The complete mitochondrial genome sequence of Korean Chilo suppressalis (Walker, 1863) (Lepidoptera: Crambidae)

Abstract

We have determined the mitochondrial genome of Chilo suppressalis (Walker, 1863) collected in Korea. The circular mitogenome of C. suppressalis was 15,341 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 622 bp. The base composition was AT-biased (93.6%). Through alignment of three C. suppresalis mitochondrial genomes, 79 single nucleotide polymorphisms (8.8%) and 291 insertions and deletions (33.3%) are identified as Korean C. suppressalis specific variations. Phylogenetic trees present that three mitochondrial genomes of C. suppressalis have enough variations within a species, which can be a candidate to understand its origin and geographical distribution using molecular marker sequences.

Keywords:

• Lepidoptera
• mitochondrial genome
• Chilo suppressalis
• Crambidae
• Korea

Chilo suppressalis (Walker, 1863), the striped stem borer, is one of the rice pests in Eastern and Southeastern Asia including China, Korea, India, and Indonesia (Park and Hyun 1990; Meng et al. 2008). Because of its ecological importance in agriculture (Pathak and Khan 1994), biological agents or sex pheromones have been developed (Beevor et al. 1990; Harry 1991; Ye et al. 2001). Till now, two complete mitochondrial genomes of C. suppressalis collected in China (Yin et al. 2011; Chai et al. 2012) were sequenced, which is a good resource to understand genetic diversity of C. suppressalis.

To understand genetic differences of C. suppressalis between Korea and China, we collected C. suppressalis in Taean-gun, South Chungcheong Province, Korea (GPS coordination is N36.875787, E126.227316). The specimens and DNA were deposited in the Insect Collection of Gyeongsang National University, South Gyeongsang Province, Korea (GNU#170303-001). Total DNA was extracted from C. suppressalis and genome sequencing was performed using HiSeq2000 at Macrogen Inc., Korea. de novo assembly was conducted by Velvet 1.2.10 (Zerbino and Birney 2008) and gaps were filled by SOAPGapCloser 1.12 (Zhao et al. 2011). All bases were confirmed by alignments against assembled sequences generated by BWA 0.7.17 (Li 2013) and SAMtools 1.9 (Li H et al. 2009). Geneious R11 11.1.5 (Biomatters Ltd, Auckland, New Zealand) was used for mitochondrial genome annotation using C. suppressalis complete mitochondrial genome (NC_015612).

The mitochondrial genome of C. suppressalis (Genbank accession is MK207057) is 15,341 bp in length. The nucleotide composition is AT-biased (79.6%). The mitogenome contains 13 protein-coding genes, two rRNAs, and 22 tRNAs. The tRNAs size ranges from 64 to 76 bp, are similar to other insects (circa 54–90 bp). Gene order of C. suppressalis mitochondrial genome is almost same to those of 22 complete mitochondrial genomes in Crambidae except that (i) tRNA-Val found between two rRNAs in four genomes, and (ii) cytochrome B enzyme gene was missing in Spoladea recurvalis (NC_027443; He et al. 2015). Their genome lengths range from 15,110 bp (Maruca testulalis; NC_024283; Zou et al. 2016) to 15,490 bp (Diatraea saccharalis; NC_013274; Li W et al. 2011): that of C.suppressalis is near to the longest. The control region presumably corresponds to the single largest non-coding AT-rich region (348 bp, A + T 95.4%).

Seven complete mitochondrial genomes from Crambidae including two mitochondrial genomes of C. suppressalis were aligned by ClustalW (Thompson et al. 2003) for constructing phylogenetic trees using maximum likelihood (bootstrap repeat is 1,000) and neighbor joining (bootstrap repeat is 10,000) methods using MEGA X (Kumar et al. 2018). From the alignment of three C. suppressalis complete mitochondrial genomes, 894 single nucleotide polymorphisms (SNPs) and 873 insertions and deletions (INDELs) are identified and among them, 79 SNPs (8.8%) and 291 INDELs (33.3%) are specific to Korean C. suppressalis. The phylogenetic trees supported by high bootstrap values present that three C. suppressalis mitochondrial genomes have enough variations within species (Figure 1). Together with these results, C. suppressalis can be a candidate to understand its origin as well as a geographical distribution based molecular marker sequences^{Figure 1}.

Figure 1. maximum likelihood (bootstrap repeat is 1,000) and neighbor joining (bootstrap repeat is 10,000) phylogenetic trees based on seven complete mitochondrial genomes in Crambidae: Korean C. suppressalis (MK207057, this study), Chinese C. suppressalis (NC_015612 and HQ860290), Chilo sacchariphagus (NC_029716), Chio auricilius (NC_024644), Diatraea saccharalis (NC_013274), and Elophila interruptalis (NC_021756). The numbers above the branches indicate bootstrap support values of maximum likelihood and neighbor joining trees.

Disclosure statement

The authors declare that they have no competing interests.

Additional information

Funding

This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development [Project No. PJ013389]” Rural Development Administration, Republic of Korea. This work was also partially supported by InfoBoss Research Grant [IBG-0008].