Document Type
Article
Original Publication Date
2013
Journal/Book/Conference Title
International Journal of Genomics
Volume
2013
DOI
10.1155/2013/832756
Date of Submission
September 2014
Abstract
Until recently, the apicomplexan parasites, Cryptosporidium hominis andC. parvum, were considered the same species. However, the two parasites, now considered distinct species, exhibit significant differences in host range, infectivity, and pathogenicity, and their sequenced genomes exhibit only 95–97% identity. The availability of the complete genome sequences of these organisms provides the potential to identify the genetic variations that are responsible for the phenotypic differences between the two parasites. We compared the genome organization and structure, gene composition, the metabolic and other pathways, and the local sequence identity between the genes of these two Cryptosporidium species. Our observations show that the phenotypic differences between C. hominisand C. parvum are not due to gross genome rearrangements, structural alterations, gene deletions or insertions, metabolic capabilities, or other obvious genomic alterations. Rather, the results indicate that these genomes exhibit a remarkable structural and compositional conservation and suggest that the phenotypic differences observed are due to subtle variations in the sequences of proteins that act at the interface between the parasite and its host.
Rights
Copyright © 2013 Aurélien J. Mazurie et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Is Part Of
VCU Microbiology and Immunology Publications
Supplementary Figure 1: Synteny of Plasmodia and Cryptosporidia genus Position of the orthologs identified in the genomes of C. parvum, P. falciparum, P. knowlesi and P. vivax. For each pair of species, a green cross denotes an ortholog present in the same strand in both genomes, while a red cross denotes an inversion.
supplementary_figure_2-compactness.pdf (29 kB)
Supplementary Figure 2: Genome Compactness Comparison of the genome compactness of well-studied apicomplexans, as the average number of putative paralogs per genes.
supplementary_figure_3-pathway_scores.pdf (962 kB)
Supplementary Figure 3: Pathway Scores See Figure 1.
supplementary_table_1-chromosomes_composition.xls (20 kB)
Supplementary Table 1: Chromosomes Composition Results of the statistical evaluation performed using the Fisher’s exact test of the enrichment of the Plasmodia chromosomes in orthologs identified in C. parvum. Values of enrichment are given as the log2 of the ratio between the fraction of orthologs in a given Plasmodium chromosome coming from a same chromosome of C. parvum, and the fraction of orthologs in the whole Plasmodium genome coming from this C. parvum chromosome. A value of 0 (ratio of 1) means that the Plasmodium chromosome contains proportionally as many orthologs from the C. parvum chromosome considered as in the whole genome. The values obtained show that the Plasmodium chromosomes significantly retain the composition of the C. parvum chromosomes. P-values below 0.05 were discarded.
supplementary_table_2-pathway_scores.xls (227 kB)
Supplementary Table 2: Pathway Scores Completeness, connectedness and support scores of the inferred metabolic pathways of C. hominis and C. parvum, along with nine other apicomplexans and an external reference, S. cerevisiae (see text).
supplementary_table_3-dn_ds.xls (812 kB)
Supplementary Table 3: Orthologs Sequence Comparison Results of the pairs of putative orthologs sequences comparisons. Identity: percentage of identity between the two protein sequences. dN/dS: non-synonymous on synonymous substitution rate ratio, or None if undefined (when dS equals to zero). Ti/Tv: transition on transversion ratio.
supplementary_table_4-protein_localizations.xls (240 kB)
Supplementary Table 4: Protein Localizations Predicted protein localization, based on the putative presence of transmembrane domains, GPI anchor and/or signal peptides (see text). For each pair of orthologs, the electronic annotation was done on the C. hominis sequence (identifier in the first column). P(signal peptide) and P(signal anchor): probability of a signal peptide and signal anchor as calculated by SignalP. # GPI anchors: putative number of GPI anchors as predicted by gpi-som. # TM domains: putative number of transmembrane helices as predicted by tmhmm.
Comments
Originally published at http://dx.doi.org/10.1155/2013/832756