Characterization of the Complete Mitochondrial Genomes of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae)

Abstract

The complete mitochondrial genomes (mitogenomes) of Cnaphalocrocis medinalis and Chilo suppressalis (Lepidoptera: Pyralidae) were determined and analyzed. The circular genomes were 15,388 bp long for C. medinalis and 15,395 bp long for C. suppressalis. Both mitogenomes contained 37 genes, with gene order similar to that of other lepidopterans. Notably, 12 protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; the cox1, cox2, and nad4 genes in the two mitogenomes had the truncated termination codons T, T, and TA, respectively, but the nad5 gene was found to use T as the termination codon only in the C. medinalis mitogenome. Additionally, the codon distribution and Relative Synonymous Codon Usage of the 13 PCGs in the C. medinalis mitogenome were very different from those in other pyralid moth mitogenomes. Most of the tRNA genes had typical cloverleaf secondary structures. However, the dihydrouridine (DHU) arm of the trnS1(AGN) gene did not form a stable stem-loop structure. Forty-nine helices in six domains, and 33 helices in three domains were present in the secondary structures of the rrnL and rrnS genes of the two mitogenomes, respectively. There were four major intergenic spacers, except for the A+T-rich region, spanning at least 12 bp in the two mitogenomes. The A+T-rich region contained an 'ATAGT(A)'-like motif followed by a poly-T stretch in the two mitogenomes. In addition, there were a potential stem-loop structure, a duplicated 25-bp repeat element, and a microsatellite '(TA)13' observed in the A+T-rich region of the C. medinalis mitogenome. A poly-T motif, a duplicated 31-bp repeat element, and a 19-bp triplication were found in the C. suppressalis mitogenome. However, there are many differences in the A+T-rich regions between the C. suppressalis mitogenome sequence in the present study and previous reports. Finally, the phylogenetic relationships of these insects were reconstructed based on amino acid sequences of mitochondrial 13 PCGs using Bayesian inference and maximum likelihood methods. These molecular-based phylogenies support the traditional morphologically based view of relationships within the Pyralidae.

Comparison of the mitochondrial genomes of the Old and New World strains of the legume pod borer, Maruca vitrata (Lepidoptera: Crambidae)

“…The AT-skew of M. vitrata (New World) was −0.002. A similar negative AT-skew was also previously reported for C. medinalis (Chai et al, 2012) and Spoladea recurvalis (He et al, 2015) (Table 2). This indicates a bias for T over A nucleotides.…”

“…Although the insect order Lepidoptera contains approximately 200,000 species, 72 complete or near complete mitogenomes representing 17 families in the lepidopteran lineage Ditrysia are available (Cameron, 2014). Among the family Crambidae, mitogenomes have been obtained for eight species: Ostrinia nubilalis and O. furnacalis (Coates et al, 2005), Diatraea saccharalis (Li et al, 2011), M. vitrata (Old World) (Margam et al, 2011b), Cnaphalocrocis medinalis (Chai et al, 2012), Chilo suppressalis (Chai et al, 2012), Paracymoriza prodigalis (Ye et al, 2013), and Spoladea recurvalis (He et al, 2015). Complete mitogenome sequences for Lepidoptera have been used to study the divergences between sibling and congeneric species (Yukuhiro et al, 2002;Coates et al, 2005) and to facilitate population-level studies .…”

“…Complete mitogenome sequences for Lepidoptera have been used to study the divergences between sibling and congeneric species (Yukuhiro et al, 2002;Coates et al, 2005) and to facilitate population-level studies . Furthermore, full mitogenomes for Lepidoptera are important for the determination of phylogenetic relationships and the identification of cryptic species Chai et al, 2012) at various taxonomic levels.…”

The complete mitochondrial genome of Pycnarmon lactiferalis (Lepidoptera: Crambidae)

“…It consists of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and an A þ T-rich region. Gene order is identical with other Pyraloidea species (Chai et al 2012;Ye et al 2013;Cao & Du 2014). There are 14 intergenic regions (except for the A þ T-rich region) ranging from 1 to 47 bp in P. lactiferalis mitochondrial genome.…”

Genetic variation of Chilo suppressalis Walker (Lepidoptera: Pyralidae) populations in Guilan and west of Mazandaran provinces analysed with RAPD markers

“…Up to now, despite the significance of RSSB, no assessment of the study about the genetic structure of RSSB by using molecular markers has been done in Iran. Papers on RSSB in other countries are limited study on geographic variation in susceptibility to Bacillus thuringiensis in China (Meng et al 2003), effects of Bt transgenic rice on RSSB and its consequences on egg parasitoid, Trichogramma brassicae (Marzban 2012), RSSB resistance to pesticides (Cao et al 2004;Li et al 2007), biochemical study (Zibaii 2008), geometric morphometric study (Zahiri et al 2006), isolation and characterisation of four polymorphic microsatellite loci ( Jiang et al 2005;Ishiguro et al 2006;Meng et al 2008), characterisation of complete mitochondrial genomes (Chai et al 2012), and limited divergence among RSSB populations caused by gene flow in southeast China . The objective of the present first study on genetic diversity of Chilo suppressalis in Iran is to explore the level of RAPD genetic variation among active RSSB populations in Guilan and west part of Mazandaran provinces, without any distinctive morphological deferens.…”