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Ding H, Dong Y, Deng Y, Xu Y, Liu Y, Wu J, Chen M, Zhang C, Liu L, Lin Y. Molecular surveillance of chloroquine resistance in Plasmodium vivax isolates from malaria cases in Yunnan Province of China using pvcrt-o gene polymorphisms. Malar J 2023; 22:338. [PMID: 37940956 PMCID: PMC10631137 DOI: 10.1186/s12936-023-04776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The efficacy of chloroquine treatment for vivax malaria has been rarely evaluated due to a lack of an appropriate testing method. The objective of this study was to conduct molecular monitoring of chloroquine resistance in Plasmodium vivax strains from vivax malaria patients in Yunnan Province, focusing on the analysis of polymorphism in the P. vivax chloroquine resistance transporter protein orthologous gene (pvcrt-o). METHODS In accordance with the principles of a cohort study, blood samples were collected from malaria cases diagnosed with a P. vivax mono-infection in Yunnan Province from 2020 to 2022. Segmental PCR was used to amplify the whole pvcrt-o gene in the blood samples and their products were subsequently sequenced. The sequencing data were arranged to obtain the full coding DNA sequence (CDS) as well as the gene's promoter region sequences. The CDSs were aligned with the reference sequence (XM_001613407.1) of the P. vivax SalI isolate to identify the mutant loci. RESULTS From a total of 375 blood samples taken from vivax malaria cases, 272 both whole gene CDSs (1272-1275 bp) and promoter DNA sequences (707 bp) of pvcrt-o gene were obtained. Among the whole CDSs, there were 7 single nucleotide polymorphic sites in which c.7 A>G was the minor allele frequency (MAF) site with 4.4% (12/272) detection rate. The mutation detection rate showed a significant decrease from 9.8% (10/102) in 2020 to 1.1% (1/92) in 2021 and 1.3% (1/78) in 2022, indicating statistical significance (χ2 = 11.256, P < 0.05). Among the identified 12 haplotypes, the majority of which were wild type (75.7%; 206/272). These four mutant haplotypes (Hap_3, Hap_5, Hap_9, and Hap_10) were classified as "K10 insertion type" and accounted for 12.1% (33/272). The detection rate of Hap_3 increased from 1.0% (1/102) in 2020 to 13.0% (12/92) in 2021 and 14.1% (11/78) in 2022, indicating statistical significance. A total of 23.8% (65/272) of the samples exhibited 14 bp (bp) deletions in the promoter region, occurring most frequently in the wild type haplotype (Hap_1) samples at a rate of 28.6% (59/206). CONCLUSIONS In recent years in Yunnan Province, a notable proportion of vivax malaria patients are infected by P. vivax strains with a "K10 insertion" and partial sequence deletions in the promoter region of the pvcrt-o gene, necessitating vigilance.
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Affiliation(s)
- Hongyun Ding
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Ying Dong
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China.
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Yanchun Xu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Yan Liu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Jing Wu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Mengni Chen
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yingkun Lin
- Center for Disease Control and Prevention, Dehong, 678499, China.
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López-Barragán MJ, Lemieux J, Quiñones M, Williamson KC, Molina-Cruz A, Cui K, Barillas-Mury C, Zhao K, Su XZ. Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum. BMC Genomics 2011; 12:587. [PMID: 22129310 PMCID: PMC3266614 DOI: 10.1186/1471-2164-12-587] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 11/30/2011] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND It has been shown that nearly a quarter of the initial predicted gene models in the Plasmodium falciparum genome contain errors. Although there have been efforts to obtain complete cDNA sequences to correct the errors, the coverage of cDNA sequences on the predicted genes is still incomplete, and many gene models for those expressed in sexual or mosquito stages have not been validated. Antisense transcripts have widely been reported in P. falciparum; however, the extent and pattern of antisense transcripts in different developmental stages remain largely unknown. RESULTS We have sequenced seven bidirectional libraries from ring, early and late trophozoite, schizont, gametocyte II, gametocyte V, and ookinete, and four strand-specific libraries from late trophozoite, schizont, gametocyte II, and gametocyte V of the 3D7 parasites. Alignment of the cDNA sequences to the 3D7 reference genome revealed stage-specific antisense transcripts and novel intron-exon splicing junctions. Sequencing of strand-specific cDNA libraries suggested that more genes are expressed in one direction in gametocyte than in schizont. Alternatively spliced genes, antisense transcripts, and stage-specific expressed genes were also characterized. CONCLUSIONS It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression.
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Affiliation(s)
- María J López-Barragán
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
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Seok JW, Lee YS, Moon EK, Lee JY, Jha BK, Kong HH, Chung DI, Hong Y. Expressed sequence tag analysis of the erythrocytic stage of Plasmodium berghei. THE KOREAN JOURNAL OF PARASITOLOGY 2011; 49:221-8. [PMID: 22072821 PMCID: PMC3210838 DOI: 10.3347/kjp.2011.49.3.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Revised: 06/01/2011] [Accepted: 06/02/2011] [Indexed: 11/23/2022]
Abstract
Rodent malaria parasites, such as Plasmodium berghei, are practical and useful model organisms for human malaria research because of their analogies to the human malaria in terms of structure, physiology, and life cycle. Exploiting the available genetic sequence information, we constructed a cDNA library from the erythrocytic stages of P. berghei and analyzed the expressed sequence tag (EST). A total of 10,040 ESTs were generated and assembled into 2,462 clusters. These EST clusters were compared against public protein databases and 48 putative new transcripts, most of which were hypothetical proteins with unknown function, were identified. Genes encoding ribosomal or membrane proteins and purine nucleotide phosphorylases were highly abundant clusters in P. berghei. Protein domain analyses and the Gene Ontology functional categorization revealed translation/protein folding, metabolism, protein degradation, and multiple family of variant antigens to be mainly prevalent. The presently-collected ESTs and its bioinformatic analysis will be useful resources to identify for drug target and vaccine candidates and validate gene predictions of P. berghei.
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Affiliation(s)
- Ji-Woong Seok
- Department of Parasitology, Kyungpook National University School of Medicine, Daegu 700-422, Korea
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Rodriguez-Soca Y, Munteanu CR, Dorado J, Rabuñal J, Pazos A, González-Díaz H. Plasmod-PPI: A web-server predicting complex biopolymer targets in plasmodium with entropy measures of protein–protein interactions. POLYMER 2010. [DOI: 10.1016/j.polymer.2009.11.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Low ETL, Alias H, Boon SH, Shariff EM, Tan CYA, Ooi LCL, Cheah SC, Raha AR, Wan KL, Singh R. Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis. BMC PLANT BIOLOGY 2008; 8:62. [PMID: 18507865 PMCID: PMC2442076 DOI: 10.1186/1471-2229-8-62] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 05/29/2008] [Indexed: 05/21/2023]
Abstract
BACKGROUND Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. RESULTS A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. CONCLUSION This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.
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Affiliation(s)
- Eng-Ti L Low
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Halimah Alias
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Soo-Heong Boon
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Asiatic Centre for Genome Technology Sdn Bhd (ACGT), Lot L3-I-1, Enterprise 4, Technology Park Malaysia, 57000 Kuala Lumpur, Malaysia
| | - Elyana M Shariff
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Myagri Associates Sdn. Bhd., 25-2, Jalan Seri Putra 1/2, Bandar Seri Putra Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Chi-Yee A Tan
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Thermo Fisher Scientific, 3, Jalan Sepadu 25/123, Taman Perindustrian Axis, Seksyen 25, 40400 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Leslie CL Ooi
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
| | - Suan-Choo Cheah
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
- Asiatic Centre for Genome Technology Sdn Bhd (ACGT), Lot L3-I-1, Enterprise 4, Technology Park Malaysia, 57000 Kuala Lumpur, Malaysia
| | - Abdul-Rahim Raha
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43300 UPM Serdang, Selangor DE, Malaysia
| | - Kiew-Lian Wan
- Malaysia Genome Institute, Heliks Emas Block, UKM-MTDC Smart Technology Centre, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor DE, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Biology Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor DE, Malaysia
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Lu F, Jiang H, Ding J, Mu J, Valenzuela JG, Ribeiro JMC, Su XZ. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics 2007; 8:255. [PMID: 17662120 PMCID: PMC1978503 DOI: 10.1186/1471-2164-8-255] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 07/27/2007] [Indexed: 11/17/2022] Open
Abstract
Background The completion of the Plasmodium falciparum genome represents a milestone in malaria research. The genome sequence allows for the development of genome-wide approaches such as microarray and proteomics that will greatly facilitate our understanding of the parasite biology and accelerate new drug and vaccine development. Designing and application of these genome-wide assays, however, requires accurate information on gene prediction and genome annotation. Unfortunately, the genes in the parasite genome databases were mostly identified using computer software that could make some erroneous predictions. Results We aimed to obtain cDNA sequences to examine the accuracy of gene prediction in silico. We constructed cDNA libraries from mixed blood stages of P. falciparum parasite using the SMART cDNA library construction technique and generated 17332 high-quality expressed sequence tags (EST), including 2198 from primer-walking experiments. Assembly of our sequence tags produced 2548 contigs and 2671 singletons versus 5220 contigs and 5910 singletons when our EST were assembled with EST in public databases. Comparison of all the assembled EST/contigs with predicted CDS and genomic sequences in the PlasmoDB database identified 356 genes with predicted coding sequences fully covered by EST, including 85 genes (23.6%) with introns incorrectly predicted. Careful automatic software and manual alignments found an additional 308 genes that have introns different from those predicted, with 152 new introns discovered and 182 introns with sizes or locations different from those predicted. Alternative spliced and antisense transcripts were also detected. Matching cDNA to predicted genes also revealed silent chromosomal regions, mostly at subtelomere regions. Conclusion Our data indicated that approximately 24% of the genes in the current databases were predicted incorrectly, although some of these inaccuracies could represent alternatively spliced transcripts, and that more genes than currently predicted have one or more additional introns. It is therefore necessary to annotate the parasite genome with experimental data, although obtaining complete cDNA sequences from this parasite will be a formidable task due to the high AT nature of the genome. This study provides valuable information for genome annotation that will be critical for functional analyses.
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Affiliation(s)
- Fangli Lu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat‑sen University, Guangzhou, Guangdong 510080, PRoC
| | - Hongying Jiang
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jinhui Ding
- Bioinformatics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jesus G Valenzuela
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - José MC Ribeiro
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Thompson J, Fernandez-Reyes D, Sharling L, Moore SG, Eling WM, Kyes SA, Newbold CI, Kafatos FC, Janse CJ, Waters AP. Plasmodium cysteine repeat modular proteins 1-4: complex proteins with roles throughout the malaria parasite life cycle. Cell Microbiol 2007; 9:1466-80. [PMID: 17253978 DOI: 10.1111/j.1462-5822.2006.00885.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Cysteine Repeat Modular Proteins (PCRMP1-4) of Plasmodium, are encoded by a small gene family that is conserved in malaria and other Apicomplexan parasites. They are very large, predicted surface proteins with multipass transmembrane domains containing motifs that are conserved within families of cysteine-rich, predicted surface proteins in a range of unicellular eukaryotes, and a unique combination of protein-binding motifs, including a >100 kDa cysteine-rich modular region, an epidermal growth factor-like domain and a Kringle domain. PCRMP1 and 2 are expressed in life cycle stages in both the mosquito and vertebrate. They colocalize with PfEMP1 (P. falciparum Erythrocyte Membrane Antigen-1) during its export from P. falciparum blood-stage parasites and are exposed on the surface of haemolymph- and salivary gland-sporozoites in the mosquito, consistent with a role in host tissue targeting and invasion. Gene disruption of pcrmp1 and 2 in the rodent malaria model, P. berghei, demonstrated that both are essential for transmission of the parasite from the mosquito to the mouse and has established their discrete and important roles in sporozoite targeting to the mosquito salivary gland. The unprecedented expression pattern and structural features of the PCRMPs thus suggest a variety of roles mediating host-parasite interactions throughout the parasite life cycle.
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Affiliation(s)
- Joanne Thompson
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK.
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Russell B, Suwanarusk R, Lek-Uthai U. Plasmodium vivax genetic diversity: microsatellite length matters. Trends Parasitol 2006; 22:399-401. [PMID: 16837246 DOI: 10.1016/j.pt.2006.06.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 06/06/2006] [Accepted: 06/29/2006] [Indexed: 10/24/2022]
Abstract
The Plasmodium vivax genome is very diverse but has a relatively low abundance of microsatellites. Leclerc et al. had shown that these di-nucleotide repeats have a low level of polymorphism, suggesting a recent bottleneck event in the evolutionary history of P. vivax. By contrast, in a recent paper, Imwong et al. show that there is a very high level of microsatellite diversity. The difference in these results is probably due to the set array lengths chosen by each group. Longer arrays are more diverse than are shorter ones because slippage mutations become exponentially more common with an increase in array length. These studies highlight the need to consider carefully the application and design of studies involving microsatellites.
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Affiliation(s)
- Bruce Russell
- International Health Program, Infectious Diseases Division, Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia.
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Abstract
T-cell-epitope mapping has emerged as one of the most powerful new drug discovery tools for a range of biomedical applications. Initially, T-cell-epitope discovery was applied to the development of vaccines for infectious diseases and cancer. T-cell-epitope-mapping applications have now expanded to include reengineering of protein therapeutics (a process now called deimmunization), as well as the fields of autoimmunity, endocrinology, allergy, transplantation and diagnostics. Research employing T-cell-epitope mapping falls within the realm of immunomics, a new field that addresses the interface between host and (pathogen) proteome, bridging informatics, genomics, proteomics, immunology and clinical medicine. This review highlights aspects of recent immunomics research that are related to the discovery of the T-cell immunome.
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Cui L, Fan Q, Hu Y, Karamycheva SA, Quackenbush J, Khuntirat B, Sattabongkot J, Carlton JM. Gene discovery in Plasmodium vivax through sequencing of ESTs from mixed blood stages. Mol Biochem Parasitol 2005; 144:1-9. [PMID: 16085323 DOI: 10.1016/j.molbiopara.2005.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 05/30/2005] [Indexed: 11/17/2022]
Abstract
Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence.
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Affiliation(s)
- Liwang Cui
- Department of Entomology, The Pennsylvania State University, 501 ASI, University Park, PA 16802, USA.
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Abstract
The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response.
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Affiliation(s)
- Jane M Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Isokpehi RD, Hide WA. Integrative analysis of intraerythrocytic differentially expressed transcripts yields novel insights into the biology of Plasmodium falciparum. Malar J 2003; 2:38. [PMID: 14617379 PMCID: PMC305352 DOI: 10.1186/1475-2875-2-38] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2003] [Accepted: 11/14/2003] [Indexed: 12/17/2022] Open
Abstract
Background The intraerythrocytic development of Plasmodium falciparum, the most virulent human malaria parasite involves asexual and gametocyte stages. There has been a significant increase in disparate datasets derived from genomic and post-genomic analysis of the parasite that necessitates delivery of integrated analysis from which biological processes important to the survival of the parasite can be determined. Methods In order to resolve genes associated with stage differentially expressed transcripts, we have developed and implemented an integrative approach that combines evidence from P. falciparum expressed sequence tags (ESTs), genomic, microarray, proteomic and gene ontology data. Results A total of 143 gametocyte-overexpressed and 51 asexual-overexpressed transcripts were identified. A subset of 74 genes associated with these transcripts showed evidence of stage-correlated protein expression, of which 53 have not been experimentally characterised. Our study has revealed (1) possible regulatory mechanisms in malaria parasites' gametocyte maturation, (2) correlation between EST and microarray data for a P. falciparum gene family to present unique EST-derived information, (3) candidate drug and antigenic targets on which computational and experimental studies can be performed, and (4) the need for more empirical studies on gene and protein expression in malaria parasites. Conclusion Applying different domains of data to the same underlying gene set has yielded novel insights into the biology of the parasite and presents an approach to appraise critically the data quality of post-genomic datasets from malaria parasites.
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Affiliation(s)
- Raphael D Isokpehi
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
| | - Winston A Hide
- South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
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Janse CJ, Haghparast A, Sperança MA, Ramesar J, Kroeze H, del Portillo HA, Waters AP. Malaria parasites lacking eef1a have a normal S/M phase yet grow more slowly due to a longer G1 phase. Mol Microbiol 2003; 50:1539-51. [PMID: 14651637 DOI: 10.1046/j.1365-2958.2003.03820.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eukaryotic elongation factor 1A (eEF1A) plays a central role in protein synthesis, cell growth and morphology. Malaria parasites possess two identical genes encoding eEF1A (eef1aa and eef1ab). Using pbeef1a-Plasmodium berghei mutants that lack an eEF1a gene, we demonstrate that the level of eEF1A production affects the proliferation of blood stages and parasite fitness. Pbeef1a- parasites can complete the vertebrate and mosquito phases of the life cycle, but the growth phase of the asexual blood stages is extended by up to 20%. Analysis of the cell cycle by flow cytometry as well as transcriptional analyses revealed that the duration of the S and M phases and the number of daughter cells produced were not detectably affected, but that the G1 phase is elongated. Thus, as in budding yeast, a growth threshold must be achieved by blood-stage Plasmodium parasites to permit transition from G1 into S/M phase. Initial analyses indicate that transcriptional events associated with gametocyte development were not remarkably retarded. Insight into protein synthesis and its influence on cell proliferation might be used to generate slow-growing (attenuated) parasites.
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Affiliation(s)
- Chris J Janse
- Malaria Group, Department of Parasitology, Leiden University Medical Centre (LUMC), PO Box 9600, 2300 RC, Leiden, The Netherlands
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Dame JB, Yowell CA, Omara-Opyene L, Carlton JM, Cooper RA, Li T. Plasmepsin 4, the food vacuole aspartic proteinase found in all Plasmodium spp. infecting man. Mol Biochem Parasitol 2003; 130:1-12. [PMID: 14550891 DOI: 10.1016/s0166-6851(03)00137-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plasmepsins are aspartic proteinases of the malaria parasite, and seven groups of plasmepsins have been identified by comparing genomic sequence data available for the genes encoding these enzymes from Plasmodium falciparum, Plasmodium vivax, Plasmodium knowlesi, Plasmodium berghei, and Plasmodium yoelii. The food vacuole plasmepsins typified by plasmepsin 4 from P. falciparum (PfPM4) constitute one of these groups. Genes encoding the ortholog of PfPM4 have been cloned from Plasmodium ovale, Plasmodium malariae, and P. vivax. In addition, P. falciparum contains three paralagous food vacuole plasmepsins or plasmepsin-like enzymes that appear to have arisen by gene duplication, plasmepsins 1 (PfPM1), 2 (PfPM2) and HAP, and all four were localized to purified food vacuole preparations by two-dimensional gel electrophoresis and mass spectroscopic analysis. The three paralogs of PfPM4 do not have counterparts in the six other Plasmodium spp. examined by genomic DNA blot analysis and by review of available genomic sequence data. The presence of these paralogs among the food vacuole plasmepsins in P. falciparum as compared with the other three species causing malaria in man will impact efforts to rationally design antimalarials targeting the food vacuole plasmepsins.
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Affiliation(s)
- John B Dame
- Department of Pathobiology, College of Veterinary Medicine, University of Florida, Box 110880, Gainesville, FL 32611-0880, USA.
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15
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Merino EF, Fernandez-Becerra C, Madeira AMBN, Machado AL, Durham A, Gruber A, Hall N, del Portillo HA. Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. Malar J 2003; 2:21. [PMID: 12914668 PMCID: PMC183858 DOI: 10.1186/1475-2875-2-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2003] [Accepted: 07/21/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium vivax is the most widely distributed human malaria, responsible for 70-80 million clinical cases each year and large socio-economical burdens for countries such as Brazil where it is the most prevalent species. Unfortunately, due to the impossibility of growing this parasite in continuous in vitro culture, research on P. vivax remains largely neglected. METHODS A pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of P. vivax was performed. To do so, 1,184 clones from a cDNA library constructed with parasites obtained from 10 different human patients in the Brazilian Amazon were sequenced. Sequences were automatedly processed to remove contaminants and low quality reads. A total of 806 sequences with an average length of 586 bp met such criteria and their clustering revealed 666 distinct events. The consensus sequence of each cluster and the unique sequences of the singlets were used in similarity searches against different databases that included P. vivax, Plasmodium falciparum, Plasmodium yoelii, Plasmodium knowlesi, Apicomplexa and the GenBank non-redundant database. An E-value of <10(-30) was used to define a significant database match. ESTs were manually assigned a gene ontology (GO) terminology RESULTS A total of 769 ESTs could be assigned a putative identity based upon sequence similarity to known proteins in GenBank. Moreover, 292 ESTs were annotated and a GO terminology was assigned to 164 of them. CONCLUSION These are the first ESTs reported for P. vivax and, as such, they represent a valuable resource to assist in the annotation of the P. vivax genome currently being sequenced. Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite.
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Affiliation(s)
- Emilio F Merino
- Departamento de Parasitologia, ICB, Universidade de São Paulo, São Paulo, Brazil
| | | | - Alda MBN Madeira
- Departamento de Patologia, FMVZ, Universidade de São Paulo, São Paulo, Brazil
| | - Ariane L Machado
- Departamento de Ciências da Computação, IME, Universidade de São Paulo, São Paulo, Brazil
| | - Alan Durham
- Departamento de Ciências da Computação, IME, Universidade de São Paulo, São Paulo, Brazil
| | - Arthur Gruber
- Departamento de Patologia, FMVZ, Universidade de São Paulo, São Paulo, Brazil
| | - Neil Hall
- The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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16
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Feng X, Carlton JM, Joy DA, Mu J, Furuya T, Suh BB, Wang Y, Barnwell JW, Su XZ. Single-nucleotide polymorphisms and genome diversity in Plasmodium vivax. Proc Natl Acad Sci U S A 2003; 100:8502-7. [PMID: 12799466 PMCID: PMC166258 DOI: 10.1073/pnas.1232502100] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The study of genetic variation in malaria parasites has practical significance for developing strategies to control the disease. Vaccines based on highly polymorphic antigens may be confounded by allelic restriction of the host immune response. In response to drug pressure, a highly plastic genome may generate resistant mutants more easily than a monomorphic one. Additionally, the study of the distribution of genomic polymorphisms may provide information leading to the identification of genes associated with traits such as parasite development and drug resistance. Indeed, the age and diversity of the human malaria parasite Plasmodium falciparum has been the subject of recent debate, because an ancient parasite with a complex genome is expected to present greater challenges for drug and vaccine development. The genome diversity of the important human pathogen Plasmodium vivax, however, remains essentially unknown. Here we analyze an approximately 100-kb contiguous chromosome segment from five isolates, revealing 191 single-nucleotide polymorphisms (SNPs) and 44 size polymorphisms. The SNPs are not evenly distributed across the segment with blocks of high and low diversity. Whereas the majority (approximately 63%) of the SNPs are in intergenic regions, introns contain significantly less SNPs than intergenic sequences. Polymorphic tandem repeats are abundant and are more uniformly distributed at a frequency of about one polymorphic tandem repeat per 3 kb. These data show that P. vivax has a highly diverse genome, and provide useful information for further understanding the genome diversity of the parasite.
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Affiliation(s)
- Xiaorong Feng
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Jane M. Carlton
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Deirdre A. Joy
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Tetsuya Furuya
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Bernard B. Suh
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Yufeng Wang
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - John W. Barnwell
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD 20892; Parasite Genomics
Group, The Institute for Genomic Research, Rockville, MD 20850;
Department of Bioinformatics, American Type
Culture Collection, Manassas, VA 20110; and
Division of Parasitic Diseases, Centers for
Disease Control and Prevention, Atlanta, GA 30341
- To whom correspondence should be addressed. E-mail:
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Abstract
With the successful completion of the project to sequence the Plasmodium falciparum genome, researchers are now turning their attention to other malaria parasite species. Here, an update on the Plasmodium vivax genome sequencing project is presented, as part of the Trends in Parasitology series of reviews expanding on various aspects of P. vivax research.
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Affiliation(s)
- Jane Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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18
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Francischetti IMB, Valenzuela JG, Pham VM, Garfield MK, Ribeiro JMC. Toward a catalog for the transcripts and proteins (sialome) from the salivary gland of the malaria vectorAnopheles gambiae. J Exp Biol 2002; 205:2429-51. [PMID: 12124367 DOI: 10.1242/jeb.205.16.2429] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARYHundreds of Anopheles gambiae salivary gland cDNA library clones have been sequenced. A cluster analysis based on sequence similarity at e-60 grouped the 691 sequences into 251 different clusters that code for proteins with putative secretory, housekeeping, or unknown functions. Among the housekeeping cDNAs, we found sequences predicted to code for novel thioredoxin, tetraspanin, hemopexin, heat shock protein, and TRIO and MBF proteins. Among secreted cDNAs, we found 21 novel A. gambiaesalivary sequences including those predicted to encode amylase, calreticulin,selenoprotein, mucin-like protein and 30-kDa allergen, in addition to antigen 5- and D7-related proteins, three novel salivary gland (SG)-like proteins and eight unique putative secreted proteins (Hypothetical Proteins, HP). The electronic version of this paper contains hyperlinks to FASTA-formatted files for each cluster with the best match to the nonredundant (NR) and conserved domain databases (CDD) in addition to CLUSTAL alignments of each cluster. The N terminus of 12 proteins (SG-1, SG-1-like 2, SG-6, HP 8, HP 9-like, 5′nucleotidase, 30-kDa protein, antigen 5- and four D7-related proteins) has been identified by Edman degradation of PVDF-transferred, SDS/PAGE-separated salivary gland proteins. Therefore, we contribute to the generation of a catalog of A. gambiae salivary transcripts and proteins. These data are freely available and will eventually become an invaluable tool to study the role of salivary molecules in parasite-host/vector interactions.
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Affiliation(s)
- Ivo M B Francischetti
- Medical Entomology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0425, USA
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19
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Hoffman SL, Subramanian GM, Collins FH, Venter JC. Plasmodium, human and Anopheles genomics and malaria. Nature 2002; 415:702-9. [PMID: 11832959 DOI: 10.1038/415702a] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Plasmodium spp. parasites that cause malaria are transmitted to humans by Anopheles spp. mosquitoes. Scientists have now amassed a great body of knowledge about the parasite, its mosquito vector and human host. Yet this year there will be 300-500 million new malaria infections and 1-3 million deaths caused by the disease. We believe that integrated analyses of genome sequence, DNA polymorphisms, and messenger RNA and protein expression profiles will lead to greater understanding of the molecular basis of vector-human and host-parasite interactions and provide strategies to build upon these insights to develop interventions to mitigate human morbidity and mortality from malaria.
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Affiliation(s)
- Stephen L Hoffman
- Celera Genomics, 45 West Gude Drive, Rockville, Maryland 20850, USA.
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20
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2002. [PMCID: PMC2448432 DOI: 10.1002/cfg.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Abstract
Almost 5 years ago, an international consortium of sequencing centers and funding agencies was formed to sequence the genome of the human malaria parasite Plasmodium falciparum. A novel chromosome by chromosome shotgun strategy was devised to sequence this very AT-rich genome. Two of the 14 chromosomes have been completed and the remaining chromosomes are in the final stages of gap closure. The consortium recently developed plans for the annotation and analysis of the complete genome sequence and its publication in 2002.
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Affiliation(s)
- M J Gardner
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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