Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.)

Abstract

Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.

Fig 1. Mitochondrial genome map of Chrysodeixis acuta.

From outer to inner, the 1st circle shows the gene map (PCGs, rRNA, tRNAs & CR) and tRNA genes are abbreviated by one letter symbols according to the IUPAC-IUB single-letter amino acid codes. The 2^nd circle shows the GC content and the 3rd shows GC skew calculated as (G-C)/ (G+C). GC content and GC skew are plotted as the deviation from the average value of the entire sequence.

Fig 2. Predicated secondary clover-leaf structures for the 22 tRNA genes of Chrysodeixis acuta.

The tRNAs are labled with abbreviation of their corresponding amino acids below each tRNA gene structure. Arms of tRNAs (clockwise from top) are the amino acid acceptor arm, TYC arm, the anticodon arm, and dihydrouridine (DHU) arm.

Fig 3. Alignment of the intergenic spacer region between trnS2 (UCN) and nad1 of several lepidopteran insects of Plusiinae subfamily.

ATACTAA motif is underlined and the TACTAAAAATAAAT is shaded.

Fig 4. Features presents A+T rich region of Chrysodeixis acuta.

The ATAGA motif is shaded, Poly-T strand is underlined, Poly-A stretch is double underlined; the single microsatellite A/T repeat sequence is dotted underlined.

Fig 5. Phylogenetic tree of 55 species from Noctuidae family species including Chrysodeixis acuta.

The analysis obtained from Bayseain Inference and Maximum Likelihood based on concatenated data of 13 PCGs genes. The numbers at nodes indicate ML bootstrap values probabilities. Accession numbers are given for species obtained from GenBank.