Characterization of the complete mitochondrial genome of Tryporyza incertulas, in comparison with seven other Pyraloidea moths

Abstract

The complete 15,223-bp mitochondrial genome (mitogenome) of Tryporyza incertulas (Walker) (Lepidoptera: Pyraloidea: Crambidae) was determined, characterized and compared with seven other species of superfamily Pyraloidea. The order of 37 genes was typical of insect mitochondrial DNA sequences described to date. Compared with other moths of Pyraloidea, the A+T biased (77.0%) of T. incertulas was the lowest. Eleven protein-coding genes (PCGs) utilized the standard ATN, but cox1 used CGA and nad4 used AAT as the initiation codons. Ten protein-coding genes had the common stop codon TAA, except nad3 having TAG as the stop codon, and cox2, nad4 using T, TA as the incomplete stop codons, respectively. All of the tRNA genes had typical cloverleaf secondary structures except trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. There was a spacer between trnQ and nad2, which was common in Lepidoptera moths. A 6-bp motif 'ATACTA' between trnS2(UCN) and nad1, a 7-bp motif "AGC(T)CTTA" between trnW and trnC and a 6-bp motif "ATGATA" of overlapping region between atp8 and atp6 were found in Pyraloidea moths. The A+T-rich region contained an 'ATAGT(A)'-like motif followed by a poly-T stretch. In addition, two potential stem-loop structures, a duplicated 19-bp repeat element, and two microsatellites '(TA)12' and '(TA)9' were observed in the A+T-rich region of T. incertulas mitogenome. Finally, the phylogenetic relationships of Pyraloidea species were constructed based on amino acid sequences of 13 PCGs of mitogenomes using Bayesian inference (BI) and maximum likelihood (ML) methods. These molecular-based phylogenies supported the morphological classification on relationships within Pyraloidea species.

Keywords: ATP synthase F0 subunit 6; ATP synthase F0 subunit 8; Ile; Leu; Mitochondrial genome; NADH dehydrogenase subunit 1; NADH dehydrogenase subunit 2; NADH dehydrogenase subunit 3; NADH dehydrogenase subunit 4; NADH dehydrogenase subunit 4l; NADH dehydrogenase subunit 5; NADH dehydrogenase subunit 6; Phe; Phylogenetic relationship; Pyraloidea; Ser; Tryporyza incertulas; atp6; atp8; cob; cox1; cox2; cox3; cytochrome b; cytochrome c oxidase subunit 1; cytochrome c oxidase subunit 2; cytochrome c oxidase subunit 3; isoleucine; leucine; mitochondrial 12s ribosomal rna; mitochondrial 16s ribosomal rna; nad1; nad2; nad3; nad4; nad4L; nad5; nad6; phenylalanine; rrnL; rrnS; serine.