Cryptosporidium serpentis is a host-adapted Cryptosporidium species that infects ectothermic reptiles, including snakes and lizards. In addition, C. serpentis is one of the few Cryptosporidium species that parasitize the stomach of the hosts. To date, the genomic data for gastric Cryptosporidium species are exclusively available for Cryptosporidium andersoni and Cryptosporidium muris, both of which infect warm-blooded hosts. To enhance our understanding of genomic features of C. serpentis, we undertook the Illumina-based whole genome sequencing of four C. serpentis isolates, and generated the first C. serpentis draft genome of 9.11 Mb in 292 scaffolds and with an N50 of 102,002 bp. Comparative genomic analyses revealed that C. serpentis shares high similarity in genomic characteristics with C. andersoni and C. muris, including genomic identity, gene content, and gene organization. We observed aerobic metabolism and a partial conventional electron transport chain in the three gastric species, which are absent in the intestinal Cryptosporidium species. This divergent metabolism of the three gastric species is likely associated with their parasitism in the stomach of hosts. However, genes involved in purine salvage pathway in C. parvum are lost in C. serpentis as well as in other gastric Cryptosporidium species. These specific gene losses may provide more insights into the anabolic capabilities of Cryptosporidium. A significant reduction in the number of multi-copy genes potentially involving the secretory pathogenesis determinants was observed in C. serpentis, which was also found in the other species with a narrow host range. Compared with the other gastric species, 19 unique genes and 67 divergent orthogroups with low identity were identified in C. serpentis. These genes/orthogroups could provide potential insights into investigating the host preference of C. serpentis and further biological studies should be performed on these genes.
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