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International Journal of Genomics
Volume 2013 (2013), Article ID 832756, 8 pages
Comparative Genomics of Cryptosporidium
1Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
2Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23284-2030, USA
3Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
Received 24 January 2013; Accepted 10 April 2013
Academic Editor: Elena Pasyukova
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.
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: 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 See Figure 1.
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 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: 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 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.