The complete mitochondrial genome of Leucoptera malifoliella Costa (Lepidoptera: Lyonetiidae)

Abstract

The mitochondrial genome (mitogenome) of Leucoptera malifoliella (=L. scitella) (Lepidoptera: Lyonetiidae) was sequenced. The size was 15,646 bp with gene content and order the same as those of other lepidopterans. The nucleotide composition of L. malifoliella mitogenome is highly A+T biased (82.57%), ranked just below Coreana raphaelis (82.66%) (Lepidoptera: Lycaenidae). All protein-coding genes (PCGs) start with the typical ATN codon except for the cox1 gene, which uses CGA as the initiation codon. Nine PCGs have the common stop codon TAA, four PCGs have the common stop codon T as incomplete stop codons, and nad4l and nad6 have TAG as the stop codon. Cloverleaf secondary structures were inferred for 22 tRNA genes, but trnS1(AGN) was found to lack the DHU stem. The secondary structure of rrnL and rrnS is generally similar to other lepidopterans but with some minor differences. The A+T-rich region includes the motif ATAGA, but the poly (T) stretch is replaced by a stem-loop structure, which may have a similar function to the poly (T) stretch. Finally, there are three long repeat (154 bp) sequences followed by one short repeat (56 bp) with four (TA)(n) intervals, and a 10-bp poly-A is present upstream of trnM. Phylogenetic analysis shows that the position of Yponomeutoidea, as represented by L. malifoliella, is the same as traditional classifications. Yponomeutoidea is the sister to the other lepidopteran superfamilies covered in the present study.

FIG. 1.

Alignment result of trnY and cox1 in 34 Lepidopterans. The dotted line and underline indicate the locations of cox1 and trnY, respectively. The overlapping base between trnY and cox1 is marked gray.

FIG. 2.

Putative secondary structures for the tRNA genes of Leucoptera malifoliella mitogenome.

FIG. 3.

Predicted rrnL secondary structure in Leucoptera malifoliella mitogenome.

FIG. 4.

Predicted rrnS secondary structure in Leucoptera malifoliella mitogenome. Tertiary interactions and base triples are shown connected by continuous lines. Base pairing is indicated as follows: Watson-Crick pairs by lines, wobble GU pairs by plus, and other noncanonical pairs by circles.

FIG. 5.

The structure of the A+T-rich region of Leucoptera malifoliella mitogenome.

FIG. 6.

Alignment of motif and Poly(T) in the A+T-rich region of 34 lepidopterans. The Poly(T) stretch is marked gray. Marked box is motif ATAGA. Underline is the stem-loop structure of Leucoptera malifoliella.

FIG. 7.

Phylogeny of lepidopteran insects. (A) Phylogenetic trees inferred from amino acid sequences and nucleotide sequences of 13 protein-coding genes (PCGs) of the mitogenome using ML analysis; the numbers above branches are bootstrap percentages; the first and second values are from amino acid sequences and nucleotide sequences, respectively. Bactrocera oleae and Anopheles gambiae were used as outgroups. (B) Phylogenetic trees inferred from amino acid sequences and nucleotide sequences of 13 PCGs of the mitogenome using Bayesian Inference (BI) analysis; the numbers above branches give posterior probabilities. In the BI tree inferred from amino acid sequences C. cephalonica is sister to the clade (Pyraloidea+(Noctuoidea+(Geometroidea+Bombycoidea))); the posterior probabilities are 100% and 90%, and the posterior probabilities of C. cephalonica in the BI tree from nucleotide sequences is 100% (not labeled). The other information on the tree is the same as in (A).

FIG. 7.

Phylogeny of lepidopteran insects. (A) Phylogenetic trees inferred from amino acid sequences and nucleotide sequences of 13 protein-coding genes (PCGs) of the mitogenome using ML analysis; the numbers above branches are bootstrap percentages; the first and second values are from amino acid sequences and nucleotide sequences, respectively. Bactrocera oleae and Anopheles gambiae were used as outgroups. (B) Phylogenetic trees inferred from amino acid sequences and nucleotide sequences of 13 PCGs of the mitogenome using Bayesian Inference (BI) analysis; the numbers above branches give posterior probabilities. In the BI tree inferred from amino acid sequences C. cephalonica is sister to the clade (Pyraloidea+(Noctuoidea+(Geometroidea+Bombycoidea))); the posterior probabilities are 100% and 90%, and the posterior probabilities of C. cephalonica in the BI tree from nucleotide sequences is 100% (not labeled). The other information on the tree is the same as in (A).