Computational protocol: The complete mitochondrial genomes for three Toxocara species of human and animal health significance

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Protocol publication

[…] Sequences were assembled manually and aligned against the complete mt genome sequence of A. suum (GenBank™ accession number NC001327) using the program Clustal X to identify gene boundaries. The open-reading frames and codon usage profiles of protein-coding genes were analyzed using the program MacVector 4.1.4 (Kodak, version 4.0). Translation initiation and translation termination codons were identified based on comparison with those reported previously for A. suum. The amino acid sequences inferred for the mt genes of three ascaridoids were aligned with those of A. simplex (GenBank™ accession number AY994157) and A. suum using Clustal X. Based on pairwise alignments, amino acid identity (%) was calculated for homologous genes. Codon usage was examined using the relationships between the nucleotide composition of codon families and amino acid occurrence, where the genetic codons are partitioned into AT-rich codons (i.e. those which are AT-rich at the first two codon positions), GC-rich codons (those which are GC-rich at the first two codon positions) and unbiased codons. For analyzing ribosomal RNA genes, putative secondary structures of 22 tRNA genes were identified using tRNAscan-SE [], or by recognizing potential secondary structures and anticodon sequences by eye by aligning sequences with those of A. simplex and A. suum. [...] Phylogenetic analyses were performed using the five ascaridoid species (T. canis, T. cati, T. malaysiensis, A. suum,A. simplex) as ingroups, and one filarioid species (O. volvulus) serving as outgroup (GenBank™ accession number AF015193), based on amino acid sequences of 12 protein-coding genes. Amino acid sequences for each gene were individually aligned using Clustal X under default setting, and then concatenated into single alignments for phylogenetic analyses. Standard unweighted maximum parsimony (MP) were performed in PAUP* 4.0b10 [] using heuristic searches with tree-bisection-reconnection branch swapping and 1000 random-addition sequence replicates with 10 trees held at each step. The Dayhoff matrix model was utilized in the analyses of neighbour joining (NJ), implemented by MEGA 3.1 [], and maximum likelihood (ML) implemented by PhyML 2.1 []. Branch supports were estimated by bootstrap analysis of 1000 replicates for NJ and MP trees, and 100 replicates for ML tree. […]

Pipeline specifications

Software tools Clustal W, MacVector, tRNAscan-SE, PAUP*, MEGA, PhyML
Applications Genome annotation, Phylogenetics
Organisms Toxocara canis, Homo sapiens, Toxocara cati, Caenorhabditis elegans, Trichinella spiralis, Ascaris suum, Anisakis simplex, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis
Diseases Animal Diseases, Ataxia Telangiectasia, Nematode Infections, Leukemia, T-Cell
Chemicals Adenosine Triphosphate