Computational protocol: The Complete Mitochondrial Genome of the Asiatic Cavity-Nesting Honeybee Apis cerana (Hymenoptera: Apidae)

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Protocol publication

[…] Sequences were assembled manually and aligned against the complete mt genome sequence of A. mellifera using the computer program Clustal×1.83 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, version4.0). Translation initiation and translation termination codons were identified based on comparison with the mt genome of A. mellifera. The amino acid sequences inferred for the mt genes of the A. cerana were aligned with those of A. mellifera by using Clustal×1.83. Based on pairwise alignments, amino acid identity (%) was calculated for homologous genes. Codon usage was examined based on the relationships between the nucleotide composition of codon families and amino acid occurrence, where the genetic codons are partitioned into AT rich codons, GC-rich codons and unbiased codons. For analyzing ribosomal RNA genes, putative secondary structures of 22 tRNA genes were identified using tRNAscan-SE , of the 22 tRNA genes, 19 were identified using tRNAscan-SE, the other 3 tRNA genes were found by eye inspection, and rRNA genes were identified by comparison with the mt genome of A. mellifera. [...] Phylogenetic relationship among the Hymenoptera were performed using the 14 Hymenoptera species () as ingroup, plus the mt DNA sequence of A. cerana obtained in the present study, using one Reduviidae species (Triatoma dimidiata, GenBank accession number AF301594) as the outgroup, based on amino acid sequences of 13 protein-coding genes. Amino acid sequences for each gene were individually aligned using Clustal×1.83 under default setting, and then concatenated into single alignments for phylogenetic analyses. Three methods, namely neighbor joining (NJ), maximum likelihood (ML) and maximum parsimony (MP), were used for phylogenetic re-constructions. Standard unweighted MP was performed using package Phylip 3.67 . NJ analysis was carried out using PAUP 4.0 Beta 10 programme , and ML analysis was performed using PUZZLE 4.1 under the default setting . The consensus tree was obtained after bootstrap analysis, with 1000 replications for NJ and MP trees, and 100 for ML tree, with values above 50% reported. […]

Pipeline specifications

Software tools Clustal W, MacVector, tRNAscan-SE, PHYLIP, PAUP*, PUZZLE
Applications Genome annotation, Phylogenetics
Organisms Apis mellifera, Apis cerana
Diseases Ataxia Telangiectasia
Chemicals Amino Acids, Nucleotides