메뉴 건너뛰기




Volumn 33, Issue 3, 2016, Pages 603-620

Population structure shapes copy number variation in malaria parasites

(18)  Cheeseman, Ian H a   Miller, Becky b   Tan, John C b   Tan, Asako b   Nair, Shalini a   Nkhoma, Standwell C c   De Donato, Marcos d   Rodulfo, Hectorina d   Dondorp, Arjen e,f   Branch, Oralee H g   Mesia, Lastenia Ruiz h   Newton, Paul f,i   Mayxay, Mayfong f,i,j   Amambua Ngwa, Alfred k   Conway, David J k,l   Nosten, François f,m   Ferdig, Michael T b   Anderson, Tim J C a  


Author keywords

copy number variation; parasitology.; population genetics

Indexed keywords

DNA HELICASE;

EID: 84964494870     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msv282     Document Type: Article
Times cited : (35)

References (88)
  • 1
    • 0032920890 scopus 로고    scopus 로고
    • Cloning of the APECED gene provides new insight into human autoimmunity
    • Aaltonen J, Bjorses P. (1999). Cloning of the APECED gene provides new insight into human autoimmunity. Ann Med. 31: 111-116
    • (1999) Ann Med , vol.31 , pp. 111-116
    • Aaltonen, J.1    Bjorses, P.2
  • 2
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • Abyzov A, Urban AE, Snyder M, Gerstein M. (2011). CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21: 974-984
    • (2011) Genome Res , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4
  • 4
    • 23044509495 scopus 로고    scopus 로고
    • Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila
    • Aminetzach YT, Macpherson JM, Petrov DA. (2005). Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila. Science 309: 764-767
    • (2005) Science , vol.309 , pp. 764-767
    • Aminetzach, Y.T.1    Macpherson, J.M.2    Petrov, D.A.3
  • 8
    • 19544366088 scopus 로고    scopus 로고
    • Are transporter genes other than the chloroquine resistance locus (pfcrt) and multidrug resistance gene (pfmdr) associated with antimalarial drug resistance'
    • Anderson TJ, Nair S, Qin H, Singlam S, Brockman A, Paiphun L, Nosten F. (2005). Are transporter genes other than the chloroquine resistance locus (pfcrt) and multidrug resistance gene (pfmdr) associated with antimalarial drug resistance'. Antimicrob Agents Chemother 49: 2180-2188
    • (2005) Antimicrob Agents Chemother , vol.49 , pp. 2180-2188
    • Anderson, T.J.1    Nair, S.2    Qin, H.3    Singlam, S.4    Brockman, A.5    Paiphun, L.6    Nosten, F.7
  • 12
    • 0024523842 scopus 로고
    • Subtelomeric chromosome deletions in field isolates of Plasmodium falciparum and their relationship to loss of cytoadherence in vitro
    • Biggs BA, Kemp DJ, Brown GV. (1989). Subtelomeric chromosome deletions in field isolates of Plasmodium falciparum and their relationship to loss of cytoadherence in vitro. Proc Natl Acad Sci U. S. A. 86: 2428-2432
    • (1989) Proc Natl Acad Sci U. S. A. , vol.86 , pp. 2428-2432
    • Biggs, B.A.1    Kemp, D.J.2    Brown, G.V.3
  • 15
    • 27644464529 scopus 로고    scopus 로고
    • Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays
    • Carret CK, Horrocks P, Konfortov B, Winzeler E, Qureshi M, Newbold C, Ivens A. (2005). Microarray-based comparative genomic analyses of the human malaria parasite Plasmodium falciparum using Affymetrix arrays. Mol Biochem Parasitol. 144: 177-186
    • (2005) Mol Biochem Parasitol , vol.144 , pp. 177-186
    • Carret, C.K.1    Horrocks, P.2    Konfortov, B.3    Winzeler, E.4    Qureshi, M.5    Newbold, C.6    Ivens, A.7
  • 21
    • 0028014644 scopus 로고
    • Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine
    • Cowman AF, Galatis D, Thompson JK. (1994). Selection for mefloquine resistance in Plasmodium falciparum is linked to amplification of the pfmdr1 gene and cross-resistance to halofantrine and quinine. Proc Natl Acad Sci U. S. A. 91: 1143-1147
    • (1994) Proc Natl Acad Sci U. S. A. , vol.91 , pp. 1143-1147
    • Cowman, A.F.1    Galatis, D.2    Thompson, J.K.3
  • 22
    • 77953067304 scopus 로고    scopus 로고
    • Smogd: Software for the measurement of genetic diversity
    • Crawford NG. (2010). Smogd: software for the measurement of genetic diversity. Mol Ecol Resour. 10: 556-557
    • (2010) Mol Ecol Resour , vol.10 , pp. 556-557
    • Crawford, N.G.1
  • 23
    • 77955275027 scopus 로고    scopus 로고
    • Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster
    • Cridland JM, Thornton KR. (2010). Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster. Genome Biol Evol. 2: 83-101
    • (2010) Genome Biol Evol , vol.2 , pp. 83-101
    • Cridland, J.M.1    Thornton, K.R.2
  • 25
    • 0037416197 scopus 로고    scopus 로고
    • Phenotypic variation of Plasmodium falciparum merozoite proteins directs receptor targeting for invasion of human erythrocytes
    • Duraisingh MT, Triglia T, Ralph SA, Rayner JC, Barnwell JW, McFadden GI, Cowman AF. (2003). Phenotypic variation of Plasmodium falciparum merozoite proteins directs receptor targeting for invasion of human erythrocytes. EMBO J. 22: 1047-1057
    • (2003) EMBO J. , vol.22 , pp. 1047-1057
    • Duraisingh, M.T.1    Triglia, T.2    Ralph, S.A.3    Rayner, J.C.4    Barnwell, J.W.5    McFadden, G.I.6    Cowman, A.F.7
  • 26
    • 79960306786 scopus 로고    scopus 로고
    • Piperaquine resistance is associated with a copy number variation on chromosome 5 in drug-pressured Plasmodium falciparum parasites
    • Eastman RT, Dharia NV, Winzeler EA, Fidock DA. (2011). Piperaquine resistance is associated with a copy number variation on chromosome 5 in drug-pressured Plasmodium falciparum parasites. Antimicrob Agents Chemother. 55: 3908-3916
    • (2011) Antimicrob Agents Chemother , vol.55 , pp. 3908-3916
    • Eastman, R.T.1    Dharia, N.V.2    Winzeler, E.A.3    Fidock, D.A.4
  • 27
    • 84871880520 scopus 로고    scopus 로고
    • Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region
    • Echeverry DF, Nair S, Osorio L, Menon S, Murillo C, Anderson TJ. (2013). Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region. BMC Genet. 14: 2
    • (2013) BMC Genet , vol.14 , pp. 2
    • Echeverry, D.F.1    Nair, S.2    Osorio, L.3    Menon, S.4    Murillo, C.5    Anderson, T.J.6
  • 28
    • 46249105777 scopus 로고    scopus 로고
    • Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster
    • Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. (2008). Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 320: 1629-1631
    • (2008) Science , vol.320 , pp. 1629-1631
    • Emerson, J.J.1    Cardoso-Moreira, M.2    Borevitz, J.O.3    Long, M.4
  • 29
    • 84886501384 scopus 로고    scopus 로고
    • Using genetic methods to define the targets of compounds with antimalarial activity
    • Flannery EL, Fidock DA, Winzeler EA. (2013). Using genetic methods to define the targets of compounds with antimalarial activity. J Med Chem. 56: 7761-7771
    • (2013) J Med Chem , vol.56 , pp. 7761-7771
    • Flannery, E.L.1    Fidock, D.A.2    Winzeler, E.A.3
  • 36
    • 14844359279 scopus 로고    scopus 로고
    • Hierfstat, a package for r to compute and test hierarchical F-statistics
    • Goudet J. (2005). Hierfstat, a package for r to compute and test hierarchical F-statistics. Mol Ecol Notes. 5: 184-186
    • (2005) Mol Ecol Notes , vol.5 , pp. 184-186
    • Goudet, J.1
  • 37
    • 84878489009 scopus 로고    scopus 로고
    • Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications
    • Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. (2013). Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog. 9: e1003375
    • (2013) PLoS Pathog , vol.9 , pp. e1003375
    • Guler, J.L.1    Freeman, D.L.2    Ahyong, V.3    Patrapuvich, R.4    White, J.5    Gujjar, R.6    Ma, P.7    DeRisi, J.8    Rathod, P.K.9
  • 38
    • 24644446846 scopus 로고    scopus 로고
    • A standardized genetic differentiation measure
    • Hedrick PW. (2005). A standardized genetic differentiation measure. Evolution 59: 1633-1638
    • (2005) Evolution , vol.59 , pp. 1633-1638
    • Hedrick, P.W.1
  • 39
    • 84876705818 scopus 로고    scopus 로고
    • Direct evidence for the adaptive role of copy number variation on antifolate susceptibility in Plasmodium falciparum
    • Heinberg A, Siu E, Stern C, Lawrence EA, Ferdig MT, Deitsch KW, Kirkman LA. (2013). Direct evidence for the adaptive role of copy number variation on antifolate susceptibility in Plasmodium falciparum. Mol Microbiol. 88: 702-712
    • (2013) Mol Microbiol , vol.88 , pp. 702-712
    • Heinberg, A.1    Siu, E.2    Stern, C.3    Lawrence, E.A.4    Ferdig, M.T.5    Deitsch, K.W.6    Kirkman, L.A.7
  • 41
    • 52449086715 scopus 로고    scopus 로고
    • Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray
    • Jiang H, Yi M, Mu J, Zhang L, Ivens A, Klimczak LJ, Huyen Y, Stephens RM, Su XZ. (2008). Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray. BMC Genomics 9: 398
    • (2008) BMC Genomics , vol.9 , pp. 398
    • Jiang, H.1    Yi, M.2    Mu, J.3    Zhang, L.4    Ivens, A.5    Klimczak, L.J.6    Huyen, Y.7    Stephens, R.M.8    Su, X.Z.9
  • 43
    • 84892421821 scopus 로고    scopus 로고
    • Copy-number changes in evolution: Rates, fitness effects and adaptive significance
    • Katju V, Bergthorsson U. (2013). Copy-number changes in evolution: rates, fitness effects and adaptive significance. Front Genet. 4: 273
    • (2013) Front Genet , vol.4 , pp. 273
    • Katju, V.1    Bergthorsson, U.2
  • 47
    • 34748900529 scopus 로고    scopus 로고
    • Antigenic variation in Plasmodium falciparum: Gene organization and regulation of the var multigene family
    • Kyes SA, Kraemer SM, Smith JD. (2007). Antigenic variation in Plasmodium falciparum: gene organization and regulation of the var multigene family. Eukaryot Cell. 6: 1511-1520
    • (2007) Eukaryot Cell , vol.6 , pp. 1511-1520
    • Kyes, S.A.1    Kraemer, S.M.2    Smith, J.D.3
  • 48
  • 55
    • 84885911072 scopus 로고    scopus 로고
    • Population genomics of rapid adaptation by soft selective sweeps
    • Messer PW, Petrov DA. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol. 28: 659-669
    • (2013) Trends Ecol Evol , vol.28 , pp. 659-669
    • Messer, P.W.1    Petrov, D.A.2
  • 60
    • 77953023691 scopus 로고    scopus 로고
    • Genetic changes during laboratory propagation: Copy number at the reticulocyte-binding protein 1 locus of Plasmodium falciparum
    • Nair S, Nkhoma S, Nosten F, Mayxay M, French N, Whitworth J, Anderson T. (2010). Genetic changes during laboratory propagation: copy number at the reticulocyte-binding protein 1 locus of Plasmodium falciparum. Mol Biochem Parasitol. 172: 145-148
    • (2010) Mol Biochem Parasitol , vol.172 , pp. 145-148
    • Nair, S.1    Nkhoma, S.2    Nosten, F.3    Mayxay, M.4    French, N.5    Whitworth, J.6    Anderson, T.7
  • 64
    • 33748074807 scopus 로고    scopus 로고
    • Expression of Plasmodium falciparum genes involved in erythrocyte invasion varies among isolates cultured directly from patients
    • Nery S, Deans AM, Mosobo M, Marsh K, Rowe JA, Conway DJ. (2006). Expression of Plasmodium falciparum genes involved in erythrocyte invasion varies among isolates cultured directly from patients. Mol Biochem Parasitol. 149: 208-215
    • (2006) Mol Biochem Parasitol , vol.149 , pp. 208-215
    • Nery, S.1    Deans, A.M.2    Mosobo, M.3    Marsh, K.4    Rowe, J.A.5    Conway, D.J.6
  • 66
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • Ohta T. (1992). The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst. 23: 263-286
    • (1992) Annu Rev Ecol Syst , vol.23 , pp. 263-286
    • Ohta, T.1
  • 67
    • 33845971545 scopus 로고    scopus 로고
    • Soft sweeps III: The signature of positive selection from recurrent mutation
    • Pennings PS, Hermisson J. (2006). Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet. 2: e186
    • (2006) PLoS Genet , vol.2 , pp. e186
    • Pennings, P.S.1    Hermisson, J.2
  • 72
    • 76749097550 scopus 로고    scopus 로고
    • The genetics of human adaptation: Hard sweeps, soft sweeps, and polygenic adaptation
    • Pritchard JK, Pickrell JK, Coop G. (2010). The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Curr Biol. 20: R208-R215
    • (2010) Curr Biol , vol.20 , pp. R208-R215
    • Pritchard, J.K.1    Pickrell, J.K.2    Coop, G.3
  • 73
    • 0034662919 scopus 로고    scopus 로고
    • Two Plasmodium falciparum genes express merozoite proteins that are related to Plasmodium vivax and Plasmodium yoelii adhesive proteins involved in host cell selection and invasion
    • Rayner JC, Galinski MR, Ingravallo P, Barnwell JW. (2000). Two Plasmodium falciparum genes express merozoite proteins that are related to Plasmodium vivax and Plasmodium yoelii adhesive proteins involved in host cell selection and invasion. Proc Natl Acad Sci U. S. A. 97: 9648-9653
    • (2000) Proc Natl Acad Sci U. S. A. , vol.97 , pp. 9648-9653
    • Rayner, J.C.1    Galinski, M.R.2    Ingravallo, P.3    Barnwell, J.W.4
  • 76
    • 0031803649 scopus 로고    scopus 로고
    • CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis
    • Savukoski M, Klockars T, Holmberg V, Santavuori P, Lander ES, Peltonen L. (1998). CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis. Nat Genet. 19: 286-288
    • (1998) Nat Genet , vol.19 , pp. 286-288
    • Savukoski, M.1    Klockars, T.2    Holmberg, V.3    Santavuori, P.4    Lander, E.S.5    Peltonen, L.6
  • 77
    • 84874209491 scopus 로고    scopus 로고
    • A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data
    • 2164-14-128
    • Sepulveda N, Campino SG, Assefa SA, Sutherland CJ, Pain A, Clark TG. (2013). A Poisson hierarchical modelling approach to detecting copy number variation in sequence coverage data. BMC Genomics 14: 128. 2164-14-128
    • (2013) BMC Genomics , vol.14 , pp. 128
    • Sepulveda, N.1    Campino, S.G.2    Assefa, S.A.3    Sutherland, C.J.4    Pain, A.5    Clark, T.G.6
  • 79
    • 0025272167 scopus 로고
    • Chromosome 9 from independent clones and isolates of Plasmodium falciparum undergoes subtelomeric deletions with similar breakpoints in vitro
    • Shirley MW, Biggs BA, Forsyth KP, Brown HJ, Thompson JK, Brown GV, Kemp DJ. (1990). Chromosome 9 from independent clones and isolates of Plasmodium falciparum undergoes subtelomeric deletions with similar breakpoints in vitro. Mol Biochem Parasitol. 40: 137-145
    • (1990) Mol Biochem Parasitol , vol.40 , pp. 137-145
    • Shirley, M.W.1    Biggs, B.A.2    Forsyth, K.P.3    Brown, H.J.4    Thompson, J.K.5    Brown, G.V.6    Kemp, D.J.7
  • 80
    • 4143139772 scopus 로고    scopus 로고
    • Selection of cysteine protease inhibitorresistant malaria parasites is accompanied by amplification of falcipain genes and alteration in inhibitor transport
    • Singh A, Rosenthal PJ. (2004). Selection of cysteine protease inhibitorresistant malaria parasites is accompanied by amplification of falcipain genes and alteration in inhibitor transport. J Biol Chem. 279: 35236-35241
    • (2004) J Biol Chem , vol.279 , pp. 35236-35241
    • Singh, A.1    Rosenthal, P.J.2
  • 81
    • 84856247679 scopus 로고    scopus 로고
    • Population genetic nature of copy number variation
    • Sjodin P, Jakobsson M. (2012). Population genetic nature of copy number variation. Methods Mol Biol. 838: 209-223
    • (2012) Methods Mol Biol , vol.838 , pp. 209-223
    • Sjodin, P.1    Jakobsson, M.2
  • 82
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Smith JM, Haigh J. (1974). The hitch-hiking effect of a favourable gene. Genet Res. 23: 23-35
    • (1974) Genet Res , vol.23 , pp. 23-35
    • Smith, J.M.1    Haigh, J.2
  • 87
    • 12344304667 scopus 로고    scopus 로고
    • Reticulocytebinding protein homologue 1 is required for sialic acid-dependent invasion into human erythrocytes by Plasmodium falciparum
    • Triglia T, Duraisingh MT, Good RT, Cowman AF. (2005). Reticulocytebinding protein homologue 1 is required for sialic acid-dependent invasion into human erythrocytes by Plasmodium falciparum. Mol Microbiol. 55: 162-174
    • (2005) Mol Microbiol , vol.55 , pp. 162-174
    • Triglia, T.1    Duraisingh, M.T.2    Good, R.T.3    Cowman, A.F.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.