title: Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes.
abstract: BACKGROUND
  Cyclospora cayetanensis is an important cause for diarrhea in children in developing countries and foodborne outbreaks of cyclosporiasis in industrialized nations. To improve understanding of the basic biology of Cyclospora spp. and development of molecular diagnostic tools and therapeutics, we sequenced the complete apicoplast and mitochondrial genomes of C. cayetanensis.
  
  
  METHODS
  The genome of one Chinese C. cayetanensis isolate was sequenced using Roche 454 and Illumina technologies. The assembled genomes of the apicoplast and mitochondrion were retrieved, annotated, and compared with reference genomes for other apicomplexans to infer genome organizations and phylogenetic relationships. Sequence variations in the mitochondrial genome were identified by comparison of two C. cayetanensis nucleotide sequences from this study and a recent publication.
  
  
  RESULTS
  The apicoplast and mitochondrial genomes of C. cayetanensis are 34,155 and 6,229 bp in size and code for 65 and 5 genes, respectively. Comparative genomic analysis showed high similarities between C. cayetanensis and Eimeria tenella in both genomes; they have 85.6% and 90.4% nucleotide sequence similarities, respectively, and complete synteny in gene organization. Phylogenetic analysis of the genomic sequences confirmed the genetic similarities between cecum-infecting avian Eimeria spp. and C. cayetanensis. Like in other coccidia, both genomes of C. cayetanensis are transcribed bi-directionally. The apicoplast genome is circular, codes for the complete machinery for protein biosynthesis, and contains two inverted repeats that differ slightly in LSU rRNA gene sequences. In contrast, the mitochondrial genome has a linear concatemer or circular mapping topology. Eight single-nucleotide and one 7-bp multiple-nucleotide variants were detected between the mitochondrial genomes of C. cayetanensis from this and recent studies.
  
  
  CONCLUSIONS
  The apicoplast and mitochondrial genomes of C. cayetanensis are highly similar to those of cecum-infecting avian Eimeria spp. in both genome organization and sequences. The availability of sequence data beyond rRNA and heat shock protein genes could facilitate studies of C. cayetanensis biology and development of genotyping tools for investigations of cyclosporiasis outbreaks.
authors.affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. kht7@cdc.gov.
authors.forename: Kevin
authors.initials: K
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. guoyaqiong1987@sina.com.|Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. guoyaqiong1987@sina.com.
authors.forename: Yaqiong
authors.initials: Y
authors.lastname: Guo
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. zhanglongxian8999@foxmail.com.
authors.forename: Longxian
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. ioy0@cdc.gov.
authors.forename: Lori A
authors.initials: LA
authors.lastname: Rowe
authors.affiliation: Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. iyd4@cdc.gov.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Roellig
authors.affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. mff3@cdc.gov.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Frace
authors.affiliation: State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. nli@ecust.edu.cn.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.affiliation: State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. xgu6@cdc.gov.|Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. xgu6@cdc.gov.
authors.forename: Shiyou
authors.initials: S
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Bioreactor Engineering, School of Resources and Environmental Engineering, East China University of Science and Technology, Shanghai, 200237, China. yyfeng@ecust.edu.cn.
authors.forename: Yaoyu
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA. lxiao@cdc.gov.
authors.forename: Lihua
authors.initials: L
authors.lastname: Xiao
mesh_terms: D000818:Animals; D063546:Apicoplasts / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D002645:Chickens; D003048:Coccidiosis / Q000469:parasitology / Q000662:veterinary*; D021744:Cyclospora / Q000737:chemistry / Q000235:genetics*; D021866:Cyclosporiasis / Q000469:parasitology*; D016054:DNA, Protozoan / Q000737:chemistry / Q000235:genetics; D004539:Eimeria / Q000737:chemistry / Q000235:genetics*; D054629:Genome, Mitochondrial; D018503:Genome, Protozoan; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011201:Poultry Diseases / Q000469:parasitology*; D012689:Sequence Homology, Nucleic Acid; D014422:Turkeys
chemical_list: D016054:DNA, Protozoan