Computational protocol: Emergence of Cryptosporidium hominis Monkey Genotype II and Novel Subtype Family Ik in the Squirrel Monkey (Saimiri sciureus) in China

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Protocol publication

[…] The nucleotide sequences obtained in this study for each locus were aligned with the corresponding Cryptosporidium reference sequences downloaded from the GenBank database, using BLAST (http://blast.ncbi.nlm.nih.gov) and ClustalX software (version 1.83; ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/). To support the genotype and subtype classification, phylogenetic analysis at each of the abovementioned loci was performed by use of the PHYLIP software, version 3.64 []. Neighbor-joining trees between different sequences were constructed to identify Cryptosporidium species and subtypes on the basis of evolutionary distances calculated using the Kimura two-parameter model. The reliability of all topology trees was evaluated by the bootstrap method with 1,000 pseudo-replicates and only values above 50% were reported. Phylograms were drawn in the MEGA 4.0 program, and sequence identity analysis was carried out using the MegAlign program in the DNAstar 6.0 software package. Moreover, to more precisely illuminate the evolutionary status of the current isolate, maximum likelihood analysis was preformed in those loci. Likewise, the bootstrap method with 1,000 pseudo-replicates was employed to assess reliability of all topology trees, and the MEGA 4.0 software was used to draw phylograms.Nucleotide sequences of the SSU rRNA, HSP70, COWP, actin, and gp60 gene fragments obtained in the present study were deposited in the GenBank database under the accession numbers KP314259–KP314263. […]

Pipeline specifications

Software tools Clustal W, PHYLIP
Application Phylogenetics
Organisms Cryptosporidium hominis, Saimiri sciureus, Campylobacter hominis
Chemicals Nucleotides