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The three common intestinal  Cryptosporidium  species in cattle differ significantly in host range, pathogenicity and public health significance. While  Cryptosporidium parvum  is pathogenic in pre-weaned calves and has a broad host range,  C. bovis  and  C. ryanae  are largely non-pathogenic and bovine-specific species in post-weaned calves. Thus far, only the genome of  C. parvum  has been sequenced. To improve our understanding of the genetic determinants of biological differences among  Cryptosporidium  spcies, we sequenced the genomes of  C. bovis  and  C. ryanae  and conducted a comparative genomics analysis. The genome of  C. bovis  has a gene content and organization more similar to  C. ryanae  than to other  Cryptosporidium  species sequenced to date; the level of similarity in amino acid and nucleotide sequences between the two species is 75.2 and 69.4 %, respectively. A total of 3723 and 3711 putative protein-encoding genes were identified in the genomes of  C. bovis  and  C. ryanae , respectively, which are fewer than the 3981 in  C. parvum . Metabolism is similar among the three species, although energy production pathways are further reduced in  C. bovis  and  C. ryanae . Compared with  C. parvum ,  C. bovis  and  C. ryanae  have lost 14 genes encoding mucin-type glycoproteins and three for insulinase-like proteases. Other gene gains and losses in the two bovine-specific and non-pathogenic species also involve the secretory pathogenesis determinants (SPDs); they have lost all genes encoding MEDLE, FLGN and SKSR proteins, and two of the three genes for NFDQ proteins, but have more genes encoding secreted WYLE proteins, secreted leucine-rich proteins and GPI-anchored adhesin PGA18. The only major difference between  C. bovis  and  C. ryanae  is in nucleotide metabolism. In addition, half of the highly divergent genes between  C. bovis  and  C. ryanae  encode secreted or membrane-bound proteins. Therefore,  C. bovis  and  C. ryanae  have gene organization and metabolic pathways similar to  C. parvum , but have lost some invasion-associated mucin glycoproteins, insulinase-like proteases, MEDLE secretory proteins and other SPDs. The multiple gene families under positive selection, such as helicase-associated domains, AMP-binding domains, protein kinases, mucins, insulinases and TRAPs could contribute to differences in host specificity and pathogenicity between  C. parvum  and  C. bovis . Biological studies should be conducted to assess the contribution of these copy number variations to the narrow host range and reduced pathogenicity of  C. bovis  and  C. ryanae .

microbial genomics

Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species