New T2T assembly ofCryptosporidium parvumIOWA annotated with reference genome gene identifiers

Abstract

ABSTRACTCryptosporidium parvumis a significant pathogen causing gastrointestinal infections in humans and animals, that is spread through the ingestion of contaminated food and water. Despite its global impact on public health, generating aC. parvumgenome sequence has always been challenging due to a lack ofin vitrocultivation systems and challenging sub-telomeric gene families. A gapless telomere to telomere genome assembly has been created forCryptosporidium parvumIOWA obtained from Bunch Grass Farms, named here as CpBGF. There are 8 chromosomes that total 9,259,183 bp. The new hybrid assembly which was generated with Illumina and Oxford Nanopore resolves complex sub-telomeric regions of chromosomes 1, 7 and 8. To facilitate ease of use and consistency with the literature, whenever possible, chromosomes have been oriented and genes in this annotation have been given the same gene IDs used in the current reference genome sequence generated in 2004. The annotation of this assembly utilized considerable RNA expression evidence, thus, untranslated regions, long noncoding RNAs and antisense RNAs are annotated. The CpBGF genome assembly serves as a valuable resource for understanding the biology, pathogenesis, and transmission ofC. parvum, and it facilitates the development of diagnostics, drugs, and vaccines against cryptosporidiosis.