title: Comparative genomic analysis of the IId subtype family of Cryptosporidium parvum.
abstract: Host adaptation is known to occur in Cryptosporidium parvum, with IIa and IId subtype families preferentially infecting calves and lambs, respectively. To improve our understanding of the genetic basis of host adaptation in Cryptosporidium parvum, we sequenced the genomes of two IId specimens and one IIa specimen from China and Egypt using the Illumina technique and compared them with the published IIa IOWA genome. Sequence data were obtained for >99.3% of the expected genome. Comparative genomic analysis identified differences in numbers of three subtelomeric gene families between sequenced genomes and the reference genome, including those encoding SKSR secretory proteins, the MEDLE family of secretory proteins, and insulinase-like proteases. These gene gains and losses compared with the reference genome were confirmed by PCR analysis. Altogether, 5,191-5,766 single nucleotide variants were seen between genomes sequenced in this study and the reference genome, with most SNVs occurring in subtelomeric regions of chromosomes 1, 4, and 6. The most highly polymorphic genes between IIa and IId encode mainly invasion-associated and immunodominant mucin proteins, and other families of secretory proteins. Further studies are needed to verify the biological significance of these genomic differences.
authors.affiliation: College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China. Electronic address: yyfeng@scau.edu.cn.
authors.forename: Yaoyu
authors.initials: Y
authors.lastname: Feng
authors.affiliation: College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.affiliation: Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Roellig
authors.affiliation: Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Alyssa
authors.initials: A
authors.lastname: Kelley
authors.affiliation: State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
authors.forename: Guangyuan
authors.initials: G
authors.lastname: Liu
authors.affiliation: Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA; Department of Zoology, Faculty of Science, Kafr El sheikh University, Kafr El Sheikh 33516, Egypt.
authors.forename: Said
authors.initials: S
authors.lastname: Amer
authors.affiliation: Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Tang
authors.affiliation: College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China.
authors.forename: Longxian
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Division of Foodborne, Waterborne and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: lxiao@cdc.gov.
authors.forename: Lihua
authors.initials: L
authors.lastname: Xiao
mesh_terms: D000818:Animals; D001483:Base Sequence; D002020:Buffaloes; D002417:Cattle; D002418:Cattle Diseases / Q000469:parasitology; D002681:China; D003457:Cryptosporidiosis / Q000469:parasitology; D016785:Cryptosporidium parvum / Q000145:classification / Q000235:genetics*; D004251:DNA Transposable Elements; D016054:DNA, Protozoan / Q000235:genetics; D004534:Egypt; D017125:Genes, Protozoan; D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods; D005838:Genotype; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D017384:Sequence Deletion; D012756:Sheep
chemical_list: D004251:DNA Transposable Elements; D016054:DNA, Protozoan
keywords: Cryptosporidium parvum; Genomics; Host adaptation; Transmission; Whole genome sequencing