Shotgun optical mapping of the entire Leishmania major Friedlin genome

Molecular and Biochemical Parasitology

Volumn 138, Issue 1, 2004, Pages 97-106

  Zhou, Shiguo ^a   Kile, Andrew ^a   Kvikstad, Erika ^a   Bechner, Mike ^a   Severin, Jessica ^a   Forrest, Dan ^a   Runnheim, Rod ^a   Churas, Chris ^a   Anantharaman, Thomas S ^a   Myler, Peter ^b   Vogt, Christy ^b   Ivens, Al ^c   Stuart, Kenneth ^b   Schwartz, David C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b SEATTLE BIOMEDICAL RESEARCH INSTITUTE   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Leishmania major Friedlin; Sequence assembly; Shotgun optical mapping

Indexed keywords

DNA FRAGMENT;

ARTICLE; CHROMOSOME SIZE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA LIBRARY; GENE DUPLICATION; GENE MAPPING; GENE SEQUENCE; GENOME; GENOME ANALYSIS; GENOME SIZE; LEISHMANIA MAJOR; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL;

ANIMALS; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOME, PROTOZOAN; IMAGE PROCESSING, COMPUTER-ASSISTED; LEISHMANIA MAJOR; RESTRICTION MAPPING;

ANIMALIA; LEISHMANIA MAJOR; PROTOZOA;

EID: 6944255631     PISSN: 01666851     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molbiopara.2004.08.002     Document Type: Article

References (53)

1. World Health Organization (WHO). WHO Leishmaniasis World Wide Web Home Page; 2003. http://www.who.int/inf-fs/en/fact116.html.
2. C.P. McHugh, P.C. Melby, and S.G. LaFon Leishmaniasis in Texas: epidemiology and clinical aspects of human cases Am J Trop Med Hyg 55 1996 547 555
3. Ellis J, Crampton J. In: Hart DT, editor. Leishmaniases: the current status and new strategies for control. New York: Plenum Press; 1989. p. 589-96.
4. R. Almeida, A. Norrish, and M. Levick From genome to vaccines: Leishmania as a model Philos Trans R Soc London B: Biol Sci 357 2002 5 11
5. A.C. Ivens, S.M. Lewis, A. Bagherzadeh, L. Zhang, H.M. Chan, and D.F. Smith A physical map of the Leishmania major Friedlin Genome Genome Res 8 1998 135 145
6. P. Wincker, C. Ravel, and C. Blaineau The Leishmania genome comprises 36 chromosomes conserved across widely divergent human pathogenic species Nucl Acids Res 24 1996 1688 1694
7. P. Bastien, C. Blaineau, and C. Britto The complete chromosomal organization of the reference strain of the Leishmania genome project, L. major Friedlin Parasitol Today 14 1998 301 303
8. A.C. Ivens, and J.M. Blackwell The Leishmania genome come of age Parasitol Today 15 1999 229 231
9. P.J. Myler, and K.D. Stuart Recent developments from the Leishmania genome project Curr Opin Microbiol 3 2000 412 416
10. P.J. Myler, L. Audleman, and T. DeVos Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes Proc Natl Acad Sci USA 96 1999 2902 2906
11. J.M. Blackwell, and S.E. Melville Status of protozoan genome analysis: trypanosomatids Parasitology 118 1999 S11 S14
12. P.D. McDonagh, P.J. Myler, and K. Stuart The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes Nucl Acids Res 28 2000 2800 2803
13. P.J. Myler, E. Sisk, and P.D. McDonagh Genomic organization and gene function in Leishmania Biochem Soc Trans 28 2000 527 531
14. P.J. Myler, S.M. Beverley, and A.K. Cruz The Leishmania genome project: new insigthts into gene organization and function Med Microbiol Immunol 190 2001 9 12
15. V. Tosato, L. Ciarloni, A. Ivens, M.A. Rajandream, B.G. Barrell, and C.V. Bruschi Secondary DNA structure analysis of the coding strand switch regions of five Leishmania major Friedlin chromosomes Curr Genet 40 2001 186 194
16. T.S. Anantharaman, B. Mishra, and D.C. Schwartz Genomics via optical mapping. 2. Ordered restriction maps J Comput Biol 4 1997 91 118
17. Anantharaman TS, Mishra B, Schwartz DC. Genomics via optical mapping. III. Contiging genomic DNA and variations. In: Courant technical report. New York: Courant Institute, New York University; 1998. p. 760.
18. T.S. Anantharaman, B. Mishra, and D.C. Schwartz Genomics via optical mapping. III. Contiging genomic DNA and variations Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology 1999 18 27
19. C. Aston, C. Hiort, and D.C. Schwartz Optical mapping: an approach for fine mapping Methods Enzymol 303 1999 55 73
20. C. Aston, B. Mishra, and D.C. Schwartz Optical mapping and its potential or large-scale sequencing projects Trends Biotechnol 17 1999 297 302
21. W. Cai, J. Jing, and B. Irvin High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping Proc Natl Acad Sci USA 95 1998 3390 3395
22. J. Jing, Z. Lai, and C. Aston Optical mapping of Plasmodium falciparum chromosome 2 Genome Res 9 1999 175 181
23. Z. Lai, J. Jing, and C. Aston A shotgun optical map of the entire Plasmodium falciparum genome Nat Genet 23 1999 309 313
24. A. Lim, E.T. Dimalanta, and K.D. Potamousis Shotgun optical maps of the whole Escherichia coli O157:H7 genome Genome Res 11 2001 1584 1593
25. J. Lin, R. Qi, and C. Aston Whole genome shotgun optical mapping of Deinococcus radiodurans Science 285 1999 1558 1562
26. S. Zhou, W. Deng, and T.S. Ananthraman A whole-genome shotgun optical map of Yersinia pestis strain KIM Appl Environ Microbiol 68 2002 6321 6331
27. S. Zhou, E. Kvikstad, and A. Kile Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly Genome Res 13 2003 2142 2151
28. D.C. Schwartz, and C.R. Cantor Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis Cell 37 1984 67 75
29. P. Bastien, C. Blaineau, and M. Pages Leishmania: sex, lies and karyotype Parasitol Today 8 1992 174 178
30. Dimalanta ET, Lim A, Runnheim R, et al. A microfluidic system for large DNA molecule arrays. Anal Chem, 2004, in press.
31. R.D. Fleischmann, M.D. Adams, and O. White Whole-genome random sequencing and assembly of Haemophilus influenzae Rd Science 269 1995 496 512
32. Bastien P, Blaineau C, Pages M. Karyotype analysis in Leishmania. In: Avila JL, Harris JR, editors. Subcelluar biochemistry, vol. 18. Intracellular parasites. New York: Plenum Press; 1992b. p. 131-87.
33. C. Ravel, P. Wincker, C. Blaineau, and M. Pages Conservation among Old World Leishmania species of six physical linkage groups defined in Leishmania infantum small chromosomes Mol Biochem Parasitol 69 1995 1 8
34. C. Britto, C. Ravel, and P. Bastien Conserved linkage groups associated with large-scale chromosomal rearrangements between old world and new world Leishmania genomes Gene 222 1998 107 117
35. S.H. Giannini, M. Schittini, J.S. Keithly, P.W. Warburton, C.R. Cantor, and L.H.T. Van Der Ploeg Karyotype analysis of Leishmania species and its use in the classification and diagnosis Science 232 1986 762 765
36. J.K. Scholler, S.G. Reed, and K. Stuart Molecular karyotypes of species and subspecies of Leishmania Mol Biochem Parasitol 20 1986 279 283
37. S.M. Beverley, R.B. Ismach, and D. McMahon-Pratt Evolution of the genus Leishmania as revealed by comparisons of the nuclear DNA restriction fragments patterns Proc Natl Acad Sci USA 84 1987 484 488
38. N. Samaras, and T.W. Spithill Molecular karyotypes of five species of Leishmania and analysis of gene locations and chromosomal rearrangements Mol Biochem Parasitol 24 1987 23 27
39. M. Pages, P. Bastien, and F. Veas Chromosome size and number polymorphisms in Leishmania infantum suggest amplication/deletion and possible genetic exchange Mol Biochem Parasitol 36 1989 161 168
40. C. Blaineau, P. Bastien, J.A. Rioux, G. Roizes, and M. Pages Long-range restriction maps of size-variable homologous chromosomes in Leishmania infantum Mol Biochem Parasitol 46 1991 293 302
41. C. Ravel, P. Dubessay, C. Britto, C. Blaineau, P. Bastien, and M. Pages High conservation of the fine-scale organization of chromosome 5 between two pathogenic Leishmania species Nucl Acids Res 27 1999 2473 2477
42. P. Wincker, C. Ravel, and C. Britto A direct method for the chromosomal assignment of DNA markers in Leishmania Gene 194 1997 77 80
43. Bastien P, Wincker P; 2003. http://www.ebi.ac.uk/parasites/LGN/lshpfggl. html.
44. X. Meng, K. Benson, K. Chada, J.E. Huff, and D.C. Schwartz Optical mapping of lambda bacteriophage clones using restriction endonucleases Nat Genet 9 1995 432 438
45. D. Grant, P. Cregan, and R.C. Shoemaker Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis Proc Natl Acad Sci USA 97 2000 168 173
46. A.L. Hughes, and R. Friedman Parallel evolution by gene duplication in the genomes of two unicellular fungi Genome Res 13 2003 794 799
47. Cavalcanti ARO, R. Ferreira, Z. Gu, and W. Li Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans J Mol Evol 56 2003 28 37
48. C. Ravel, P. Wincker, C. Blaineau, C. Britto, P. Basitien, and M. Pages Medium-range restriction maps of five chromosomes of Leishmania infantum and localization of size-variable regions Genomics 35 1996 509 516
49. S.M. Sunkin, P. Kiser, P.J. Myler, and K. Stuart The size difference between Leishmania major Friedlin chromosome one homologues is localized to sub-telomeric repeats at one chromosomal end Mol Biochem Parasitol 109 2000 1 5
50. D.M. Iovannisci, and S.M. Beverley Structural alterations of chromosome 2 in Leishmania major as evidence for ploidy, including spontaneous amplification of the mini-exon array Mol Biochem Parasitol 34 1989 177 188
51. S. Martinez-Calvillo, S.M. Sunkin, S. Yan, M. Fox, K. Stuart, and P.J. Myler Genomic organization and functional characterization of the Leishmania major Fridlin ribosomal RNA gene locus Mol Biochem Parasitol 116 2001 147 157
52. Zhou S, Kile A, Bechner M, et al. A single molecule approach to bacterial genomics via optical mapping. J Bacteriol, in press.
53. S. Tamar, C. Dumas, and B. Papadopoulou Chromosome structure and sequence organization between pathogenic and nonpathogenic Leishmania spp Mol Biochem Parasitol 111 2000 401 414