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Mensah BA, Akyea-Bobi NE, Ghansah A. Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub-Saharan Africa. FRONTIERS IN EPIDEMIOLOGY 2022; 2:939291. [PMID: 38455324 PMCID: PMC10911004 DOI: 10.3389/fepid.2022.939291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/10/2022] [Indexed: 03/09/2024]
Abstract
Transmission dynamics is an important indicator for malaria control and elimination. As we move closer to eliminating malaria in Sub-Saharan Africa (sSA), transmission indices with higher resolution (genomic approaches) will complement our current measurements of transmission. Most of the present programmatic knowledge of malaria transmission patterns are derived from assessments of epidemiologic and clinical data, such as case counts, parasitological estimates of parasite prevalence, and Entomological Inoculation Rates (EIR). However, to eliminate malaria from endemic areas, we need to track changes in the parasite population and how they will impact transmission. This is made possible through the evolving field of genomics and genetics, as well as the development of tools for more in-depth studies on the diversity of parasites and the complexity of infections, among other topics. If malaria elimination is to be achieved globally, country-specific elimination activities should be supported by parasite genomic data from regularly collected blood samples for diagnosis, surveillance and possibly from other programmatic interventions. This presents a unique opportunity to track the spread of malaria parasites and shed additional light on intervention efficacy. In this review, various genetic techniques are highlighted along with their significance for an enhanced understanding of transmission patterns in distinct topological settings throughout Sub-Saharan Africa. The importance of these methods and their limitations in malaria surveillance to guide control and elimination strategies, are explored.
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Affiliation(s)
- Benedicta A. Mensah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nukunu E. Akyea-Bobi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Roy S, Bhandari V, Barman M, Kumar P, Bhanot V, Arora JS, Singh S, Sharma P. Population Genetic Analysis of the Theileria annulata Parasites Identified Limited Diversity and Multiplicity of Infection in the Vaccine From India. Front Microbiol 2021; 11:579929. [PMID: 33552006 PMCID: PMC7854550 DOI: 10.3389/fmicb.2020.579929] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Apicomplexan parasite Theileria annulata causes significant economic loss to the livestock industry in India and other tropical countries. In India, parasite control is mainly dependent on the live attenuated schizont vaccine and the drug buparvaquone. For effective disease control, it is essential to study the population structure and genetic diversity of the Theileria annulata field isolates and vaccine currently used in India. Methodology/Results: A total of 125 T. annulata isolates were genotyped using 10 microsatellite markers from four states belonging to different geographical locations of India. Limited genetic diversity was observed in the vaccine isolates when compared to the parasites in the field; a level of geographical substructuring was evident in India. The number of genotypes observed per infection was highest in India when compared to other endemic countries, suggesting high transmission intensity and abundance of ticks in the country. A reduced panel of four markers can be used for future studies in these for surveillance of the T. annulata parasites in India. Conclusion: High genetic variation between the parasite populations in the country suggests their successful spread in the field and could hamper the disease control programs. Our findings provide the baseline data for the diversity and population structure of T. annulata parasites from India. The low diversity in the vaccine advocates improving the current vaccine, possibly by increasing its heterozygosity. The reduced panel of the markers identified in this study will be helpful in monitoring parasite and its reintroduction after Theileria eradication.
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Affiliation(s)
- Sonti Roy
- National Institute of Animal Biotechnology, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, India
| | | | | | - Pankaj Kumar
- Division of Livestock and Fisheries Management, ICAR-Research Complex for Eastern Region, Patna, India
| | - Vandna Bhanot
- Disease Investigation Laboratory, Lala Lajpat Rai University of Veterinary and Animal Sciences, Ambala, India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Punjab, India
| | - Satparkash Singh
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Punjab, India
| | - Paresh Sharma
- National Institute of Animal Biotechnology, Hyderabad, India
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Huang F, Jacob CG, Takala-Harrison S, Adams M, Yang HL, Liu H, Xia ZG, Zhou SS, Tang LH, Plowe CV. Genomic Epidemiology of Antimalarial Drug Resistance in Plasmodium falciparum in Southern China. Front Cell Infect Microbiol 2021; 10:610985. [PMID: 33489939 PMCID: PMC7820777 DOI: 10.3389/fcimb.2020.610985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/20/2020] [Indexed: 12/05/2022] Open
Abstract
Emerging artemisinin resistance in Southeast Asia poses a significant risk to malaria control and eradication goals, including China’s plan to eliminate malaria nationwide by 2020. Plasmodium falciparum was endemic in China, especially in Southern China. Parasites from this region have shown decreased susceptibility to artemisinin and delayed parasite clearance after artemisinin treatment. Understanding the genetic basis of artemisinin resistance and identifying specific genetic loci associated with this phenotype is crucial for surveillance and containment of resistance. In this study, parasites were collected from clinical patients from Yunnan province and Hainan island. The parasites were genotyped using a P. falciparum-specific single nucleotide polymorphism (SNP) microarray. The SNP profiles examined included a total of 27 validated and candidate molecular markers of drug resistance. The structure of the parasite population was evaluated by principal component analysis by using the EIGENSOFT program, and ADMIXTURE was used to calculate maximum likelihood estimates for the substructure analysis. Parasites showed a high prevalence of resistance haplotypes of pfdhfr and pfdhps and moderate prevalence of pfcrt. There was no mutation identified on pfmdr1. Candidate SNPs on chromosomes 10, 13, and 14 that were associated with delayed parasite clearance showed a low prevalence of mutants. Parasites from Southern China were clustered and separated from those from Southeast Asia. Parasites from Yunnan province were substructured from parasites from Hainan island. This study provides evidence for a genomic population with drug resistance in Southern China and also illustrates the utility of SNP microarrays for large-scale parasite molecular epidemiology.
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Affiliation(s)
- Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | | | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Heng-Lin Yang
- Malaria Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Hui Liu
- Malaria Department, Yunnan Institute of Parasitic Diseases, Puer, China
| | - Zhi-Gui Xia
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Shui-Sen Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
| | - Lin-Hua Tang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Chinese Center for Tropical Diseases Research, Key Laboratory of Parasite and Vector Biology, Ministry of Health, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, China
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4
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Daniels RF, Schaffner SF, Dieye Y, Dieng G, Hainsworth M, Fall FB, Diouf CN, Ndiop M, Cisse M, Gueye AB, Sarr O, Guinot P, Deme AB, Bei AK, Sy M, Thwing J, MacInnis B, Earle D, Guinovart C, Sene D, Hartl DL, Ndiaye D, Steketee RW, Wirth DF, Volkman SK. Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal. Malar J 2020; 19:276. [PMID: 32746830 PMCID: PMC7397603 DOI: 10.1186/s12936-020-03346-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/25/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. METHODS A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. RESULTS Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. CONCLUSIONS These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.
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Affiliation(s)
- Rachel F. Daniels
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA
| | | | | | | | | | - Fatou B. Fall
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | - Medoune Ndiop
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | | | - Oumar Sarr
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | - Awa B. Deme
- Dantec Teaching and Research Hospital, Dakar, Senegal
| | - Amy K. Bei
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA
| | - Mouhamad Sy
- Dantec Teaching and Research Hospital, Dakar, Senegal
| | - Julie Thwing
- grid.416738.f0000 0001 2163 0069Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | | | | | - Doudou Sene
- Senegal National Malaria Control Programme, Dakar, Senegal
| | - Daniel L. Hartl
- grid.38142.3c000000041936754XHarvard University, Cambridge, MA USA
| | - Daouda Ndiaye
- grid.8191.10000 0001 2186 9619Cheikh Anta Diop University, Dakar, Senegal
| | | | - Dyann F. Wirth
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA
| | - Sarah K. Volkman
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA ,grid.28203.3b0000 0004 0378 6053Simmons University, Boston, MA USA
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5
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Ye R, Tian Y, Huang Y, Zhang Y, Wang J, Sun X, Zhou H, Zhang D, Pan W. Genome-Wide Analysis of Genetic Diversity in Plasmodium falciparum Isolates From China-Myanmar Border. Front Genet 2019; 10:1065. [PMID: 31737048 PMCID: PMC6830057 DOI: 10.3389/fgene.2019.01065] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/03/2019] [Indexed: 12/29/2022] Open
Abstract
Plasmodium falciparum isolates from China-Myanmar border (CMB) have experienced regional special selective pressures and adaptive evolution. However, the genomes of P. falciparum isolates from this region to date are poorly characterized. Herein, we performed whole-genome sequencing of 34 P. falciparum isolates from CMB and a series of genome-wide sequence analyses to reveal their genetic diversity, population structures, and comparisons with the isolates from other epidemic regions (Thai-Cambodia border, Thai-Myanmar border, and West Africa). Totally 59,720 high-quality single-nucleotide polymorphisms (SNPs) were identified in the P. falciparum isolates from CMB, with average nucleotide diversity (π = 4.59 × 10-4) and LD decay (132 bp). The Tajima's D and Fu and Li's D values of the CMB isolates were -0.8 (p < 0.05) and -0.84 (p < 0.05), respectively, suggesting a demographic history of recent population expansion or purifying selection. Moreover, 78 genes of the parasite were identified that could be under positive selection, including those genes conferring drug resistance such as pfubp1. In addition, 33 SNPs were identified for tracing the source of the parasites with a high accuracy by analysis of the most differential SNPs among the four epidemic regions. Collectively, our data demonstrated high diversity of the CMB isolates' genomes forming a distinct population, and the identification of 33-SNP barcode provides a valuable surveillance of parasite migration among the regions.
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Affiliation(s)
- Run Ye
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yini Tian
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yufu Huang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Yilong Zhang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Jian Wang
- Yunnan Institute of Parasitic Diseases, Puer, China
| | - Xiaodong Sun
- Yunnan Institute of Parasitic Diseases, Puer, China
| | | | - Dongmei Zhang
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
| | - Weiqing Pan
- Department of Tropical Diseases, Naval Medical University, Shanghai, China
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Apinjoh TO, Ouattara A, Titanji VPK, Djimde A, Amambua-Ngwa A. Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa? Malar J 2019; 18:217. [PMID: 31242921 PMCID: PMC6595576 DOI: 10.1186/s12936-019-2844-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The intensification of malaria control interventions has resulted in its global decline, but it remains a significant public health burden especially in sub-Saharan Africa (sSA). Knowledge on the parasite diversity, its transmission dynamics, mechanisms of adaptation to environmental and interventional pressures could help refine or develop new control and elimination strategies. Critical to this is the accurate assessment of the parasite’s genetic diversity and monitoring of genetic markers of anti-malarial resistance across all susceptible populations. Such wide molecular surveillance will require selected tools and approaches from a variety of ever evolving advancements in technology and the changing epidemiology of malaria. The choice of an effective approach for specific endemic settings remains challenging, particularly for countries in sSA with limited access to advanced technologies. This article examines the current strategies and tools for Plasmodium falciparum genetic diversity typing and resistance monitoring and proposes how the different tools could be employed in resource-poor settings. Advanced approaches enabling targeted deep sequencing is valued as a sensitive method for assessing drug resistance and parasite diversity but remains out of the reach of most laboratories in sSA due to the high cost of development and maintenance. It is, however, feasible to equip a limited number of laboratories as Centres of Excellence in Africa (CEA), which will receive and process samples from a network of peripheral laboratories in the continent. Cheaper, sensitive and portable real-time PCR methods can be used in peripheral laboratories to pre-screen and select samples for targeted deep sequence or genome wide analyses at these CEAs.
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Affiliation(s)
- Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Amed Ouattara
- School of Medicine, University of Maryland, College Park, Baltimore, USA
| | - Vincent P K Titanji
- Faculty of Science, Engineering and Technology, Cameroon Christian University, Bali, Cameroon
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
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7
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Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nat Commun 2019; 10:2665. [PMID: 31209259 PMCID: PMC6572796 DOI: 10.1038/s41467-019-10121-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 04/17/2019] [Indexed: 02/08/2023] Open
Abstract
Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
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Affiliation(s)
- Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | | | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Yao Li
- Center for Geospatial Information Science, University of Maryland, College Park, MD, 20742, USA
| | - Sonia Agrawal
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David L Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Khan Daun Penh, Phnom Penh, Cambodia
| | - Mark M Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, 1202, Switzerland
| | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, 11191, Myanmar
| | | | - Myaing M Nyunt
- Duke Global Health Institute, Duke University, Durham, NC, 27710, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Stewart
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Fulakeza J, McNitt S, Vareta J, Saidi A, Mvula G, Taylor T, Mathanga DP, Small DS, Skarbinski J, Gutman JR, Seydel K. Comparison of msp genotyping and a 24 SNP molecular assay for differentiating Plasmodium falciparum recrudescence from reinfection. Malar J 2019; 18:84. [PMID: 30885193 PMCID: PMC6423793 DOI: 10.1186/s12936-019-2695-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/01/2019] [Indexed: 08/23/2023] Open
Abstract
Background Current World Health Organization guidelines for conducting anti-malarial drug efficacy clinical trials recommend genotyping Plasmodium falciparum genes msp1 and msp2 to distinguish recrudescence from reinfection. A more recently developed potential alternative to this method is a molecular genotyping assay based on a panel of 24 single nucleotide polymorphism (SNP) markers. Methods Performance parameters of these two genotyping methods were compared using data from two recently completed drug efficacy trials. Blood samples from two anti-malarial therapeutic trials were analysed by both msp genotyping and the 24 SNP assay. Additionally, to conserve time and resources, the statistical program R was used to select the most informative SNPs for a set of unrelated Malawian samples to develop a truncated SNP-based assay for the region surrounding Blantyre, Malawi. The ability of this truncated assay to distinguish reinfection from recrudescence when compared to the full 24 SNP assay was then analysed using data from the therapeutic trials. Results A total of 360 samples were analysed; 66 for concordance of msp and SNP barcoding methodologies, and 294 for assessing the most informative of the 24 SNP markers. SNP genotyping performed comparably to msp genotyping, with only one case of disagreement among the 50 interpretable results, where the SNP assay identified the sample as reinfection and the msp typing as recrudescence. Furthermore, SNP typing was more robust; only 6% of samples were uninterpretable by SNP typing, compared to 19.7% when msp genotyping was used. For discriminating reinfection from recrudescence, a truncated 6 SNP assay was found to perform at 95.1% the accuracy of the full 24 SNP bar code. Conclusions The use of SNP analysis has similar sensitivity to the standard msp genotyping in determining recrudescence from reinfection. Although more expensive, SNP typing is faster and less work intensive. Limiting the assay to those SNPs most informative in the geographical region of interest may further decrease the workload and the cost, making this technique a feasible and affordable alternative in drug efficacy trials. Electronic supplementary material The online version of this article (10.1186/s12936-019-2695-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Fulakeza
- Department of Biomedical Sciences, University of Malawi, College of Medicine, P/Bag 360, Chichiri, Blantyre 3, Malawi
| | - Sarah McNitt
- Department of Cell and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jimmy Vareta
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Alex Saidi
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Godfrey Mvula
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi
| | - Terrie Taylor
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi.,Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - Don P Mathanga
- Department of Biomedical Sciences, University of Malawi, College of Medicine, P/Bag 360, Chichiri, Blantyre 3, Malawi
| | - Dylan S Small
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, USA
| | | | - Julie R Gutman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, US Center for Disease Control and Prevention, Atlanta, USA
| | - Karl Seydel
- Blantyre Malaria Project, University of Malawi College of Medicine, Blantyre, Malawi. .,Department of Osteopathic Medical Specialties, College of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA.
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9
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Yin F, Liu Z, Liu J, Liu A, Salih DA, Li Y, Liu G, Luo J, Guan G, Yin H. Population Genetic Analysis of Theileria annulata from Six Geographical Regions in China, Determined on the Basis of Micro- and Mini-satellite Markers. Front Genet 2018. [PMID: 29515624 PMCID: PMC5826064 DOI: 10.3389/fgene.2018.00050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Theileria annulata, a tick-borne apicomplexan protozoan, causes a lymphoproliferative disease of cattle with high prevalence in tropical and sub-tropical regions. Understanding the genetic diversity and structure of local populations will provide more fundamental knowledge for the population genetics and epidemics of protozoa. In this study, 78 samples of T. annulata collected from cattle/yaks representing 6 different geographic populations in China were genotyped using eight micro- and mini-satellite markers. High genetic variation within population, moderate genetic differentiation, and high level of diversity co-occurring with significant linkage disequilibrium were observed, which indicates there is gene flow between these populations in spite of the existence of reproductive and geographical barriers among populations. Furthermore, some degree of genetic differentiation was also found between samples from China and Oman. These findings provide a first glimpse of the genetic diversity of the T. annulata populations in China, and might contribute to the knowledge of distribution, dynamics, and epidemiology of T. annulata populations and optimize the management strategies for control.
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Affiliation(s)
- Fangyuan Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhijie Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Junlong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Aihong Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | | | - Youquan Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guiquan Guan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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10
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Lo E, Hemming-Schroeder E, Yewhalaw D, Nguyen J, Kebede E, Zemene E, Getachew S, Tushune K, Zhong D, Zhou G, Petros B, Yan G. Transmission dynamics of co-endemic Plasmodium vivax and P. falciparum in Ethiopia and prevalence of antimalarial resistant genotypes. PLoS Negl Trop Dis 2017; 11:e0005806. [PMID: 28746333 PMCID: PMC5546713 DOI: 10.1371/journal.pntd.0005806] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 08/07/2017] [Accepted: 07/13/2017] [Indexed: 11/19/2022] Open
Abstract
Ethiopia is one of the few African countries where Plasmodium vivax is co-endemic with P. falciparum. Malaria transmission is seasonal and transmission intensity varies mainly by landscape and climate. Although the recent emergence of drug resistant parasites presents a major issue to malaria control in Ethiopia, little is known about the transmission pathways of parasite species and prevalence of resistant markers. This study used microsatellites to determine population diversity and gene flow patterns of P. falciparum (N = 226) and P. vivax (N = 205), as well as prevalence of drug resistant markers to infer the impact of gene flow and existing malaria treatment regimes. Plasmodium falciparum indicated a higher rate of polyclonal infections than P. vivax. Both species revealed moderate genetic diversity and similar population structure. Populations in the northern highlands were closely related to the eastern Rift Valley, but slightly distinct from the southern basin area. Gene flow via human migrations between the northern and eastern populations were frequent and mostly bidirectional. Landscape genetic analyses indicated that environmental heterogeneity and geographical distance did not constrain parasite gene flow. This may partly explain similar patterns of resistant marker prevalence. In P. falciparum, a high prevalence of mutant alleles was detected in codons related to chloroquine (pfcrt and pfmdr1) and sulfadoxine-pyrimethamine (pfdhps and pfdhfr) resistance. Over 60% of the samples showed pfmdr1 duplications. Nevertheless, no mutation was detected in pfK13 that relates to artemisinin resistance. In P. vivax, while sequences of pvcrt-o were highly conserved and less than 5% of the samples showed pvmdr duplications, over 50% of the samples had pvmdr1 976F mutation. It remains to be tested if this mutation relates to chloroquine resistance. Monitoring the extent of malaria spread and markers of drug resistance is imperative to inform policy for evidence-based antimalarial choice and interventions. To effectively reduce malaria burden in Ethiopia, control efforts should focus on seasonal migrant populations.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antimalarials/pharmacology
- Child
- Child, Preschool
- Drug Resistance
- Endemic Diseases
- Ethiopia/epidemiology
- Female
- Gene Flow
- Genes, Protozoan
- Genetics, Population
- Genotype
- Humans
- Infant
- Infant, Newborn
- Malaria, Falciparum/epidemiology
- Malaria, Falciparum/parasitology
- Malaria, Falciparum/transmission
- Malaria, Vivax/epidemiology
- Malaria, Vivax/parasitology
- Malaria, Vivax/transmission
- Male
- Microsatellite Repeats
- Middle Aged
- Plasmodium falciparum/drug effects
- Plasmodium falciparum/genetics
- Plasmodium falciparum/isolation & purification
- Plasmodium vivax/drug effects
- Plasmodium vivax/genetics
- Plasmodium vivax/isolation & purification
- Prevalence
- Young Adult
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Affiliation(s)
- Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail: (EL); (GY)
| | | | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Jennifer Nguyen
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Estifanos Kebede
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Endalew Zemene
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Sisay Getachew
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Kora Tushune
- Department of Health Services Management, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Daibin Zhong
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Guofa Zhou
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Beyene Petros
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, United States of America
- * E-mail: (EL); (GY)
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11
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Fouad H, Hongjie L, Hosni D, Wei J, Abbas G, Ga'al H, Jianchu M. Controlling Aedes albopictus and Culex pipiens pallens using silver nanoparticles synthesized from aqueous extract of Cassia fistula fruit pulp and its mode of action. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2017; 46:558-567. [PMID: 28541740 DOI: 10.1080/21691401.2017.1329739] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Mosquitoes act as key vector for transmission of devastating parasites and pathogens which affect millions of people globally. In this research, the green synthesis of silver nanoparticles of Cassia fistula fruit pulp as an innovative and operative tool against vector mosquitoes is presented. Silver nanoparticles were characterized by a series of techniques including Fourier transform infrared spectroscopy, Transmission Electron Microscope and confirmed by Scanning Electron Microscope, UV-Vis spectrophotometry and X-ray diffraction. Silver nanoparticles were highly effective against the larvae (I-IV instar) and pupae of Aedes albopictus and Culex pipiens pallens after 24, 48 and 72 h of treatment. Ae. albopictus had LC50 values ranging from 8.3 mg/L (I instar) to 17.3 mg/L (pupae) and LC50 ranging from 1.1 mg/L (I instar) to 19.0 mg/L (pupae) against Cx. pipiens pallens. The systemic effect of AgNPs was further assessed in the fourth instar larvae of Ae. albopictus and Cx. pipiens pallens by measuring the levels of total proteins and activity of two important marker enzymes: Acetylcholinesterase and α- and β-carboxylesterase. Overall, the findings of the study suggest that the use of Cassia fistula-fruit pulp extract mediated synthesis of silver nanoparticles can be used for controlling vector mosquitoes. This is the first report on the mosquito larvicidal and pupicidal activity of AgNPs synthesized by Cassia fistula fruit pulp and its possible mechanism of action.
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Affiliation(s)
- Hatem Fouad
- a Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects , Institute of Insect Sciences, Zhejiang University , Hangzhou , Zhejiang , PR China.,b Department of Field Crop Pests , Plant Protection Research Institute, Agricultural Research Center , Cairo , Egypt
| | - Li Hongjie
- a Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects , Institute of Insect Sciences, Zhejiang University , Hangzhou , Zhejiang , PR China
| | - Dawood Hosni
- c Department of Agriculture Chemistry, Faculty of Agriculture , Mansoura University , Mansoura , Egypt
| | - Jiqian Wei
- d Hangzhou General Station of Plant Protection and Soil Fertilizer , Hangzhou , Zhejiang , PR China
| | - Ghulam Abbas
- e Department of Chemical Engineering , University of Gujrat , Gujrat , Pakistan
| | - Hassan Ga'al
- a Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects , Institute of Insect Sciences, Zhejiang University , Hangzhou , Zhejiang , PR China
| | - Mo Jianchu
- a Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects , Institute of Insect Sciences, Zhejiang University , Hangzhou , Zhejiang , PR China
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12
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Duffy CW, Ba H, Assefa S, Ahouidi AD, Deh YB, Tandia A, Kirsebom FCM, Kwiatkowski DP, Conway DJ. Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution. Mol Ecol 2017; 26:2880-2894. [PMID: 28214367 PMCID: PMC5485074 DOI: 10.1111/mec.14066] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 02/03/2017] [Accepted: 02/03/2017] [Indexed: 01/29/2023]
Abstract
To determine whether the major human malaria parasite Plasmodium falciparum exhibits fragmented population structure or local adaptation at the northern limit of its African distribution where the dry Sahel zone meets the Sahara, samples were collected from diverse locations within Mauritania over a range of ~1000 km. Microsatellite genotypes were obtained for 203 clinical infection samples from eight locations, and Illumina paired‐end sequences were obtained to yield high coverage genomewide single nucleotide polymorphism (SNP) data for 65 clinical infection samples from four locations. Most infections contained single parasite genotypes, reflecting low rates of transmission and superinfection locally, in contrast to the situation seen in population samples from countries further south. A minority of infections shared related or identical genotypes locally, indicating some repeated transmission of parasite clones without recombination. This caused some multilocus linkage disequilibrium and local divergence, but aside from the effect of repeated genotypes there was minimal differentiation between locations. Several chromosomal regions had elevated integrated haplotype scores (|iHS|) indicating recent selection, including those containing drug resistance genes. A genomewide FST scan comparison with previous sequence data from an area in West Africa with higher infection endemicity indicates that regional gene flow prevents genetic isolation, but revealed allele frequency differentiation at three drug resistance loci and an erythrocyte invasion ligand gene. Contrast of extended haplotype signatures revealed none to be unique to Mauritania. Discrete foci of infection on the edge of the Sahara are genetically highly connected to the wider continental parasite population, and local elimination would be difficult to achieve without very substantial reduction in malaria throughout the region.
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Affiliation(s)
- Craig W Duffy
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Hampate Ba
- Institut National de Recherche en Sante Publique, Nouakchott, Mauritania
| | - Samuel Assefa
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Ambroise D Ahouidi
- Laboratory of Bacteriology and Virology, Le Dantec Hospital, Cheikh Anta Diop University, Dakar, Senegal
| | - Yacine B Deh
- Institut National de Recherche en Sante Publique, Nouakchott, Mauritania
| | - Abderahmane Tandia
- Institut National de Recherche en Sante Publique, Nouakchott, Mauritania
| | - Freja C M Kirsebom
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | | | - David J Conway
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Keppel St, London, WC1E 7HT, UK
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13
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Chang HH, Worby CJ, Yeka A, Nankabirwa J, Kamya MR, Staedke SG, Dorsey G, Murphy M, Neafsey DE, Jeffreys AE, Hubbart C, Rockett KA, Amato R, Kwiatkowski DP, Buckee CO, Greenhouse B. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites. PLoS Comput Biol 2017; 13:e1005348. [PMID: 28125584 PMCID: PMC5300274 DOI: 10.1371/journal.pcbi.1005348] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/09/2017] [Accepted: 01/05/2017] [Indexed: 12/24/2022] Open
Abstract
As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings.
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Affiliation(s)
- Hsiao-Han Chang
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Colin J. Worby
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Adoke Yeka
- Makerere University School of Public Health, College of Health Sciences, Kampala, Uganda
- Infectious Disease Research Collaboration, Kampala, Uganda
| | - Joaniter Nankabirwa
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Moses R. Kamya
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Sarah G. Staedke
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Maxwell Murphy
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
| | - Daniel E. Neafsey
- Genome Sequencing and Analysis Program, Broad Institute, Cambridge, Massachusetts, United States
| | - Anna E. Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Roberto Amato
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P. Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States
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14
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Patnaik BB, Wang TH, Kang SW, Hwang HJ, Park SY, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JS, Han YS, Park HS, Lee YS. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery. PLoS One 2016; 11:e0148622. [PMID: 26872384 PMCID: PMC4752248 DOI: 10.1371/journal.pone.0148622] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/20/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae), is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS) technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction. RESULTS The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO) terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2) were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs) were identified from 61,141 unigenes (size of >1 kb) with the most abundant being dinucleotide repeats. CONCLUSIONS This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata. The transcriptome provides a comprehensive sequence resource for the conservation of genetic information in this species and enrichment of the genetic database. The development of molecular markers will assist in the genetic improvement of C. plicata.
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Affiliation(s)
- Bharat Bhusan Patnaik
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- Trident School of Biotech Sciences, Trident Academy of Creative Technology (TACT), Bhubaneswar- 751024, Odisha, India
| | - Tae Hun Wang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Hee-Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - So Young Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Eun Bi Park
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Jong Min Chung
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Dae Kwon Song
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
| | - Changmu Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Soonok Kim
- National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Jun Sang Lee
- Institute of Environmental Research, Kangwon National University, 1 Kangwondaehak-gil, Chuncheon-si, Gangwon-do, 200-701, Republic of Korea
| | - Yeon Soo Han
- College of Agriculture and Life Science, Chonnam National University, 300 Yongbong-Dong, Buk-gu, Gwangju, 500-757, Republic of Korea
| | - Hong Seog Park
- Research Institute, GnC BIO Co., LTD., 621-6 Banseok-dong, Yuseong-gu, Daejeon, 305-150, Republic of Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, 22 Soonchunhyangro, Shinchang-myeon, Asan, Chungchungnam-do, 336-745, Republic of Korea
- * E-mail:
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