Cryptosporidium spp. are apicomplexan parasites that infect humans and a variety of animals (Checkley et al., 2015). They colonize the gastrointestinal epithelial cells of the host, causing moderate to severe diarrhea in young animals and immunocompromised individuals (Guerin and Striepen, 2020). Nearly 50 species and ∼120 genotypes of Cryptosporidium spp. have been identified (Ryan et al., 2021a). Among them, Cryptosporidium parvum, Cryptosporidium meleagridis, and Cryptosporidium ubiquitum are important zoonotic species that infect various animals, while others are mostly host-adapted species with limited host ranges, such as Cryptosporidium hominis, Cryptosporidium canis, Cryptosporidium felis, Cryptosporidium bovis, Cryptosporidium ryanae, and Cryptosporidium xiaoi (Xiao, 2010, Ryan et al., 2021b).

Cryptosporidium xiaoi is the most commonly reported species in sheep and goats, especially in less intensive farming areas. Since the first report of ovine cryptosporidiosis in 1974 (Barker and Carbonell, 1974), C. parvum and C. ubiquitum have emerged as the major causative agents of cryptosporidiosis in sheep and goats (Feng and Xiao, 2017). In 2007, a novel genotype was identified in sheep and yaks, and named as a C. bovis-like genotype due to its genetic similarity to C. bovis in the ssrRNA gene (Feng et al., 2007, Navarro-i-Martinez et al., 2007, Santin et al., 2007). However, sequence differences in the 70 kDa heat shock protein (hsp70) and actin genes, and biological characteristics, indicated that the C. bovis-like genotype represented a new species named C. xiaoi (Fayer and Santin, 2009). In recent years, the host-specific C. xiaoi has been extensively reported in sheep and goats worldwide (Guo et al., 2021, Chen et al., 2022). In addition, C. xiaoi infections have occasionally been reported in HIV/AIDS patients (Adamu et al., 2014).

The increased availability of whole-genome data has greatly facilitated the study of genetic diversity and evolution among Cryptosporidium spp. Since the genomes of C. parvum and C. hominis were sequenced in 2004 (Abrahamsen et al., 2004, Xu et al., 2004), at least 15 Cryptosporidium spp. with different host ranges have been sequenced (Fan et al., 2019, Xu et al., 2020, Li et al., 2021, Li et al., 2023) , and their genomes are publicly available in the CryptoDB database (https://cryptodb.org/cryptodb/app) (Warrenfeltz et al., 2020) and NCBI database (https://www.ncbi.nlm.nih.gov/assembly/?term=cryptosporidium). Comparative genomics has revealed similar genomic features among these sequenced Cryptosporidium spp., such as the ∼9.0 Mb of genome size and synteny in gene organization. However, the subtelomeric genes encoding invasion-related mucin-like glycoproteins (MUC), insulinase-like proteases (INS), and MEDLE proteins in the host-adapted C. canis, C. felis, C. bovis, and C. ryanae are less abundant than in C. parvum and closely related Cryptosporidium spp. Similar reductive evolution has also been found in metabolism, particularly in the electron transport system (Fan et al., 2019, Xu et al., 2020, Li et al., 2021). These apparent genetic changes likely reflect the adaptive evolution of Cryptosporidium spp. to different host environments.

Subtelomere instability is a potential trigger for the adaptation of organisms to different living environments. The subtelomeres are defined as regions immediately adjacent to the telomeric repeats and are reservoirs of highly divergent genes (Olovnikov et al., 2021). Diversification of subtelomeric genes has been reported across various organisms and may play an indispensable role in shaping their biological characteristics. For example, sequence variations in subtelomeric genes encoding β-galactosidase enable yeast to adapt to diverse nutritional conditions (Mason and McEachern, 2018). In the Plasmodium spp. apicomplexan parasites, the subtelomeric gene families encoding variant surface antigens (VSAs) are involved in pathogenesis and host immune evasion (Jemmely et al., 2010). As a result, vsa gene sequences show extensive sequence polymorphism among Plasmodium spp. parasitizing different animals (Castillo et al., 2019). Similarly, sequence variations of secretory protein-encoding genes have been detected in subtelomeric regions of different Cryptosporidium spp. and C. parvum subtypes with distinct host ranges (Widmer et al., 2012, Xu et al., 2019, Xu et al., 2020, Jia et al., 2022). These increased nucleotide differences reflect adaptive evolution of divergent Cryptosporidium spp. and subtypes to their hosts.

In this study, we sequenced the genomes of two C. xiaoi isolates obtained from sheep. Results of comparative genomic analysis showed low nucleotide divergence between the sheep-derived C. xiaoi isolates H2942 and T52996, which belong to two different subtype families. In comparison, there are extensive nucleotide sequence differences between C. xiaoi and C. bovis genomes, especially in subtelomeric regions. These sequences and possible species-specific genes encode mainly secretory proteins with disordered regions and have gone through positive selection. They could contribute to different host preferences of C. xiaoi and C. bovis.