Table 2.

Timeline and progression of genomic research in Cryptosporidium species.

Year	The Greatest Milestone	Genomic Approach	Outcome of Study	Reference
1999	Initial genomic exploration into C. parvum Iowa strain	Random sequence analysis	✓Sequence survey comprising only 2.5% of the C. parvum genome ✓The disadvantage of the method is the limited availability of gene sequences in the public databases at the time	[13]
2000	First cDNA sequence survey of C. parvum Iowa oocysts/sporozoites	Random sequence analysis with GSS approach to gene discovery	✓First broad-based molecular views into the basic biology and cellular metabolism of this experimentally intractable apicomplexan parasite	[6]
2004	Complete genome sequencing of C. parvum Iowa type II strain	Whole-genome with shotgun Sanger sequencing	✓Whole genome was sequenced from a plasmid insert library ✓“HAPPY” map was used to create a scaffold and order the sequence contigs	[11]
2004	Complete genome sequencing C. hominis TU502	Whole-genome with shotgun Sanger sequencing	✓Whole genome was sequenced from a plasmid insert library ✓“HAPPY” map was not available; the authors constructed large (~7–8-fold coverage) bacterial artificial chromosome (BAC) libraries for this species and used the C. parvum “HAPPY” map to guide assembly	[19]
2012	Comparative genome analysis of two C. parvum isolates (TU114 and C. parvum Iowa)	Whole-genome sequencing	✓Small number of highly diverged genes ✓Transporter genes’ over-representation indicates species-specific infection ability	[12]
2015	Sequencing of genomes C. chipmunk genotype I	Whole genome sequencing	✓Subtyping tool based on two markers for genetic characterization of C. chipmunk genotype I was developed ✓C. chipmunk genotype I isolates from humans and wildlife are genetically similar	[23]
2015	Comparative genome analysis of C. hominis and C. parvum	Whole genome sequencing	✓Occurrence of genetic recombination in virulent ✓C. hominis subtypes and telomeric gene duplications in C. parvum ✓Sequence similarity and recombination in the gp60 region indicate a potential role in the emergence of highly transmissible C. hominis subtypes	[14]
2016	Sequencing of genomes: C. meleagridis UKMEL1, C. baileyi TAMU-09Q1 and C. hominis TU502_2012 and UKH1	Draft genome sequencing	✓The genome assembly of C. hominis is significantly more complete and less fragmented than the previous version ✓The first versions of genome sequence assemblies and annotations for each isolate	[7]
2016	Genome sequencing of Cryptosporidium spp. in clinical samples	Single-cell sequencing	✓Workflow for whole genome sequencing of single cells of the parasite ✓Combining sequence data from all single-cell genomes, almost the entire reference genome (99.7%) was accounted for, and most of this (98.8%) was described at > 20× coverage	[21]
2017	Sequencing of the genomes of two specimens of C. parvum form China and Egypt	Whole genome sequencing	✓Differences in subtelomeric gene families, such as SKSR, MEDLE proteins, and insulinase-like proteases, found between sequenced and reference genomes ✓Most polymorphic genes between genomes mainly encode invasion-related mucin proteins and other secretory protein families	[15]
2018	Analysis of genetic diversity of C. hominis infections in slum-dwelling infants in Bangladesh	Long-read resequencing	✓High rates of sexual recombination and regions of the genome that were highly polymorphic, suggesting areas under selection	[22]
2018	Analysis of a zoonotic isolate of C. parvum UKP1 isolated from a person with cryptosporidiosis	Draft genome sequencing	✓Sequences needed to identify markers important in distinguishing routes of transmission and potential virulence traits for better epidemiological analysis and risk assessment	[8]
2020	Comparative analysis of Cryptosporidium species that infect humans	Whole-genome sequencing	✓Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed	[16]
2020	Sequencing of the genomes of C. bovis and C. ryanae	Whole-genome sequencing	✓The genome of C. bovis has a gene content and organization more similar to C. ryanae than to other Cryptosporidium species sequenced to date	[9]