Complete sequence of the mitochondrial genome of the Japanese buff-tip moth, Phalera flavescens (Lepidoptera: Notodontidae)

Abstract

ABSTRACT. We sequenced the complete mitochondrial genome of Phalera flavescens. The mitogenome is 15,659 bp in length, including 13 protein-coding genes (atp6, atp8, cox1-3, nad1-6, nad4L, cob), two ribosomal RNAs (rrnS and rrnL), 22 transfer RNAs and an AT-rich region, a putative control region (D-loop). Gene order and orientation were found to be identical to those of other completely sequenced lepidopteran mitogenomes. All 13 protein-coding genes start with the common codon ATN, except for the cox1 gene, which uses CGA as the initial codon. Nine of the 13 protein-coding genes stop with codon TAA, while the cox1, cox2, nad5, and nad4 genes stop with the single nucleotide T. All tRNA genes can be folded into canonical cloverleaf secondary structure, except for trnS1, which loses the ''DHU'' arm. Six overlapping sequences totaling 20 bp (1-8 bp for each sequence) and 16 intergenic spacer sequences, totaling 276 bp (1-58 bp for each sequence) are scattered throughout the genome; the largest intergenic spacer is located between the trnQ and nad2 genes. A microsatellitelike structure (AT) 6 ACC(AT) 6 and 16-bp poly-T elements preceded by the ATTTA motif are present in the D-loop region. Additionally, unexpectedly, an extra 190-bp insertion, with unknown function, was found in the small subunit rRNA gene (rrnS); this gene is the longest known (1020 bp) among all of the Lepidoptera.

Characterization of the Complete Mitochondrial Genome of Leucoma salicis (Lepidoptera: Lymantriidae) and Comparison with Other Lepidopteran Insects

“…The relative synonymous codon usage of the 13 protein-coding genes (PCGs) in L. salicis is consistent with those of published lepidopteran sequences. Similarly, codons with A or T in the third codon position being overrepresented relative to other synonymous codons, is consistent with previous observations of lepidopterans9; likewise the absence or underrepresentation of high-GC codons1820.…”

The complete mitochondrial genome of Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae)

“…The gene order and arrangement are consistent with all other lepidopterans (e.g. Yang et al 2009;Sun et al 2012;Hao et al 2013;Wu et al 2016). The A þ T content of the whole mitogenome is 79.8%, which is generally in accordance with other four determined Zygaenoidea mitogenomes.…”

How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

“…While many of these may seem minor – for example, tRNAs annotated to be 1 bp too long or too short – they still result in inaccurate homology statements when aligning genes for phylogenetic analysis. Other errors, however, are quite substantial and radically change gene alignments with other species – for example, the rrnS gene of Phalera Hübner was annotated to be 190 bp too short due to an unrecognized 225 bp repeat in the middle of the gene (Sun et al ., ). Some errors are due to errors in earlier publications being propagated into later mt genome annotations.…”