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Comparative genomic analysis of the principal
- Source :
- PeerJ
- Publication Year :
- 2020
-
Abstract
- Cryptosporidium parasites are ubiquitous and can infect a broad range of vertebrates and are considered the most frequent protozoa associated with waterborne parasitic outbreaks. The intestine is the target of three of the species most frequently found in humans: C. hominis, C. parvum, and. C. meleagridis. Despite the recent advance in genome sequencing projects for this apicomplexan, a broad genomic comparison including the three species most prevalent in humans have not been published so far. In this work, we downloaded raw NGS data, assembled it under normalized conditions, and compared 23 publicly available genomes of C. hominis, C. parvum, and C. meleagridis. Although few genomes showed highly fragmented assemblies, most of them had less than 500 scaffolds and mean coverage that ranged between 35X and 511X. Synonymous single nucleotide variants were the most common in C. hominis and C. meleagridis, while in C. parvum, they accounted for around 50% of the SNV observed. Furthermore, deleterious nucleotide substitutions common to all three species were more common in genes associated with DNA repair, recombination, and chromosome-associated proteins. Indel events were observed in the 23 studied isolates that spanned up to 500 bases. The highest number of deletions was observed in C. meleagridis, followed by C. hominis, with more than 60 species-specific deletions found in some isolates of these two species. Although several genes with indel events have been partially annotated, most of them remain to encode uncharacterized proteins.
- Subjects :
- Bioinformatics
Molecular biology
030231 tropical medicine
Cryptosporidium
Genomics
comparative genomics
Biology
Microbiology
Genome
General Biochemistry, Genetics and Molecular Biology
DNA sequencing
Computational biology
03 medical and health sciences
0302 clinical medicine
Genetic variation
Indel
Gene
Taxonomy
030304 developmental biology
Whole genome sequencing
Comparative genomics
Genetics
Whole-genome sequencing
0303 health sciences
General Neuroscience
General Medicine
biology.organism_classification
NGS
Parasitology
General Agricultural and Biological Sciences
High-throughput nucleotide sequencing
De novo genome assembly
Subjects
Details
- ISSN :
- 21678359
- Volume :
- 8
- Database :
- OpenAIRE
- Journal :
- PeerJ
- Accession number :
- edsair.doi.dedup.....b4317e8323f0bc0bf6c2eeeafb74a366