Computational protocol: Novel type of linear mitochondrial genomes with dual flip-flop inversion system in apicomplexan parasites, Babesia microti and Babesia rodhaini

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Protocol publication

[…] Nucleotide sequences of the mt genomes from B. microti and B. rodhaini and their deduced amino acid sequences were aligned with reported sequences from P. falciparum (M76611), B. bovis (AB499088), T. annulata (NW_001091933), T. equi (AB499091) and T. parva (AB499089) by Clustal W [] with manual correction. Protein-coding regions were inferred using previously annotated sequences from T. parva and B. bovis.To identify putative rRNA genes, mt DNA sequences or annotated rRNA gene fragments from B. bovis (EU075182) and T. parva (Z23263) were used as a query under suggested algorithm parameters [] in NCBI BLAST 2.2 []. In silico analysis was also performed with Probalign beta version 1.2 [] and SSEARCH 3.5 [] using known rRNA gene fragments and suggested advanced search options [,]. Newly identified candidate rRNA genes were, likewise, used as input sequences. Information from sequence alignments using CLUSTAL W [] and putative base-pairings between fragments proposed for T. parva mt rRNA fragments [,] were used to determine the termini of candidate rRNA genes. [...] Concatenated amino acid sequences of COX1 and COB (696 sites) from 17 apicomplexan parasites (Additional file : Table S4) were used for phylogenetic analysis. A free living dinoflagellate, Crypthecodinium cohnii[,], was included as an outgroup. COX3 were not used for phylogenetic analysis, due to very high divergence in Babesia/Theileria species []. We constructed the ML phylogenetic tree by the PROML program in PHYLIP version 3.68 []. CODEML program in PAML version 4.2 [] was used to estimate the Γ shape parameter value α. Bootstrap analysis was done by applying PROML to 100 re-sampled datasets produced by SEQBOOT program in PHYLIP. BP values were calculated for internal branches of the ML-tree using CONSENSE in PHYLIP. […]

Pipeline specifications

Software tools Clustal W, BLASTN, Probalign, PHYLIP, PAML
Applications Phylogenetics, Amino acid sequence alignment
Organisms Babesia microti, Homo sapiens, Brucella microti
Diseases Babesiosis, Malaria