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. 2015 Nov 9:5:16324.
doi: 10.1038/srep16324.

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference

Juan P Isaza  1   2 , Ana Luz Galván  1 , Victor Polanco  3 , Bernice Huang  4 , Andrey V Matveyev  4 , Myrna G Serrano  4 , Patricio Manque  3 , Gregory A Buck  4 , Juan F Alzate  1   2
Affiliations

Revisiting the reference genomes of human pathogenic Cryptosporidium species: reannotation of C. parvum Iowa and a new C. hominis reference

Juan P Isaza et al. Sci Rep. .

Abstract

Cryptosporidium parvum and C. hominis are the most relevant species of this genus for human health. Both cause a self-limiting diarrhea in immunocompetent individuals, but cause potentially life-threatening disease in the immunocompromised. Despite the importance of these pathogens, only one reference genome of each has been analyzed and published. These two reference genomes were sequenced using automated capillary sequencing; as of yet, no next generation sequencing technology has been applied to improve their assemblies and annotations. For C. hominis, the main challenge that prevents a larger number of genomes to be sequenced is its resistance to axenic culture. In the present study, we employed next generation technology to analyse the genomic DNA and RNA to generate a new reference genome sequence of a C. hominis strain isolated directly from human stool and a new genome annotation of the C. parvum Iowa reference genome.

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Figures

Figure 1
Figure 1. Frequency of genes with introns across chromosomes and number of exons per gene.
Bar charts showing (a) Distribution of genes with introns in C. parvum Iowa chromosomes and b) exons distribution among genes of C. parvum Iowa genome (intronless genes were excluded). IGA (Blue) stands for Improved Genome Annotation (this work) and OGA (Orange) stand for Original Genome Annotation.
Figure 2
Figure 2. Phylogenetic position of C. hominis UdeA01 based on partial sequence of GP60 gene.
Phylogenetic tree based on partial sequence of GP60 gene from different isolates of C. hominis and C. parvum. The tree was constructed by Neighbour-Joining method and 1, 000 bootstrap replicates. Bootstrap values above 50 are shown. The tree was rooted with the GP60 sequence of C. parvum Iowa.
Figure 3
Figure 3. Circular representation of C. hominis UdeA01 genome.
Graphical representation of C. hominis UdeA01 chromosomes. Circles from outer to inner represents: Chromosomes (grey); histogram of read coverage in windows size of 10 kb (red); forward CDSs (blue); reverse CDSs (blue); C. hominis TU502 – C. hominis UdeA01 intergenic region SNPs density (orange) and coding region SNPs density (green); “C. hominis TU502 new” – C. hominis UdeA01 intergenic region SNPs density (orange) and coding region SNPs density (green); C. hominis UKH1 – C. hominis UdeA01 intergenic region SNPs density (orange) and coding region SNPs density (green); C. parvum Iowa – C. hominis UdeA01 intergenic region SNPs density (orange) and coding region SNPs density (green); GC content in window size of 10 kb (yellow). Black bars in chromosome circle represents the remaining gaps. Three pink bars represent the telomeric region where it was reached. Red bars over CDS circles represent the location of eleven genes of C. hominis UdeA01 absent in C. parvum Iowa genome.
Figure 4
Figure 4. Gene Ontology enrichment analysis of highly divergent genes between C. hominis isolates.
Gene Ontology enrichment analysis for (a) 77 highly divergent genes between C. hominis TU502 and C. hominis UdeA01 (test) whole putative C. hominis UdeA01 proteome (reference). (b) 37 highly divergent genes between C. hominis UdeA01 and C. hominis UKH1 (test) whole putative C. hominis UdeA01 proteome (reference). GO terms found over/under represented by a two-tailed Fisher Exact test with a p-value below 0.05.
Figure 5
Figure 5. Gene Ontology (GO) terms overrepresented in the highly divergent genes with specific SNPs of C. hominis TU502.
Gene Ontology enrichment analysis for highly divergent genes with specific SNPs of C. hominis TU502 (test) whole putative C. hominis UdeA01 proteome (reference). GO terms found over/under represented by a two-tailed Fisher Exact test with a p-value below 0.05
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