Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista1,2,
- Yiran Li2,
- Adam Sateriale3,
- Mandy J. Sanders4,
- Karen L. Brooks4,
- Alan Tracey4,
- Brendan R.E. Ansell5,
- Aaron R. Jex5,
- Garrett W. Cooper6,
- Ethan D. Smith6,
- Rui Xiao2,
- Jennifer E. Dumaine3,
- Peter Georgeson6,7,8,
- Bernard J. Pope6,7,9,10,
- Matthew Berriman4,
- Boris Striepen3,
- James A. Cotton4 and
- Jessica C. Kissinger1,2,11
- 1Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA;
- 2Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA;
- 3Department of Pathology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- 4The Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom;
- 5Faculty of Veterinary and Agricultural Sciences, The University of Melbourne and Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia;
- 6Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne VIC 3000, Australia;
- 7Melbourne Bioinformatics, The University of Melbourne, Parkville VIC 3010, Australia;
- 8University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Melbourne VIC 3000, Australia;
- 9Department of Surgery (Royal Melbourne Hospital), Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne 3010, Australia;
- 10Department of Medicine, Central Clinical School, Faculty of Medicine Nursing and Health Sciences, Monash University, Melbourne 3004, Australia;
- 11Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
Abstract
Cryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, the Cryptosporidium community has only had access to a good, but incomplete, Cryptosporidium parvum IOWA reference genome sequence. Incomplete reference sequences hamper annotation, experimental design, and interpretation. We have generated a new C. parvum IOWA genome assembly supported by Pacific Biosciences (PacBio) and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related species: C. parvum, Cryptosporidium hominis, and Cryptosporidium tyzzeri. We made 1926 C. parvum annotation updates based on experimental evidence. They include new transporters, ncRNAs, introns, and altered gene structures. The new assembly and annotation revealed a complete Dnmt2 methylase ortholog. Comparative annotation between C. parvum, C. hominis, and C. tyzzeri revealed that most “missing” orthologs are found, suggesting that the biological differences between the species must result from gene copy number variation, differences in gene regulation, and single-nucleotide variants (SNVs). Using the new assembly and annotation as reference, 190 genes are identified as evolving under positive selection, including many not detected previously. The new C. parvum IOWA reference genome assembly is larger, gap free, and lacks ambiguous bases. This chromosomal assembly recovers all 16 chromosome ends, 13 of which are contiguously assembled. The three remaining chromosome ends are provisionally placed. These ends represent duplication of entire chromosome ends including subtelomeric regions revealing a new level of genome plasticity that will both inform and impact future research.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275325.121.
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Freely available online through the Genome Research Open Access option.
- Received February 11, 2021.
- Accepted November 10, 2021.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
