Characterization of the complete mitochondrial genome of Orthaga olivacea Warre (Lepidoptera Pyralidae) and comparison with other Lepidopteran insects

Abstract

Orthaga olivacea Warre (Lepidoptera: Pyralidae) is an important agricultural pest of camphor trees (Cinnamomum camphora). To further supplement the known genome-level features of related species, the complete mitochondrial genome of Orthaga olivacea is amplified, sequenced, annotated, analyzed, and compared with 58 other species of Lepidopteran. The complete sequence is 15,174 bp, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Base composition is biased toward adenine and thymine (79.02% A+T) and A+T skew are slightly negative. Twelve of the 13 PCGs use typical ATN start codons. The exception is cytochrome oxidase 1 (cox1) that utilizes a CGA initiation codon. Nine PCGs have standard termination codon (TAA); others have incomplete stop codons, a single T or TA nucleotide. All the tRNA genes have the typical cloverleaf secondary structure, except for trnS (AGN) , in which dihydrouridine (DHU) arm fails to form a stable stem-loop structure. The A+T-rich region (293 bp) contains a typical Lepidopter motifs 'ATAGA' followed by a 17 bp poly-T stretch, and a microsatellite-like (AT) 13 repeat. Codon usage analysis revealed that Asn, Ile, Leu2, Lys, Tyr and Phe were the most frequently used amino acids, while Cys was the least utilized. Phylogenetic analysis suggested that among sequenced lepidopteran mitochondrial genomes, Orthaga olivacea Warre was most closely related to Hypsopygia regina, and confirmed that Orthaga olivacea Warre belongs to the Pyralidae family.

Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects

“…The TAA stop codon was the most common among these PCGs (nad2, cox1, atp8, atp6, cox3, nad3, nad5, nad4L, nad6, cytb), while nad1 utilized a TAG stop codon, and nad4 and cox2 harbored incomplete stop codons (T) (Table 1). This is a common conserved mitogenomic feature among invertebrates [17][18][19] , and this single T residue can be still be recognized by endonucleases during polycistronic pre-mRNA transcription, with polyadenylation from contiguous PCGs ultimately yielding a functional stop codon 5,20,21 . Next, we assessed codon usage among a range of Lepidopteran species, including three Noctuoidae members as well as Bombycoidea, Tortricoidea, and Geometroidea members (Fig.…”

The complete mitochondrial genome of Orthaga achatina (Lepidoptera: Pyralidae)

“…The phylogenetic tree and AAI heatmap of each protein was visualized using EVOLVIEW version 2 (https://evolgenius.info//evolview-v2) (He et al 2016). Phylogenetic analyses showed similar relationships among sampled families as shown in Yang et al (2020). Each clade showed a monophyletic cluster and the following clades were highly supported (Figure 1): (1) Pyralidae þ Crambidae; and…”

“…Pyralidae is the largest family in Lepidoptera, with more than 25,000 species in the world, some of which are pests of agricultural and forestry plants, such as Orthaga (Yang et al 2020). Orthaga achatina Butler (Lepidoptera: Pyralidae) is the most serious pest of camphor trees (Cinnamomum camphora) in China, Korea, Japan, and Malaysia (Wu 2006).…”

“…Orthaga achatina can also feed on other Lauraceae plants, such as Lindera glauca and Cinnamomum cassia, causing serious defoliation (Long et al 2017). Mitochondrial genome has high mutation rate and low DNA recombination rate, which is of great significance in insect phylogenetic analysis (Gai et al 2020;Yang et al 2020). However, the mitochondrial genome of O. achatina has not been publicly reported.…”

“…All protein-coding genes (PCGs) are initiated with ATN as the starting codon except the cox1, which is no justification for continued speculation about polynucleotide start codon similar to other Lepidoptera insects (Singh et al 2017;Liu et al 2018;Yang et al 2020). Ten PCGs had canonical stop codons TAA or TAG, while three had incomplete termination codons single T (cox3 and atp6) or TA (nad4L).…”