the first genetic linkage map of Japanese gentian (Gentianaceae). BMC Genomics 2012. [PMID: 23186361 PMCID: PMC3561071 DOI: 10.1186/1471-2164-13-672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Background Japanese gentians (Gentiana triflora and Gentiana scabra) are amongst the most popular floricultural plants in Japan. However, genomic resources for Japanese gentians have not yet been developed, mainly because of the heterozygous genome structure conserved by outcrossing, the long juvenile period, and limited knowledge about the inheritance of important traits. In this study, we developed a genetic linkage map to improve breeding programs of Japanese gentians. Results Enriched simple sequence repeat (SSR) libraries from a G. triflora double haploid line yielded almost 20,000 clones using 454 pyrosequencing technology, 6.7% of which could be used to design SSR markers. To increase the number of molecular markers, we identified three putative long terminal repeat (LTR) sequences using the recently developed inter-primer binding site (iPBS) method. We also developed retrotransposon microsatellite amplified polymorphism (REMAP) markers combining retrotransposon and inter-simple sequence repeat (ISSR) markers. In addition to SSR and REMAP markers, modified amplified fragment length polymorphism (AFLP) and random amplification polymorphic DNA (RAPD) markers were developed. Using 93 BC1 progeny from G. scabra backcrossed with a G. triflora double haploid line, 19 linkage groups were constructed with a total of 263 markers (97 SSR, 97 AFLP, 39 RAPD, and 30 REMAP markers). One phenotypic trait (stem color) and 10 functional markers related to genes controlling flower color, flowering time and cold tolerance were assigned to the linkage map, confirming its utility. Conclusions This is the first reported genetic linkage map for Japanese gentians and for any species belonging to the family Gentianaceae. As demonstrated by mapping of functional markers and the stem color trait, our results will help to explain the genetic basis of agronomic important traits, and will be useful for marker-assisted selection in gentian breeding programs. Our map will also be an important resource for further genetic analyses such as mapping of quantitative trait loci and map-based cloning of genes in this species.
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Affiliation(s)
- Takashi Nakatsuka
- Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, Iwate 024-0003, Japan
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Gallardo CE, Correa C, Morales P, Sáez PA, Pastenes L, Méndez MA. Validation of a cheap and simple nondestructive method for obtaining
AFLP
s and
DNA
sequences (mitochondrial and nuclear) in amphibians. Mol Ecol Resour 2012; 12:1090-6. [PMID: 22978706 DOI: 10.1111/1755-0998.12013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/07/2012] [Accepted: 08/14/2012] [Indexed: 11/26/2022]
Affiliation(s)
- C. E. Gallardo
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
| | - C. Correa
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Alameda 340 PO Box 114‐D Santiago Chile
| | - P. Morales
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
| | - P. A. Sáez
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
| | - L. Pastenes
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
| | - M. A. Méndez
- Laboratorio de Genética y Evolución Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Las Palmeras 3425, Ñuñoa PO Box 653 Santiago Chile
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Leishmania AFLP: Paving the way towards improved molecular assays and markers of diversity. INFECTION GENETICS AND EVOLUTION 2011; 11:960-7. [DOI: 10.1016/j.meegid.2011.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/14/2011] [Accepted: 03/14/2011] [Indexed: 11/24/2022]
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Guan L, Shiraishi S. Improved AFLP protocol using dual-suppression PCR and its application to species with large genomes. Mol Ecol Resour 2011; 11:854-61. [PMID: 21676205 DOI: 10.1111/j.1755-0998.2011.03029.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To improve the amplified fragment length polymorphism assay, dual-suppression PCR was introduced into the preamplification step of the assay. The dual-suppression PCR blocked completely the amplification of fragments with the same sequence (Bsp1407I-Bsp1407I or NlaIII-NlaIII) at both ends and amplified selectively fragments with different adaptor sequences (Bsp1407I-NlaIII) at each end. Two protocols, referred to as A and B, were established for species with medium- and large-sized genomes, respectively. Both protocols incorporated the dual-suppression PCR. Protocol A resulted in high-quality electrophoretic profiles for black cottonwood and rice, which have medium-sized genomes. In protocol B, an intensely selective PCR step was added to protocol A. Protocol B yielded profiles for Japanese black pine and Japanese cedar that were improved significantly relative to protocol A: the number of strong peaks increased and that of low peaks decreased. Japanese black pine and Japanese cedar have large genomes. The optimal profiles were generated with a total of eight or nine selective nucleotides.
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Affiliation(s)
- Lanhua Guan
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka 812-8581, Japan
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He SP, Sun JL, Zhang C, Du XM. Identification of exotic genetic components and DNA methylation pattern analysis of three cotton introgression lines from Gossypium bickii. Mol Biol 2011. [DOI: 10.1134/s002689331102018x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Zhang L, Yang G, Guo S, Wei Q, Zou G. Construction of a genetic linkage map for silver carp (Hypophthalmichthys molitrix). Anim Genet 2011; 41:523-30. [PMID: 20331598 DOI: 10.1111/j.1365-2052.2010.02031.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For silver carp (Hypophthalmichthys molitrix), a combined microsatellite (or simple sequence repeat) and amplified fragment length polymorphism (AFLP) sex average linkage map was constructed. A total of 483 markers (245 microsatellites and 238 AFLPs) were assigned to 33 linkage groups. The map spanned 1352.2 cM, covering 86.4% of the estimated genome size of silver carp. The maximum and average spaces between 420 loci were 21.5 cM and 3.2 cM, respectively. The length of linkage groups ranged from 3.6 cM to 98.5 cM with an average of 41.0 cM. The number of markers per group varied from 2 to 44 with an average of 14.6. The AFLP markers significantly improved the integrity of microsatellite-based linkage groups and increased the genome coverage and marker evenness. A genome-wide recombination suppression was observed in male. In an extreme case, six microsatellites co-segregated in male, but spanned a 45.1 cM region in female.
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Affiliation(s)
- L Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Harel-Beja R, Tzuri G, Portnoy V, Lotan-Pompan M, Lev S, Cohen S, Dai N, Yeselson L, Meir A, Libhaber SE, Avisar E, Melame T, van Koert P, Verbakel H, Hofstede R, Volpin H, Oliver M, Fougedoire A, Stalh C, Fauve J, Copes B, Fei Z, Giovannoni J, Ori N, Lewinsohn E, Sherman A, Burger J, Tadmor Y, Schaffer AA, Katzir N. A genetic map of melon highly enriched with fruit quality QTLs and EST markers, including sugar and carotenoid metabolism genes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:511-33. [PMID: 20401460 DOI: 10.1007/s00122-010-1327-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/22/2010] [Indexed: 05/03/2023]
Abstract
A genetic map of melon enriched for fruit traits was constructed, using a recombinant inbred (RI) population developed from a cross between representatives of the two subspecies of Cucumis melo L.: PI 414723 (subspecies agrestis) and 'Dulce' (subspecies melo). Phenotyping of 99 RI lines was conducted over three seasons in two locations in Israel and the US. The map includes 668 DNA markers (386 SSRs, 76 SNPs, six INDELs and 200 AFLPs), of which 160 were newly developed from fruit ESTs. These ESTs include candidate genes encoding for enzymes of sugar and carotenoid metabolic pathways that were cloned from melon cDNA or identified through mining of the International Cucurbit Genomics Initiative database (http://www.icugi.org/). The map covers 1,222 cM with an average of 2.672 cM between markers. In addition, a skeleton physical map was initiated and 29 melon BACs harboring fruit ESTs were localized to the 12 linkage groups of the map. Altogether, 44 fruit QTLs were identified: 25 confirming QTLs described using other populations and 19 newly described QTLs. The map includes QTLs for fruit sugar content, particularly sucrose, the major sugar affecting sweetness in melon fruit. Six QTLs interacting in an additive manner account for nearly all the difference in sugar content between the two genotypes. Three QTLs for fruit flesh color and carotenoid content were identified. Interestingly, no clear colocalization of QTLs for either sugar or carotenoid content was observed with over 40 genes encoding for enzymes involved in their metabolism. The RI population described here provides a useful resource for further genomics and metabolomics studies in melon, as well as useful markers for breeding for fruit quality.
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Affiliation(s)
- R Harel-Beja
- Department of Vegetable Research, Agricultural Research Organization, Newe Ya'ar Research Center, P.O. Box 1021, Ramat Yishay, 30095, Israel
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Gort G, van Eeuwijk FA. Codominant scoring of AFLP in association panels. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:337-51. [PMID: 20237752 PMCID: PMC2886132 DOI: 10.1007/s00122-010-1313-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 03/01/2010] [Indexed: 05/11/2023]
Abstract
A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy-Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics.
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Development and evaluation of different PCR-based typing methods for discrimination ofLeishmania donovaniisolates from Nepal. Parasitology 2010; 137:947-57. [DOI: 10.1017/s0031182009991752] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
SUMMARYIntroduction.Leishmania donovani, the causative agent of visceral leishmaniasis in the Indian subcontinent, has been reported to be genetically homogeneous. In order to support ongoing initiatives to eliminate the disease, highly discriminative tools are required for documenting the parasite population and dynamics.Methods.Thirty-four clinical isolates ofL.donovanifrom Nepal were analysed on the basis of size and restriction endonuclease polymorphisms of PCR amplicons from kinetoplast minicircle DNA, 5 nuclear microsatellites, and nuclear loci encoding glycoprotein 63, cysteine proteinase B, and hydrophilic acylated surface protein B. We present and validate a procedure allowing standardized analysis of kDNA fingerprint patterns.Results.Our results show that parasites are best discriminated on the basis of kinetoplast minicircle DNA (14 genotypes) and 1 microsatellite defining 7 genotypes, while the remaining markers discriminated 2 groups or were monomorphic. Combination of all nuclear markers revealed 8 genotypes, while extension with kDNA data yielded 18 genotypes.Conclusion.We present tools that allow discrimination of closely relatedL.donovanistrains circulating in the Terai region of Nepal. These can be used to study the micro-epidemiology of parasite populations, determine the geographical origin of infections, distinguish relapses from re-infection, and monitor the spread of particular variants.
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Van der Auwera G, Bhattarai NR, Odiwuor S, Vuylsteke M. Remarks on identification of amplified fragment length polymorphisms linked to SAG resistance in Leishmania. Acta Trop 2010; 113:92-3. [PMID: 19800857 DOI: 10.1016/j.actatropica.2009.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 09/10/2009] [Accepted: 09/23/2009] [Indexed: 11/29/2022]
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Lu Y, Curtiss J, Miranda D, Hughs E, Zhang J. ATG-anchored AFLP (ATG-AFLP) analysis in cotton. PLANT CELL REPORTS 2008; 27:1645-1653. [PMID: 18584177 DOI: 10.1007/s00299-008-0568-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 05/20/2008] [Accepted: 05/26/2008] [Indexed: 05/26/2023]
Abstract
Amplified fragment length polymorphism (AFLP) marker system has had broad applications in biology. However, the anonymous AFLP markers are mainly amplified from non-coding regions, limiting their usefulness as a functional marker system. To take advantages of the traditional AFLP techniques, we propose substitution of a restriction enzyme that recognizes a restriction site containing ATG, called ATG-anchored AFLP (ATG-AFLP) analysis. In this study, we chose NsiI (recognizing ATGCAT) to replace EcoRI in combination with MseI to completely digest genomic DNA. One specific adaptor, one pre-selective primer and six selective amplification primers for the NsiI site were designed for ligation and PCR. Six NsiI and eight MseI primers generated a total of 1,780 ATG-AFLP fragments, of which 750 (42%) were polymorphic among four genotypes from two cultivated cotton species (Upland cotton, Gossypium hirsutum and Pima cotton, G. barbadense). The number of ATG-AFLP markers was sufficient to separate the four genotypes into two groups, consistent with their evolutionary and breeding history. Our results also showed that ATG-AFLP generated less number of total and polymorphic fragments per primer combination (2-3 vs. 4-5) than conventional AFLP within Upland cotton. Using a recombination inbred line (RIL) population, 62 polymorphic ATG-AFLP markers were mapped to 19 linkage groups with known chromosome anchored simple sequence repeat (SSR) markers. Of the nine ATG-AFLP fragments randomly chosen, three were found to be highly homologous to cotton cDNA sequences. An in-silico analysis of cotton and Arabidopsis cDNA confirmed that the ATG-anchored enzyme combination NsiI/MseI did generate more fragments than the EcoRI/MseI combination.
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Affiliation(s)
- Yingzhi Lu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
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High-density linkage maps and sex-linked markers for the black tiger shrimp (Penaeus monodon). Genetics 2008; 179:917-25. [PMID: 18558652 DOI: 10.1534/genetics.107.080150] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report on the construction of sex-specific high-density linkage maps and identification of sex-linked markers for the black tiger shrimp (Penaeus monodon). Overall, we identified 44 male and 43 female linkage groups (2n = 88) from the analysis of 2,306 AFLP markers segregating in three full-sib families, covering 2,378 and 2,362 cM, respectively. Twenty-one putatively homologous linkage groups, including the sex-linkage groups, were identified between the female and male linkage maps. Six sex-linked AFLP marker alleles were inherited from female parents in the three families, suggesting that the P. monodon adopts a WZ-ZZ sex-determining system. Two sex-linked AFLP markers, one of which we converted into an allele-specific assay, confirmed their association with sex in a panel of 52 genetically unrelated animals.
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Picard Y, Roumagnac P, Legrand D, Humeau L, Robène-Soustrade I, Chiroleu F, Gagnevin L, Pruvost O. Polyphasic characterization of Xanthomonas axonopodis pv. allii associated with outbreaks of bacterial blight on three Allium species in the Mascarene archipelago. PHYTOPATHOLOGY 2008; 98:919-925. [PMID: 18943210 DOI: 10.1094/phyto-98-8-0919] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Based on the number of new reports during the last two decades, bacterial blight of onion (Allium cepa) is considered an emerging disease. The causal agent, Xanthomonas axonopodis pv. allii, is pathogenic to several Allium species after inoculation, but outbreaks worldwide have been primarily reported on onion. We describe a unique epidemiological situation in Réunion Island, France, with concomitant outbreaks on three Allium species, onion, leek (A. porrum), and garlic (A. sativum). There was no host specialization within Allium spp. among strains associated with the three host species. Based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism, strains associated with these outbreaks in Réunion Island were highly related genetically to strains isolated from diseased plant samples and contaminated seed lots in the neighboring island of Mauritius, where the disease has occurred since 1984. All AFLP haplotypes were identified as X. axonopodis pv. allii based on polymerase chain reaction analysis using specific primers, biochemical tests, and/or pathogenicity tests. Two genetically related groups of strains (A and B) that can be distinguished by AFLP, differential utilization of three carbon sources, and xanthomonadin pigment production were detected initially after establishment of the pathogen. In less than 10 years after the establishment of the pathogen there was nearly an extinction of group A strains in Réunion Island, suggesting differences in fitness between strains in the two groups.
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Affiliation(s)
- Y Picard
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université, Pôle de Protection des Plantes, La Réunion, France
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Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology. BMC Genomics 2008; 9:347. [PMID: 18652646 PMCID: PMC2515857 DOI: 10.1186/1471-2164-9-347] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 07/24/2008] [Indexed: 01/06/2023] Open
Abstract
Background After 10-year-use of AFLP (Amplified Fragment Length Polymorphism) technology for DNA fingerprinting and mRNA profiling, large repertories of genome- and transcriptome-derived sequences are available in public databases for model, crop and tree species. AFLP marker systems have been and are being extensively exploited for genome scanning and gene mapping, as well as cDNA-AFLP for transcriptome profiling and differentially expressed gene cloning. The evaluation, annotation and classification of genomic markers and expressed transcripts would be of great utility for both functional genomics and systems biology research in plants. This may be achieved by means of the Gene Ontology (GO), consisting in three structured vocabularies (i.e. ontologies) describing genes, transcripts and proteins of any organism in terms of their associated cellular component, biological process and molecular function in a species-independent manner. In this paper, the functional annotation of about 8,000 AFLP-derived ESTs retrieved in the NCBI databases was carried out by using GO terminology. Results Descriptive statistics on the type, size and nature of gene sequences obtained by means of AFLP technology were calculated. The gene products associated with mRNA transcripts were then classified according to the three main GO vocabularies. A comparison of the functional content of cDNA-AFLP records was also performed by splitting the sequence dataset into monocots and dicots and by comparing them to all annotated ESTs of Arabidopsis and rice, respectively. On the whole, the statistical parameters adopted for the in silico AFLP-derived transcriptome-anchored sequence analysis proved to be critical for obtaining reliable GO results. Such an exhaustive annotation may offer a suitable platform for functional genomics, particularly useful in non-model species. Conclusion Reliable GO annotations of AFLP-derived sequences can be gathered through the optimization of the experimental steps and the statistical parameters adopted. The Blast2GO software was shown to represent a comprehensive bioinformatics solution for an annotation-based functional analysis. According to the whole set of GO annotations, the AFLP technology generates thorough information for angiosperm gene products and shares common features across angiosperm species and families. The utility of this technology for structural and functional genomics in plants can be implemented by serial annotation analyses of genome-anchored fragments and organ/tissue-specific repertories of transcriptome-derived fragments.
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Affiliation(s)
- Alessandro Botton
- Department of Environmental Agronomy and Crop Science, University of Padova, Viale dell'Università 16, Campus of Agripolis, 35020 Legnaro, Italy.
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Hoeberichts FA, Vaeck E, Kiddle G, Coppens E, van de Cotte B, Adamantidis A, Ormenese S, Foyer CH, Zabeau M, Inzé D, Périlleux C, Van Breusegem F, Vuylsteke M. A Temperature-sensitive mutation in the Arabidopsis thaliana phosphomannomutase gene disrupts protein glycosylation and triggers cell death. J Biol Chem 2007; 283:5708-18. [PMID: 18086684 DOI: 10.1074/jbc.m704991200] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eukaryotic phosphomannomutases (PMMs) catalyze the interconversion of mannose 6-phosphate to mannose 1-phosphate and are essential to the biosynthesis of GDP-mannose. As such, plant PMMs are involved in ascorbic acid (AsA) biosynthesis and N-glycosylation. We report on the conditional phenotype of the temperature-sensitive Arabidopsis thaliana pmm-12 mutant. Mutant seedlings were phenotypically similar to wild type seedlings when grown at 16-18 degrees C but died within several days after transfer to 28 degrees C. This phenotype was observed throughout both vegetative and reproductive development. Protein extracts derived from pmm-12 plants had lower PMM protein and enzyme activity levels. In vitro biochemical analysis of recombinant proteins showed that the mutant PMM protein was compromised in its catalytic efficiency (K cat/K m). Despite significantly decreased AsA levels in pmm-12 plants, AsA deficiency could not account for the observed phenotype. Since, at restrictive temperature, total glycoprotein patterns were altered and glycosylation of protein-disulfide isomerase was perturbed, we propose that a deficiency in protein glycosylation is responsible for the observed cell death phenotype.
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Affiliation(s)
- Frank A Hoeberichts
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent University, 9052 Gent, Belgium
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van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJT. Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2007; 2:e1172. [PMID: 18000544 PMCID: PMC2048665 DOI: 10.1371/journal.pone.0001172] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 10/25/2007] [Indexed: 11/18/2022] Open
Abstract
Application of single nucleotide polymorphisms (SNPs) is revolutionizing human bio-medical research. However, discovery of polymorphisms in low polymorphic species is still a challenging and costly endeavor, despite widespread availability of Sanger sequencing technology. We present CRoPS™ as a novel approach for polymorphism discovery by combining the power of reproducible genome complexity reduction of AFLP® with Genome Sequencer (GS) 20/GS FLX next-generation sequencing technology. With CRoPS, hundreds-of-thousands of sequence reads derived from complexity-reduced genome sequences of two or more samples are processed and mined for SNPs using a fully-automated bioinformatics pipeline. We show that over 75% of putative maize SNPs discovered using CRoPS are successfully converted to SNPWave® assays, confirming them to be true SNPs derived from unique (single-copy) genome sequences. By using CRoPS, polymorphism discovery will become affordable in organisms with high levels of repetitive DNA in the genome and/or low levels of polymorphism in the (breeding) germplasm without the need for prior sequence information.
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Vuylsteke M, Peleman JD, van Eijk MJT. AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis. Nat Protoc 2007; 2:1399-413. [PMID: 17545977 DOI: 10.1038/nprot.2007.174] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although DNA microarrays are currently the standard tool for genome-wide expression analysis, their application is limited to organisms for which the complete genome sequence or large collections of known transcript sequences are available. Here, we describe a protocol for cDNA-AFLP, an AFLP-based transcript profiling method that allows genome-wide expression analysis in any species without the need for prior sequence knowledge. In essence, the cDNA-AFLP method involves reverse transcription of mRNA into double-stranded cDNA, followed by restriction digestion, ligation of specific adapters and fractionation of this mixture of cDNA fragments into smaller subsets by selective PCR amplification. The resulting cDNA-AFLP fragments are separated on high-resolution gels, and visualization of cDNA-AFLP fingerprints is described using either a conventional autoradiography platform or an automated LI-COR system. Observed differences in band intensities between samples provide a good measure of the relative differences in the gene expression levels. Identification of differentially expressed genes can be accomplished by purifying cDNA-AFLP fragments from sequence gels and subsequent sequencing. This method has found widespread use as an attractive technology for gene discovery on the basis of fragment detection and for temporal quantitative gene expression analysis. The protocol can be completed in 3-4 d.
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Affiliation(s)
- Marnik Vuylsteke
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Ghent, Belgium.
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