Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade

Nature Genetics

Volumn 44, Issue 9, 2012, Pages 1051-1055

  Tachibana, Shin Ichiro ^a,k   Sullivan, Steven A ^b   Kawai, Satoru ^c   Nakamura, Shota ^a   Kim, Hyunjae R ^b   Goto, Naohisa ^a   Arisue, Nobuko ^a   Palacpac, Nirianne M Q ^a   Honma, Hajime ^a   Yagi, Masanori ^a   Tougan, Takahiro ^a   Katakai, Yuko ^d   Kaneko, Osamu ^e   Mita, Toshihiro ^f   Kita, Kiyoshi ^g   Yasutomi, Yasuhiro ^h   Sutton, Patrick L ^b   Shakhbatyan, Rimma ^b   Horii, Toshihiro ^a   Yasunaga, Teruo ^a   Barnwell, John W ⁱ   Escalante, Ananias A ^j   Carlton, Jane M ^b   Tanabe, Kazuyuki ^a   more..

^a OSAKA UNIVERSITY   (Japan)

^b NEW YORK UNIVERSITY   (United States)

^c DOKKYO MEDICAL UNIVERSITY   (Japan)

^d The Corporation for Production and Research of Laboratory Primates   (Japan)

^e NAGASAKI UNIVERSITY   (Japan)

^f JUNTENDO UNIVERSITY   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h NATIONAL INSTITUTE OF BIOMEDICAL INNOVATION   (Japan)

ⁱ CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^j ARIZONA STATE UNIVERSITY   (United States)

^k KYOTO UNIVERSITY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CELL INVASION; COPY NUMBER VARIATION; ERYTHROCYTE; GENE DUPLICATION; GENE FREQUENCY; GENE SEQUENCE; GENETIC VARIABILITY; HAPLORHINI; MALARIA; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMODIUM CYNOMOLGI; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UNINDEXED SEQUENCE;

ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; GENES, PROTOZOAN; GENOME, PROTOZOAN; HAPLORHINI; MALARIA; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MONKEY DISEASES; PHYLOGENY; PLASMODIUM CYNOMOLGI; PLASMODIUM VIVAX; SEQUENCE ANALYSIS, DNA;

CERCOPITHECIDAE; PLASMODIUM CYNOMOLGI; PLASMODIUM KNOWLESI; PLASMODIUM VIVAX; SIMIAE;

EID: 84865683097     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2375     Document Type: Article

References (38)

1. Mendis, K., Sina, B.J., Marchesini, P. & Carter, R. The neglected burden of Plasmodium vivax malaria. Am. J. Trop. Med. Hyg. 64, 97-106 (2001). (Pubitemid 32552576)
2. Mueller, I. et al. Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria parasite. Lancet Infect. Dis. 9, 555-566 (2009).
3. Baird, J.K. Resistance to chloroquine unhinges vivax malaria therapeutics. Antimicrob. Agents Chemother. 55, 1827-1830 (2011).
4. Rayner, J.C., Liu, W., Peeters, M., Sharp, P.M. & Hahn, B.H. A plethora of Plasmodium species in wild apes: a source of human infection? Trends Parasitol. 27, 222-229 (2011).
5. Cornejo, O.E. & Escalante, A.A. The origin and age of Plasmodium vivax. Trends Parasitol. 22, 558-563 (2006). (Pubitemid 44716726)
6. Escalante, A.A. et al. A monkey's tale: the origin of Plasmodium vivax as a human malaria parasite. Proc. Natl. Acad. Sci. USA 102, 1980-1985 (2005). (Pubitemid 40261998)
7. Mu, J. et al. Host switch leads to emergence of Plasmodium vivax malaria in humans. Mol. Biol. Evol. 22, 1686-1693 (2005). (Pubitemid 41373579)
8. Singh, B. et al. A large focus of naturally acquired Plasmodium knowlesi infections in human beings. Lancet 363, 1017-1024 (2004). (Pubitemid 38410774)
9. Pain, A. et al. The genome of the simian and human malaria parasite Plasmodium knowlesi. Nature 455, 799-803 (2008).
10. Eyles, D.E., Coatney, G.R. & Getz, M.E. Vivax-type malaria parasite of macaques transmissible to man. Science 131, 1812-1813 (1960).
11. Gibbs, R.A. et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316, 222-234 (2007). (Pubitemid 46633091)
12. Carlton, J.M. et al. Comparative genomics of the neglected human malaria parasite Plasmodium vivax. Nature 455, 757-763 (2008).
13. Saxena, A.K., Wu, Y. & Garboczi, D.N. Plasmodium p25 and p28 surface proteins: potential transmission-blocking vaccines. Eukaryot. Cell 6, 1260-1265 (2007). (Pubitemid 47257695)
14. Iyer, J., Gruner, A.C., Renia, L., Snounou, G. & Preiser, P.R. Invasion of host cells by malaria parasites: a tale of two protein families. Mol. Microbiol. 65, 231-249 (2007). (Pubitemid 47052720)
15. Okenu, D.M., Malhotra, P., Lalitha, P.V., Chitnis, C.E. & Chauhan, V.S. Cloning and sequence analysis of a gene encoding an erythrocyte binding protein from Plasmodium cynomolgi. Mol. Biochem. Parasitol. 89, 301-306 (1997). (Pubitemid 27435100)
16. Coatney, G.R., Collins, W.E., Warren, M. & Contacos, P.G. The Primate Malarias (US Department of Health, Education and Welfare, Washington, DC, 1971).
17. Cunningham, D., Lawton, J., Jarra, W., Preiser, P. & Langhorne, J. The pir multigene family of Plasmodium: antigenic variation and beyond. Mol. Biochem. Parasitol. 170, 65-73 (2010).
18. al-Khedery, B., Barnwell, J.W. & Galinski, M.R. Antigenic variation in malaria: a 3′ genomic alteration associated with the expression of a P. knowlesi variant antigen. Mol. Cell 3, 131-141 (1999). (Pubitemid 29292614)
19. Krotoski, W.A. The hypnozoite and malarial relapse. Prog. Clin. Parasitol. 1, 1-19 (1989).
20. Campbell, T.L., De Silva, E.K., Olszewski, K.L., Elemento, O. & Llinas, M. Identifcation and genome-wide prediction of DNA binding specifcities for the ApiAP2 family of regulators from the malaria parasite. PLoS Pathog. 6, e1001165 (2010).
21. Mu, J. et al. Genome-wide variation and identifcation of vaccine targets in the Plasmodium falciparum genome. Nat. Genet. 39, 126-130 (2007). (Pubitemid 46026512)
22. Volkman, S.K. et al. A genome-wide map of diversity in Plasmodium falciparum. Nat. Genet. 39, 113-119 (2007). (Pubitemid 46026510)
23. Xie, C. & Tammi, M.T. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 80 (2009).
24. Lee, K.S. et al. Plasmodium knowlesi: reservoir hosts and tracking the emergence in humans and macaques. PLoS Pathog. 7, e1002015 (2011).
25. Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426 (1986). (Pubitemid 16010523)
26. Doi, M. et al. Worldwide sequence conservation of transmission-blocking vaccine candidate Pvs230 in Plasmodium vivax. Vaccine 29, 4308-4315 (2011).
27. Carlton, J.M., Sina, B.J. & Adams, J.H. Why is Plasmodium vivax a neglected tropical disease? PLoS Negl. Trop. Dis. 5, e1160 (2011).
28. Ohtsubo, Y., Ikeda-Ohtsubo, W., Nagata, Y. & Tsuda, M. GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 9, 376 (2008).
29. Cantarel, B.L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188-196 (2008).
30. Popendorf, K., Tsuyoshi, H., Osana, Y. & Sakakibara, Y. Murasaki: a fast, parallelizable algorithm to fnd anchors from multiple genomes. PLoS ONE 5, e12651 (2010).
31. Thompson, J.D., Higgins, D.G. & Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specifc gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680 (1994). (Pubitemid 24354800)
32. Felsenstein, J. PHYLIP, Phylogeny Inference Package, 3.6a3 edn (University of Washington, Seattle, 2005).
33. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586-1591 (2007). (Pubitemid 47236688)
34. Ning, Z., Cox, A.J. & Mullikin, J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729 (2001). (Pubitemid 33040499)
35. Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
36. Tamura, K., Dudley, J., Nei, M. & Kumar, S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599 (2007). (Pubitemid 47236692)
37. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
38. Edgar, R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004). (Pubitemid 38832724)