title: Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium.
abstract: BACKGROUND
  Infections with Taenia solium are the most common cause of adult acquired seizures worldwide, and are the leading cause of epilepsy in developing countries. A better understanding of the genetic diversity of T. solium will improve parasite diagnostics and transmission pathways in endemic areas thereby facilitating the design of future control measures and interventions. Microsatellite markers are useful genome features, which enable strain typing and identification in complex pathogen genomes. Here we describe microsatellite identification and characterization in T. solium, providing information that will assist in global efforts to control this important pathogen.
  
  
  METHODS
  For genome sequencing, T. solium cysts and proglottids were collected from Huancayo and Puno in Peru, respectively. Using next generation sequencing (NGS) and de novo assembly, we assembled two draft genomes and one hybrid genome. Microsatellite sequences were identified and 36 of them were selected for further analysis. Twenty T. solium isolates were collected from Tumbes in the northern region, and twenty from Puno in the southern region of Peru. The size-polymorphism of the selected microsatellites was determined with multi-capillary electrophoresis. We analyzed the association between microsatellite polymorphism and the geographic origin of the samples.
  
  
  RESULTS
  The predicted size of the hybrid (proglottid genome combined with cyst genome) T. solium genome was 111 MB with a GC content of 42.54%. A total of 7,979 contigs (>1,000 nt) were obtained. We identified 9,129 microsatellites in the Puno-proglottid genome and 9,936 in the Huancayo-cyst genome, with 5 or more repeats, ranging from mono- to hexa-nucleotide. Seven microsatellites were polymorphic and 29 were monomorphic within the analyzed isolates. T. solium tapeworms were classified into two genetic groups that correlated with the North/South geographic origin of the parasites.
  
  
  CONCLUSIONS
  The availability of draft genomes for T. solium represents a significant step towards the understanding the biology of the parasite. We report here a set of T. solium polymorphic microsatellite markers that appear promising for genetic epidemiology studies.
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Mónica J
authors.initials: MJ
authors.lastname: Pajuelo
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: María
authors.initials: M
authors.lastname: Eguiluz
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Eric
authors.initials: E
authors.lastname: Dahlstrom
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: David
authors.initials: D
authors.lastname: Requena
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Frank
authors.initials: F
authors.lastname: Guzmán
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ramirez
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sheen
authors.affiliation: Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
authors.forename: Michael
authors.initials: M
authors.lastname: Frace
authors.affiliation: Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
authors.forename: Scott
authors.initials: S
authors.lastname: Sammons
authors.affiliation: Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
authors.forename: Vitaliano
authors.initials: V
authors.lastname: Cama
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Sarah
authors.initials: S
authors.lastname: Anzick
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Dan
authors.initials: D
authors.lastname: Bruno
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Siddhartha
authors.initials: S
authors.lastname: Mahanty
authors.affiliation: Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
authors.forename: Patricia
authors.initials: P
authors.lastname: Wilkins
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Theodore
authors.initials: T
authors.lastname: Nash
authors.affiliation: Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru.
authors.forename: Armando
authors.initials: A
authors.lastname: Gonzalez
authors.affiliation: Departamento de Microbiología, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima Peru.|Instituto Nacional de Ciencias Neurológicas. Lima, Peru.
authors.forename: Héctor H
authors.initials: HH
authors.lastname: García
authors.affiliation: Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Robert H
authors.initials: RH
authors.lastname: Gilman
authors.affiliation: Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, Montana, United States of America.
authors.forename: Steve
authors.initials: S
authors.lastname: Porcella
authors.affiliation: Laboratorio de Bioinformatica y Biologia Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
authors.forename: Mirko
authors.initials: M
authors.lastname: Zimic
mesh_terms: D000328:Adult; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D018509:DNA, Helminth / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D049751:Genome, Helminth / Q000235:genetics*; D005838:Genotype; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010568:Peru / Q000453:epidemiology; D017422:Sequence Analysis, DNA; D041201:Taenia solium / Q000235:genetics* / Q000302:isolation & purification; D013622:Taeniasis / Q000453:epidemiology / Q000469:parasitology*
chemical_list: D018509:DNA, Helminth