title: Shotgun optical mapping of the entire Leishmania major Friedlin genome.
abstract: Leishmania is a group of protozoan parasites which causes a broad spectrum of diseases resulting in widespread human suffering and death, as well as economic loss from the infection of some domestic animals and wildlife. To further understand the fundamental genomic architecture of this parasite, and to accelerate the on-going sequencing project, a whole-genome XbaI restriction map was constructed using the optical mapping system. This map supplemented traditional physical maps that were generated by fingerprinting and hybridization of cosmid and P1 clone libraries. Thirty-six optical map contigs were constructed for the corresponding known 36 chromosomes of the Leishmania major Friedlin genome. The chromosome sizes ranged from 326.9 to 2821.3 kb, with a total genome size of 34.7 Mb; the average XbaI restriction fragment was 25.3 kb, and ranged from 15.7 to 77.8 kb on a per chromosomes basis. Comparison between the optical maps and the in silico maps of sequence drawn from completed, nearly finished, or large sequence contigs showed that optical maps served several useful functions within the path to create finished sequence by: guiding aspects of the sequence assembly, identifying misassemblies, detection of cosmid or PAC clones misplacements to chromosomes, and validation of sequence stemming from varying degrees of finishing. Our results also showed the potential use of optical maps as a means to detect and characterize map segmental duplication within genomes.
authors.affiliation: Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA.
authors.forename: Shiguo
authors.initials: S
authors.lastname: Zhou
authors.forename: Andrew
authors.initials: A
authors.lastname: Kile
authors.forename: Erika
authors.initials: E
authors.lastname: Kvikstad
authors.forename: Mike
authors.initials: M
authors.lastname: Bechner
authors.forename: Jessica
authors.initials: J
authors.lastname: Severin
authors.forename: Dan
authors.initials: D
authors.lastname: Forrest
authors.forename: Rod
authors.initials: R
authors.lastname: Runnheim
authors.forename: Chris
authors.initials: C
authors.lastname: Churas
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Anantharaman
authors.forename: Peter
authors.initials: P
authors.lastname: Myler
authors.forename: Christy
authors.initials: C
authors.lastname: Vogt
authors.forename: Al
authors.initials: A
authors.lastname: Ivens
authors.forename: Kenneth
authors.initials: K
authors.lastname: Stuart
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
mesh_terms: D000818:Animals; D015252:Deoxyribonucleases, Type II Site-Specific / Q000378:metabolism; D016521:Electrophoresis, Gel, Pulsed-Field; D018503:Genome, Protozoan; D007091:Image Processing, Computer-Assisted; D018320:Leishmania major / Q000235:genetics*; D015183:Restriction Mapping / Q000379:methods*
chemical_list: C025580:endodeoxyribonuclease XBAI; D015252:Deoxyribonucleases, Type II Site-Specific