Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
[Preprint]. 2024 Feb 17:2024.02.16.580748.
doi: 10.1101/2024.02.16.580748.

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

Lasya R Penumarthi  1   2 , Rodrigo P Baptista  1   2 , Megan S Beaudry  3 , Travis C Glenn  1   3   4 , Jessica C Kissinger  1   2   4
Affiliations

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

Lasya R Penumarthi et al. bioRxiv. .

Update in

Abstract

Cryptosporidium spp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants and immunosuppressed populations as well as animals. Although most human Cryptosporidium infections are caused by C. parvum and C. hominis, there are several other human-infecting species including C. meleagridis, which is commonly observed in developing countries. Here, we polished and annotated a long-read genome sequence assembly for C. meleagridis TU1867, a species which infects birds and humans. The genome sequence was generated using a combination of whole genome amplification (WGA) and long-read Oxford Nanopore Technologies sequencing. The assembly was then polished with Illumina data. The chromosome-level genome assembly is 9.2 Mbp with a contig N50 of 1.1 Mb. Annotation revealed 3,923 protein-coding genes. A BUSCO analysis indicates a completeness of 96.6% (n=446), including 430 (96.4%) single-copy and 1 (0.224%) duplicated apicomplexan conserved gene(s). The new C. meleagridis genome assembly is nearly gap-free and provides a valuable new resource for the Cryptosporidium community and future studies on evolution and host-specificity.

Keywords: Oxford Nanopore; Whole genome amplification; comparative genomics; functional annotation.

PubMed Disclaimer

Conflict of interest statement

Competing interests The authors declare no competing interests.

Figures

Figure 1.
Figure 1.. DNA synteny plot of the eight chromosome level contigs of CmTU1867 (left hemisphere) and CmUKMEL1 (right hemisphere).
Jupiterplot between the previous CmUKMEL1 genome sequence and the new CmTU1867 genome sequence. Ribbons are colored with respect to the reference genome (CmTU1867).
Figure 2.
Figure 2.. Protein synteny analysis of the eight chromosome-level contigs of CmTU1967 (right hemisphere) and Cryptosporidium parvum, CpBGF (left hemisphere).
Circos plot rings, moving from the center to the exterior illustrate shared ortholog clusters between CmTU1867 and CpBGF, number of base pairs in 50,000 bp increments, GC content histogram, and gene density. Locations of rRNA genes are as indicated.
Figure 3.
Figure 3.. Venn diagram of ortholog search results following manual validation.
Orthogroup comparison among the new CmTU1867, the previous CmUKMEL1, and the newly released reference genome, CpBGF. See Figure 5 for the pre-validation results. Arrows link gene IDs to their orthogroups.
Figure 4.
Figure 4.. Experimental workflow for genome sequencing, assembly, annotation, and analysis.
Bioinformatics workflow for assembly and annotation of the DNA derived from CmTU1867 WGA. Green boxes represent main initial steps as well as new data used for parts of the pipeline and blue boxes represent subsequent downstream analyses of the data generated. Please refer to methods for additional details.
Figure 5.
Figure 5.. Ortholog search results shown in a Venn diagram.
Orthogroup comparison among the new CmTU1867, the previous CmUKMEL1, and the newly released reference genome, CpBGF prior to validation and correction. Arrows point to orthogroups containing the indicated gene IDs.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Putignani L. et al. Characterization of a mitochondrion-like organelle in Cryptosporidium parvum. Parasitology 129, 1–18 (2004). - PubMed
    1. Hlavsa M. C. et al. Outbreaks Associated with Treated Recreational Water - United States, 2000–2014. MMWR Morb Mortal Wkly Rep 67, 547–551 (2018). 10.15585/mmwr.mm6719a3 - DOI - PMC - PubMed
    1. Kotloff K. L. et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet 382, 209–222 (2013). 10.1016/S0140-6736(13)60844-2 - DOI - PubMed
    1. Girma M., Teshome W., Petros B. & Endeshaw T. Cryptosporidiosis and Isosporiasis among HIV-positive individuals in south Ethiopia: a cross sectional study. BMC Infect Dis 14, 100 (2014). 10.1186/1471-2334-14-100 - DOI - PMC - PubMed
    1. Investigators M.-E. N. The MAL-ED study: a multinational and multidisciplinary approach to understand the relationship between enteric pathogens, malnutrition, gut physiology, physical growth, cognitive development, and immune responses in infants and children up to 2 years of age in resource-poor environments. Clin Infect Dis 59 Suppl 4, S193–206 (2014). 10.1093/cid/ciu653 - DOI - PubMed

Publication types