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Cryptosporidium has been recently identified as the second most important cause for diarrhea in the Global Enterics Multi-Center Study (GEMS).Among the 26 established Cryptosporidium species and over 40 recognized genotypes,only a handful are considered major human pathogens,especially Cryptosporidium hominis and Cryptosporidium parvum,with the latter also infecting ruminants.Our understanding of the genetic basis for host specificity in Cryptosporidium spp.is hampered by the unavailability of effective cultivation and animal models and genetic manipulation tools,and limited availability of whole genome sequence data fromarange of Cryptosporidium species with different host specificities.In this study,we sequenced the newly recognized Cryptosporidium tyzzeri,which is genetically related to C.hominis and C.parvum but uses mice as natural hosts.Altogether,8.633 Mb ofnucleotides in 695 assembled contigs were obtained by 454 sequencing from a whole genome-amplified product ofC.tyzzeri oocysts purified from a domestic mouse in the Czech Republic.569 of the contigs or 8.625 Mb of the nucleotides were mapped to the 8 chromosomes ofC.parvum,representing about 95% of the complete genome.The genome ofC.tyzzeri had 97.2% and96.7%nucleotide sequence identity to genomes ofC.parvum and C.hominis,respectively,and an almost complete syntanyin gene organization tothe two previously sequenced species.No major insertions and deletions were observed between C.tyzzeri and C.parvum.Genome-wide SNP analysis showed almost identical SNP patterns among the three species; i.e.,genes or intergenic regions with high sequence polymorphism showed mostly high sequencevariations amongallthree species,with a few noticeable exceptions in chromosomes 4 (around NT 444200),7 (around NT 684500 and 911-400),and 8 (around NT 325100 and 1043800).In addition,relatively large insertions or deletions wereidentified in a few functional genes.The structural,compositional,and sequence conservation among three closely related Cryptosporidium species suggests that host specificity is probably determined bysubtle variations in the sequences of proteins that interact with the host elements.