Mitochondrial Genome Sequence and Expression Profiling for the Legume Pod Borer Maruca vitrata (Lepidoptera: Crambidae)

Abstract

We report the assembly of the 14,054 bp near complete sequencing of the mitochondrial genome of the legume pod borer (LPB), Maruca vitrata (Lepidoptera: Crambidae), which we subsequently used to estimate divergence and relationships within the lepidopteran lineage. The arrangement and orientation of the 13 protein-coding, 2 rRNA, and 19 tRNA genes sequenced was typical of insect mitochondrial DNA sequences described to date. The sequence contained a high A+T content of 80.1% and a bias for the use of codons with A or T nucleotides in the 3rd position. Transcript mapping with midgut and salivary gland ESTs for mitochondrial genome annotation showed that translation from protein-coding genes initiates and terminates at standard mitochondrial codons, except for the coxI gene, which may start from an arginine CGA codon. The genomic copy of coxII terminates at a T nucleotide, and a proposed polyadenylation mechanism for completion of the TAA stop codon was confirmed by comparisons to EST data. EST contig data further showed that mature M. vitrata mitochondrial transcripts are monocistronic, except for bicistronic transcripts for overlapping genes nd4/nd4L and nd6/cytb, and a tricistronic transcript for atp8/atp6/coxIII. This processing of polycistronic mitochondrial transcripts adheres to the tRNA punctuated cleavage mechanism, whereby mature transcripts are cleaved only at intervening tRNA gene sequences. In contrast, the tricistronic atp8/atp6/coxIII in Drosophila is present as separate atp8/atp6 and coxIII transcripts despite the lack of an intervening tRNA. Our results indicate that mitochondrial processing mechanisms vary between arthropod species, and that it is crucial to use transcriptional information to obtain full annotation of mitochondrial genomes.

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

“…The aim of this study was achieved by defining the previously undetermined levels of mitochondrial genome variation between strains of M. vitrata. In doing so, a substitution bias at non-synonymous sites was defined, which is typical for highly conserved mitochondrial PCG, including the previously published mitogenome coxI by Margam et al (2011b). This short-term change identified here provides valuable information regarding variation between geographically distinct strains of a species that is analogous to that shown by comparisons between other closely related insect species (Coates et al, 2005;Coates, 2014).…”

“…CGA was used as the start codon for cox1 as previously reported for lepidopterans such as Bombyx mori (Yukuhiro et al, 2002), O. nubilalis and O. furnacalis (Coates et al, 2005), S. recurvalis (He et al, 2015), Adoxophyes honmai , C. raphaelis , Antheraea pernyi , B. mandarina , Ochrogaster lunifer (Salvato et al, 2008), Artogeia melete , Eriogyna pyretorum , Hyphantria cunea (Liao et al, 2010) and M. vitrata (Old World) (Margam et al, 2011b). The termination codon TAA was used in all PCGs with the exception of nad3, which had TAG.…”

“…We observed the motif ATAG immediately upstream of the CGA start codon of the M. vitrata (New World) cox1 gene. This motif is conserved in some lepidopteran mitogenomes and lacking in others (Margam et al, 2011b). Among the available crambid mitogenomes, O. furnacalis and O. nubilalis both have the motif TTAG upstream of the start codon of the cox1 gene, while M. vitrata (Old World) has ATAG.…”

“…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 .…”

Mitochondrial Genomes of Lepidopteran Insects Considered Crop Pests

“…In contrast, an atypical isoleucine codon (ATT) was used to initiate protein synthesis in the ATP8, NAD2, NAD3, and NAD5 genes. Arginine (CGA) was used for the COI gene for which a nucleotide sequence of four or six base pairs has been proposed, much like TTAG in Maruca vitrata [42], to serve in a nonstandard initiation process located immediately upstream from the putative arginine CGA start codon of COI. In T. solanivora, this tetranucleotide sequence consisted of TTGG.…”