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. 2022 Feb 15:11:giac010.
doi: 10.1093/gigascience/giac010.

Fully resolved assembly of Cryptosporidium parvum

Vipin K Menon  1 , Pablo C Okhuysen  2 , Cynthia L Chappell  3 , Medhat Mahmoud  1 , Medhat Mahmoud  1 , Qingchang Meng  1 , Harsha Doddapaneni  1 , Vanesa Vee  1 , Yi Han  1 , Sejal Salvi  1 , Sravya Bhamidipati  1 , Kavya Kottapalli  1 , George Weissenberger  1 , Hua Shen  1 , Matthew C Ross  4 , Kristi L Hoffman  4 , Sara Javornik Cregeen  4 , Donna M Muzny  1 , Ginger A Metcalf  1 , Richard A Gibbs  1 , Joseph F Petrosino  4 , Fritz J Sedlazeck  1
Affiliations

Fully resolved assembly of Cryptosporidium parvum

Vipin K Menon et al. Gigascience. .

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.

Keywords: Cryptosporidium; assembly; assembly comparisons; nanopore.

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Conflict of interest statement

F.J.S. has presented at both ONT- and Pacific Biosciences–sponsored conferences. The authors declare that they have no other competing interests.

Figures

Figure 1
Figure 1
: Workflow for the generation of Cryptosporidium parvum assembly.
Figure 2
Figure 2
: Read length distribution and cumulative coverage over the Oxford Nanopore sequencing. We obtained a total of 53× coverage with long reads and even 10× coverage with reads larger than 30 kb (x axis). The longest read measured was 808 kb.
Figure 3
Figure 3
: Assembly comparisons. (A) The Canu assembly shows a high concordance with the previously published C. parvum assembly (GCA_015245375.1) [27] (dot plots) and agreements in length (bottom). Nevertheless, clear assembly differences are visual when comparing it to GCA_000165345.1 [13]. (B) The Flye assembly vs the C. parvum assembly (GCA_015245375.1) shows large disagreements. Contig 3 is merged between 2 different Cryptosporidium chromosomes, and 1 chromosome is missing. Also, the length comparison (bottom) shows discrepancies in the beginning, highlighting a very short contig in the end (green track). Interestingly GCA_000165345.1 shows structural differences over both assemblies, likely indicating errors in the previous reference.
See this image and copyright information in PMC

References

    1. Dong S, Yang Y, Wang Y, et al. Prevalence of Cryptosporidium infection in the global population: a systematic review and meta-analysis. Acta Parasitol. 2020;65(4):882–9. - PubMed
    1. Head MG, Brown RJ, Newell M-L, et al. The allocation of USdollar;105 billion in global funding from G20 countries for infectious disease research between 2000 and 2017: a content analysis of investments. Lancet Glob Health. 2020;8(10):e1295–304. - PMC - PubMed
    1. Fayer R, Morgan U, Upton SJ. Epidemiology of Cryptosporidium: transmission, detection and identification. Int J Parasitol. 2000;30(12-13):1305–22. - PubMed
    1. Fayer R. Cryptosporidium: a water-borne zoonotic parasite. Vet Parasitol. 2004;126(1-2):37–56. - PubMed
    1. Xiao L, Feng Y. Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis. Food Waterborne Parasitol. 2017;8-9:14–32. - PMC - PubMed

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