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

Abstract

The complete mitochondrial genome (mitogenome) of Leucoma salicis (Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other than cox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences. All tRNA genes had typical clover-leaf secondary structures, except for the tRNA^Ser (AGN), in which the dihydrouridine (DHU) arm could not form a stable stem-loop structure. The A + T-rich region of 325 bp had several distinctive features, including the motif 'ATAGA' followed by an 18 bp poly-T stretch, a microsatellite-like (AT)₇ element, and an 11-bp poly-A present immediately upstream of tRNA^Met. Relationships among 32 insect species were determined using Maximum Likelihood (ML), Neighbor Joining (NJ) and Bayesian Inference (BI) phylogenetic methods. These analyses confirm that L. salicis belongs to the Lymantriidae; and that Lymantriidae is a member of Noctuoidea, and is a sister taxon to Erebidae, Nolidae and Noctuidae, most closely related to Erebidae.

Figure 1. Map of the mitogenome of L. salicis.

tRNA genes are labeled according to the IUPAC-IUB three-letter amino acids; cox1, cox2 and cox3 refer to the cytochrome c oxidase subunits; cob refers to cytochrome b; nad1-nad6 refer to NADH dehydrogenase components; rrnL and rrnS refer to ribosomal RNAs.

Figure 2. Comparison of codon usage within the mitochondrial genome of members of the Lepidoptera.

Lowercase letters (a,b,c,d and e) above species names represent the superfamily to which the species belongs (a: Noctuoidea, b: Geometroidea, c: Bombycoidea, d: Pyraloidea, e: Tortricoidea).

Figure 3. Codon distribution in members of the Lepidoptera.

CDspT = codons per thousand codons.

Figure 4. Relative Synonymous Codon Usage (RSCU) of the mitochondrial genome of five superfamilies in the Lepidoptera.

Codon families are plotted on the x-axis. Codons indicated above the bar are not present in the mitogenome.

Figure 5. Predicted secondary structures of the 22 tRNA genes of the L. salicis mitogenome.

Figure 6

(A) Alignment of the intergenic spacer region between tRNA^Ser (UCN) and nad1 of several Lepidopteran insects. (B) Features present in the A + T-rich region of L. salicis. The ‘ATATG’ motif is shaded. The poly-A stretch is double underlined, and the poly-T stretch is underlined. The single microsatellite T/A repeat sequence is indicated by dotted underlining.

Figure 7

(A) Tree showing the phylogenetic relationships among 32 species, constructed using Maximum Likelihood with 1000 bootstrap replicates. (B) Neighbor Joining (NJ) tree, with 1000 bootstrap replicates. (C) Tree constructed using Bayesian Inference (BI) MCMC consensus tree, with posterior probabilities shown at nodes. Drosophila melanogaster (NC_025936) and Locusta migratoria (NC_002084) were used as outgroups.