Fully resolved assembly of Cryptosporidium parvum

Abstract

Background Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. Findings Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. Conclusions This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.

Long-read genome assembly and gene model annotations for the rodent malaria parasite Plasmodium yoelii 17XNL

“…As widely available Nanopore sequencing chemistries (Q10) yield a systematic error, Nanopore data are often paired with Illumina data to provide error correction. The sequencing error rates from Illumina are typically above 99.9% and can be used with polishing algorithms to identify errors in assemblies that were produced with long, noisy reads ( 18 , 19 ). We also generated high-fidelity PacBio sequencing data to access the feasibility of genome assembly without the need for error correction.…”

“…With the advent of more accurate long-read sequencing technologies, there has been a renewed interest in sequencing the Plasmodium genomes and transcriptomes, including those of another P. yoelii strain, PyN67, which has been used to study genetic polymorphisms and drug responses ( 17 ). In addition, the genomes of other apicomplexan parasites, such as Cryptosporidium and Babesia species, have now been established using a combination of long-read Nanopore sequencing and short-read Illumina sequencing ( 18 , 19 , 20 ).…”

Long-Read Genome Assembly and Gene Model Annotations for the Rodent Malaria ParasitePlasmodium yoelii17XNL

“…As widely available Nanopore sequencing chemistries (Q10) yield a systematic error, Nanopore data are often paired with Illumina data to provide error correction. The sequencing error rates from Illumina are typically above 99.9% and can be used with polishing algorithms to identify errors in assemblies that were produced with long, noisy reads (18, 19). A detailed outline of our experimental methods is included in Supplemental Figure 1.…”

A Thorny Tale of Parasites: Screening for Enteric Protozoan Parasites in Hedgehogs from Portugal

“…Even when comparing studies employing PCR, the implementation of distinct oligonucleotide primers targeting different regions may contribute to disparities in sensitivities. The isolate was classified as C. parvum, one of the most common species of Cryptosporidium found in humans, with a global prevalence of 7.6% [39]. Given the synanthropic presence of hedgehogs in urban areas and their proximity to humans, concerns about their possible role as hosts for C. parvum should be considered.…”