메뉴 건너뛰기




Volumn 12, Issue 1, 2012, Pages 149-159

Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

Author keywords

Diversity; Drug resistance; Leishmania infantum; Population genetics; Population markers; Visceral leishmaniasis

Indexed keywords

ANTIMONY;

EID: 83555178358     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.11.005     Document Type: Article
Times cited : (48)

References (65)
  • 2
    • 77958134755 scopus 로고    scopus 로고
    • Ascertainment biases in SNP chips affect measures of population divergence
    • Albrechtsen A., Nielsen F.C., Nielsen R. Ascertainment biases in SNP chips affect measures of population divergence. Mol. Biol. Evol. 2010, 27(11):2534-2547.
    • (2010) Mol. Biol. Evol. , vol.27 , Issue.11 , pp. 2534-2547
    • Albrechtsen, A.1    Nielsen, F.C.2    Nielsen, R.3
  • 5
    • 0032900678 scopus 로고    scopus 로고
    • Median-joining networks for inferring intraspecific phylogenies
    • Bandelt H.J., Forster P., Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 1999, 16:37-48.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 37-48
    • Bandelt, H.J.1    Forster, P.2    Röhl, A.3
  • 6
    • 77953614765 scopus 로고    scopus 로고
    • Development and evaluation of different PCR-based typing methods for discrimination of Leishmania donovani isolates from Nepal
    • Bhattarai N.R., Dujardin J.C., Rijal S., De Doncker S., Boelaert M., Van der Auwera G. Development and evaluation of different PCR-based typing methods for discrimination of Leishmania donovani isolates from Nepal. Parasitology 2010, 137(6):947-957.
    • (2010) Parasitology , vol.137 , Issue.6 , pp. 947-957
    • Bhattarai, N.R.1    Dujardin, J.C.2    Rijal, S.3    De Doncker, S.4    Boelaert, M.5    Van der Auwera, G.6
  • 9
    • 0035895258 scopus 로고    scopus 로고
    • High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
    • Buetow K.H., Edmonson M., MacDonald R., Clifford R., Yip P., Kelley J., Little D.P., Strausberg R., Koester H., Cantor C.R., Braun A. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl Acad. Sci. USA 2001, 98(2):581-584.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , Issue.2 , pp. 581-584
    • Buetow, K.H.1    Edmonson, M.2    MacDonald, R.3    Clifford, R.4    Yip, P.5    Kelley, J.6    Little, D.P.7    Strausberg, R.8    Koester, H.9    Cantor, C.R.10    Braun, A.11
  • 10
    • 39549123620 scopus 로고    scopus 로고
    • A Leishmania infantum cytosolic tryparedoxin activates B cells to secrete interleukin-10 and specific immunoglobulin
    • Cabral S.M., Silvestre R.L., Santarém N.M., Tavares J.C., Silva A.F., Cordeiro-da-Silva A. A Leishmania infantum cytosolic tryparedoxin activates B cells to secrete interleukin-10 and specific immunoglobulin. Immunology 2008, 1234:555-565.
    • (2008) Immunology , vol.1234 , pp. 555-565
    • Cabral, S.M.1    Silvestre, R.L.2    Santarém, N.M.3    Tavares, J.C.4    Silva, A.F.5    Cordeiro-da-Silva, A.6
  • 14
    • 0037346501 scopus 로고    scopus 로고
    • Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets
    • Dieringer D., Schlötterer C. Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes 2003, 3(1):167-169.
    • (2003) Mol. Ecol. Notes , vol.3 , Issue.1 , pp. 167-169
    • Dieringer, D.1    Schlötterer, C.2
  • 16
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • Drummond A.J., Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 2007, 7:214.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 18
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    • Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 2005, 14(8):2611-2620.
    • (2005) Mol. Ecol. , vol.14 , Issue.8 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 19
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    • Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 2003, 164(4):1567-1587.
    • (2003) Genetics , vol.164 , Issue.4 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 21
    • 0042351392 scopus 로고    scopus 로고
    • A2rel: a constitutively expressed Leishmania gene linked to an amastigote-stage-specific gene
    • Ghedin E., Charest H., Matlashewski G. A2rel: a constitutively expressed Leishmania gene linked to an amastigote-stage-specific gene. Mol. Biochem. Parasitol. 1998, 93(1):23-29.
    • (1998) Mol. Biochem. Parasitol. , vol.93 , Issue.1 , pp. 23-29
    • Ghedin, E.1    Charest, H.2    Matlashewski, G.3
  • 22
    • 43149120377 scopus 로고    scopus 로고
    • Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness
    • Hamblin M.T., Warburton M.L., Buckler E.S. Empirical comparison of Simple Sequence Repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2007, 2(12):e1367.
    • (2007) PLoS One , vol.2 , Issue.12
    • Hamblin, M.T.1    Warburton, M.L.2    Buckler, E.S.3
  • 23
    • 68949103876 scopus 로고    scopus 로고
    • Inferring weak population structure with the assistance of sample group information
    • Hubisz M., Falush D., Stephens M., Pritchard J.K. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 2009, 9(5):1322-1332.
    • (2009) Molecular Ecology Resources , vol.9 , Issue.5 , pp. 1322-1332
    • Hubisz, M.1    Falush, D.2    Stephens, M.3    Pritchard, J.K.4
  • 24
    • 0024372736 scopus 로고
    • The " hitchhiking effect" revisited
    • Kaplan N.L., Hudson R.R., Langley C.H. The " hitchhiking effect" revisited. Genetics 1989, 123(4):887-899.
    • (1989) Genetics , vol.123 , Issue.4 , pp. 887-899
    • Kaplan, N.L.1    Hudson, R.R.2    Langley, C.H.3
  • 26
    • 74149087390 scopus 로고    scopus 로고
    • Amplified fragment length polymorphism (AFLP) analysis is useful for distinguishing Leishmania species of visceral and cutaneous forms
    • Kumar A., Boggula V.R., Misra P., Sundar S., Shasany A.K., Dube A. Amplified fragment length polymorphism (AFLP) analysis is useful for distinguishing Leishmania species of visceral and cutaneous forms. Acta Trop. 2010, 113(2):202-206.
    • (2010) Acta Trop. , vol.113 , Issue.2 , pp. 202-206
    • Kumar, A.1    Boggula, V.R.2    Misra, P.3    Sundar, S.4    Shasany, A.K.5    Dube, A.6
  • 27
    • 26944475928 scopus 로고    scopus 로고
    • Analysis of ribosomal DNA internal transcribed spacer sequences of the Leishmania donovani complex
    • Kuhls K., Mauricio I.L., Pratlong F., Presber W., Schönian G. Analysis of ribosomal DNA internal transcribed spacer sequences of the Leishmania donovani complex. Microbes Infect. 2005, 7(11-12):1224-1234.
    • (2005) Microbes Infect. , vol.7 , Issue.11-12 , pp. 1224-1234
    • Kuhls, K.1    Mauricio, I.L.2    Pratlong, F.3    Presber, W.4    Schönian, G.5
  • 28
    • 33847348111 scopus 로고    scopus 로고
    • Multilocus microsatellite typing (MLMT) reveals genetically isolated populations between and within the main endemic regions of visceral leishmaniasis
    • Kuhls K., Keilonat L., Ochsenreither S., Schaar M., Schweynoch C., Presber W., Schönian G. Multilocus microsatellite typing (MLMT) reveals genetically isolated populations between and within the main endemic regions of visceral leishmaniasis. Microbes Infect. 2007, 9(3):334-343.
    • (2007) Microbes Infect. , vol.9 , Issue.3 , pp. 334-343
    • Kuhls, K.1    Keilonat, L.2    Ochsenreither, S.3    Schaar, M.4    Schweynoch, C.5    Presber, W.6    Schönian, G.7
  • 33
    • 79951475133 scopus 로고    scopus 로고
    • A decade's perspective on DNA sequencing technology
    • Mardis E.R. A decade's perspective on DNA sequencing technology. Nature 2011, 470(7333):198-203.
    • (2011) Nature , vol.470 , Issue.7333 , pp. 198-203
    • Mardis, E.R.1
  • 34
    • 33744967724 scopus 로고    scopus 로고
    • Towards multilocus sequence typing of the Leishmania donovani complex: resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GPI, NH1, NH2, PGD)
    • Mauricio I.L., Yeo M., Baghaei M., Doto D., Pratlong F., Zemanova E., Dedet J.P., Lukes J., Miles M.A. Towards multilocus sequence typing of the Leishmania donovani complex: resolving genotypes and haplotypes for five polymorphic metabolic enzymes (ASAT, GPI, NH1, NH2, PGD). Int. J. Parasitol. 2006, 36(7):757-769.
    • (2006) Int. J. Parasitol. , vol.36 , Issue.7 , pp. 757-769
    • Mauricio, I.L.1    Yeo, M.2    Baghaei, M.3    Doto, D.4    Pratlong, F.5    Zemanova, E.6    Dedet, J.P.7    Lukes, J.8    Miles, M.A.9
  • 35
    • 1642271573 scopus 로고    scopus 로고
    • The SNP workshop group SNPs in ecology, evolution and conservation
    • Morin P.A., Luikart G., Wayne R.K. The SNP workshop group SNPs in ecology, evolution and conservation. Trends Ecol. Evol. 2004, 19:208-216.
    • (2004) Trends Ecol. Evol. , vol.19 , pp. 208-216
    • Morin, P.A.1    Luikart, G.2    Wayne, R.K.3
  • 36
    • 0016629918 scopus 로고
    • The bottleneck eVect and genetic variability in populations
    • Nei M., Maruyama T., Chakraborty R. The bottleneck eVect and genetic variability in populations. Evolution 1975, 29:1-10.
    • (1975) Evolution , vol.29 , pp. 1-10
    • Nei, M.1    Maruyama, T.2    Chakraborty, R.3
  • 37
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: predicting amino acid changes that affect protein function
    • Ng P.C., Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003, 31(13):3812-3814.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.13 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 39
    • 32344451312 scopus 로고    scopus 로고
    • Multilocus microsatellite typing as a new tool for discrimination of Leishmania infantum MON-1 strains
    • Ochsenreither S., Kuhls K., Schaar M., Presber W., Schonian G. Multilocus microsatellite typing as a new tool for discrimination of Leishmania infantum MON-1 strains. J. Clin. Microbiol. 2006, 44:495-503.
    • (2006) J. Clin. Microbiol. , vol.44 , pp. 495-503
    • Ochsenreither, S.1    Kuhls, K.2    Schaar, M.3    Presber, W.4    Schonian, G.5
  • 40
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 41
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: server and survey
    • Ramensky V., Bork P., Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002, 30(17):3894-3900.
    • (2002) Nucleic Acids Res. , vol.30 , Issue.17 , pp. 3894-3900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 46
    • 0347362518 scopus 로고    scopus 로고
    • Informativeness of genetic markers for inference of ancestry
    • Rosenberg N.A., Li L.M., Ward R., Pritchard J.K. Informativeness of genetic markers for inference of ancestry. Am. J. Hum. Genet. 2003, 73(6):1402-1422.
    • (2003) Am. J. Hum. Genet. , vol.73 , Issue.6 , pp. 1402-1422
    • Rosenberg, N.A.1    Li, L.M.2    Ward, R.3    Pritchard, J.K.4
  • 47
    • 43549096649 scopus 로고    scopus 로고
    • Post-translational modification of cellular proteins during Leishmania donovani differentiation
    • Rosenzweig D., Smith D., Myler P.J., Olafson R.W., Zilberstein D. Post-translational modification of cellular proteins during Leishmania donovani differentiation. Proteomics 2008, 8(9):1843-1850.
    • (2008) Proteomics , vol.8 , Issue.9 , pp. 1843-1850
    • Rosenzweig, D.1    Smith, D.2    Myler, P.J.3    Olafson, R.W.4    Zilberstein, D.5
  • 48
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987, 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 49
    • 33646066009 scopus 로고    scopus 로고
    • Upregulation of surface proteins in Leishmania donovani isolated from patients of post kala-azar dermal leishmaniasis
    • Salotra P., Duncan R.C., Singh R., Subba Raju B.V., Sreenivas G., Nakhasi H.L. Upregulation of surface proteins in Leishmania donovani isolated from patients of post kala-azar dermal leishmaniasis. Microbes Infect. 2006, 8(3):637-644.
    • (2006) Microbes Infect. , vol.8 , Issue.3 , pp. 637-644
    • Salotra, P.1    Duncan, R.C.2    Singh, R.3    Subba Raju, B.V.4    Sreenivas, G.5    Nakhasi, H.L.6
  • 51
    • 77951623346 scopus 로고    scopus 로고
    • Comparative in vivo expression of amastigote up regulated Leishmania genes in three different forms of Leishmaniasis
    • Sharma P., Gurumurthy S., Duncan R., Nakhasi H.L., Salotra P. Comparative in vivo expression of amastigote up regulated Leishmania genes in three different forms of Leishmaniasis. Parasitol Int. 2010, 59(2):262-264.
    • (2010) Parasitol Int. , vol.59 , Issue.2 , pp. 262-264
    • Sharma, P.1    Gurumurthy, S.2    Duncan, R.3    Nakhasi, H.L.4    Salotra, P.5
  • 53
    • 3342920601 scopus 로고    scopus 로고
    • Prospects for inferring very large phylogenies by using the neighbor-joining method
    • Tamura K., Nei M., Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 2004, 101:11030-11035.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 11030-11035
    • Tamura, K.1    Nei, M.2    Kumar, S.3
  • 54
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
    • Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, 28(10):2731-2739.
    • (2011) Mol. Biol. Evol. , vol.28 , Issue.10 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 55
    • 70349481004 scopus 로고    scopus 로고
    • Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison
    • Tokarska M., Marshall T., Kowalczyk R., Wójcik J.M., Pertoldi C., Kristensen T.N., Loeschcke V., Gregersen V.R., Bendixen C. Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison. Heredity 2009, 103(4):326-332.
    • (2009) Heredity , vol.103 , Issue.4 , pp. 326-332
    • Tokarska, M.1    Marshall, T.2    Kowalczyk, R.3    Wójcik, J.M.4    Pertoldi, C.5    Kristensen, T.N.6    Loeschcke, V.7    Gregersen, V.R.8    Bendixen, C.9
  • 56
    • 31344433668 scopus 로고    scopus 로고
    • Characterization and conservation of genetic diversity in subdivided populations
    • Toro M.A., Caballero A. Characterization and conservation of genetic diversity in subdivided populations. Philos. Trans. R. Soc. B Biol. Sci. 2005, 360(1459):1367-1378.
    • (2005) Philos. Trans. R. Soc. B Biol. Sci. , vol.360 , Issue.1459 , pp. 1367-1378
    • Toro, M.A.1    Caballero, A.2
  • 58
    • 77953128783 scopus 로고    scopus 로고
    • Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers
    • Van Inghelandt D., Melchinger A.E., Lebreton C., Stich B. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theor. Appl. Genet. 2010, 120(7):1289-1299.
    • (2010) Theor. Appl. Genet. , vol.120 , Issue.7 , pp. 1289-1299
    • Van Inghelandt, D.1    Melchinger, A.E.2    Lebreton, C.3    Stich, B.4
  • 60
    • 83555176551 scopus 로고    scopus 로고
    • WHO Expert Committee on the Control of the Leishmaniases. Control of the leishmaniases. WHO Technical Report Series 949, Geneva, Switzerland.
    • WHO Expert Committee on the Control of the Leishmaniases. 2010. Control of the leishmaniases. WHO Technical Report Series 949, Geneva, Switzerland.
    • (2010)
  • 62
    • 77954761899 scopus 로고    scopus 로고
    • Elevated levels of tryparedoxin peroxidase in antimony unresponsive Leishmania donovani field isolates
    • Wyllie S., Mandal G., Singh N., Sundar S., Fairlamb A.H., Chatterjee M. Elevated levels of tryparedoxin peroxidase in antimony unresponsive Leishmania donovani field isolates. Mol. Biochem. Parasitol. 2010, 173(2):162-164.
    • (2010) Mol. Biochem. Parasitol. , vol.173 , Issue.2 , pp. 162-164
    • Wyllie, S.1    Mandal, G.2    Singh, N.3    Sundar, S.4    Fairlamb, A.H.5    Chatterjee, M.6
  • 63
    • 84890417804 scopus 로고
    • The genetical structure of populations
    • Wright S. The genetical structure of populations. Ann. Eugenics 1951, 15:323-354.
    • (1951) Ann. Eugenics , vol.15 , pp. 323-354
    • Wright, S.1
  • 64
    • 33846239241 scopus 로고    scopus 로고
    • The Leishmania donovani complex: genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH, & FH), new targets for multilocus sequence typing
    • Zemanová E., Jirků M., Mauricio I.L., Horák A., Miles M.A., Lukes J. The Leishmania donovani complex: genotypes of five metabolic enzymes (ICD, ME, MPI, G6PDH, & FH), new targets for multilocus sequence typing. Int. J. Parasitol. 2007, 37(2):149-160.
    • (2007) Int. J. Parasitol. , vol.37 , Issue.2 , pp. 149-160
    • Zemanová, E.1    Jirků, M.2    Mauricio, I.L.3    Horák, A.4    Miles, M.A.5    Lukes, J.6
  • 65
    • 0035117857 scopus 로고    scopus 로고
    • Characterization of the A2-A2rel gene cluster in Leishmania donovani: involvement of A2 in visceralization during infection
    • Zhang W.W., Matlashewski G. Characterization of the A2-A2rel gene cluster in Leishmania donovani: involvement of A2 in visceralization during infection. Mol. Microbiol. 2001, 39(4):935-948.
    • (2001) Mol. Microbiol. , vol.39 , Issue.4 , pp. 935-948
    • Zhang, W.W.1    Matlashewski, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.