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ISSN : 1225-0171(Print)
ISSN : 2287-545X(Online)
Korean Journal of Applied Entomology Vol.62 No.4 pp.347-354
DOI : https://doi.org/10.5656/KSAE.2023.11.0.055

Complete Mitochondrial Genome of Mythimna loreyi (Duponchel, 1827) (Lepidoptera: Noctuidae) in South Korea

Na Ra Jeong1, Dagyeong Jeong2, Gwan-Seok Lee1, Wonhoon Lee1,3*
1Department of Plant Medicine and Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
2Crop Protection Division, National Institute of Agricultural Sciences, RDA, Wanju 55365, Korea
3Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
*Corresponding author:wonhoon@gnu.ac.kr
November 5, 2023 November 25, 2023 November 27, 2023

Abstract


Mythimna loreyi (Duponchel, 1827) (Lepidoptera: Noctuidae) is a pest that damages agricultural plants, such as rice, wheat, and maize. We sequenced the entire 15,314-bp mitochondrial genome of this species. It has a typical set of genes (13 proteincoding genes, two ribosomal RNA genes, and 22 transfer RNA genes) as well as one major non-coding A+T-rich region. Using concatenated sequences of 13 protein-coding genes and two rRNAs (13,376 bp, including gaps), phylogenetic analysis demonstrated that the sister relationship between M. loreyi and M. separata had the highest nodal support. The monophyly of each family (Noctuidae, Euteliidae, Nolidae, Erebidae, and Notodontidae) of the superfamily Noctuoidea was supported by the highest nodal support.


Mitochondrial genome , Mythimna loreyi , Noctuidae , Rice armyworm , South Korea

국내 뒷흰가는줄무늬밤나방의 미토콘드리아 게놈(mitochondrial genome) 분석

정나라1, 정다경2, 이관석1, 이원훈1,3*
1경상국립대학교 식물의학과
2국립농업과학원 작물보호과
3경상국립대학교 농업생명과학연구원

초록


뒷흰가는줄무늬밤나방은 쌀, 밀, 옥수수와 같은 농작물에 피해를 주는 해충이다. 본 연구에서는 국내 뒷흰가는줄무늬밤나방의 미토콘드리아 게놈(15,314b)을 분석하였다. 13개의PCG와2개의 rRNA (13,376bp)를 연결한 서열을 사용한 계통발생 분석 결과, 뒷흰가는줄무늬밤나방과 멸 강나방 사이의 가장 높은 노드 수치로 자매분류군을 형성하였다. 밤나방상과(Noctuoidea)의 각 과(Noctuidae, Euteliidae, Nolidae, Erebidae 및 Notodontidae)들은 가장 높은 노드수치로 단계통을 형성하였다.


미토콘드리아게놈 , 뒷흰가는줄무늬밤나방 , 밤나방과 , 한국

    Mythimna loreyi (Duponchel, 1827) (Lepidoptera: Noctuidae) is distributed in Asia, Africa, Australia, and the Middle East (CABI, 2023) and is known to cause damage to Poaceae species such as rice, wheat, maize, sugarcane, barley, and sorghum (El‐Sherif, 1972;Harai, 1975). In South Korea, M. loreyi was first collected at an adult stage in 1982 (Ahn et al., 1994) and has recently been shown to damage maize in South Korea (Nam et al., 2020).

    M. separata is a well-known migratory insect in the genus Mythimna. M. separata can fly 12 km in 12 h in the laboratory (Li et al., 1964). M. loreyi has also been described as a migratory insect in Europe (Sparks et al., 2007), with a flight range of 32 km in 12 h. M. loreyi has been found in South Korea since 1982, but the economic impact and distribution have yet to be calculated. In South Korea, M. loreyi is frequently found in the same field as M. sepatata. However, these two species cannot be distinguished based on their morphological characteristics at the larval stage (Kim et al., 2020). This suggests that M. loreyi could be confused with M. separata (Nam et al., 2020).

    The insect mitochondrial genome (mitogenome) is a circular molecule, 14–19 kb in size, and contains 22 transfer RNA (tRNA) genes and two ribosomal RNA genes encoding small and large subunit rRNAs (rrnS and rrnL), which are involved in the translation of 13 protein-coding genes (PCGs), and a large non-coding element termed the A + T-rich region, which contains both the origin for replication and transcription (Moritz et al., 1987;Wolstenholme, 1992;Cameron, 2014). Owing to their unique features, including the conservation of coding content, maternal inheritance, and rapid evolution, mitogenome sequences have been widely used as informative molecular markers for diverse evolutionary studies among species in the fields of molecular evolution, phylogenetics, population genetics, and comparative and evolutionary genomics (Harrison, 1989;Boore, 1999;Whinnett et al., 2005;Lopez-Vaamonde et al., 2012;Timmermans et al., 2014). To date, two M. loreyi mitogenomes have been reported in GenBank. However, one (MZ853169) has unpublished data, while another (MT506351) was used in the development of loop-mediated isothermal amplification (LAMP) (Nam et al., 2020). As yet, there have been no reports on its genome structure and features.

    To better understand the insect mitogenome, taxon and genome sampling must be expanded. The analysis of the M. loreyi mitogenome has increased our understanding of insect mitogenomes and provided new insights into the mechanisms underpinning mitochondrial DNA evolution, particularly gene rearrangements. In this study, the entire mitogenome of M. loreyi was newly sequenced, and the mitogenome was then submitted to phylogenetic studies involving comparison with M. separata, which has a similar larval morphology.

    Materials and Methods

    Genomic DNA extraction

    One wild adult was collected in a pheromone trap in Goheung, Jeollanam Province, South Korea (34° 38' 28.8" N, 127° 24' 39.6" E) for the study. Following the manufacturer's instructions, genomic DNA was extracted from the hind legs using an AccuPrep® Genomic DNA Extraction Kit, and 100% ethanol (Bioneer, Daejeon, Korea). Excess DNA and specimens were deposited at the Gyeongsang National University, Jinju, South Korea.

    Mitochondrial genome sequencing

    Using the extracted DNA, three long overlapping fragments (LFs; COI-ND5, ND5-lrRNA, and ND1-COI) were amplified using three sets of primers developed based on previously reported M. loreyi data. The developed primers were used to amplify 25 overlapping short fragments (SF) using the LFs as templates. The following settings were used for the LF polymerase chain reaction (PCR): 4 min initial denaturation at 94°C, followed by 30 cycles of 10 sec at 98°C, 15 min at 50°C, and a final 10-min extension at 72°C. SF PCR was performed as follows: initial denaturation for 4 min at 94°C, followed by 35 cycles of 1 min at 94°C, 1 min at 48°C, and 1 min at 72°C, with a final 7 min extension at 72°C. AccuPower PCR PreMix (Bioneer, Daejeon, Korea) was used for PCR. To validate effective DNA amplification, electrophoresis was performed on a 1.5% agarose gel using 0.5 × TAE buffer. All products were sequenced bidirectionally.

    Because clear direct sequences of M. loreyi SF13 and SF22 could not be obtained, they were sequenced after cloning, whereas the remaining SFs were sequenced directly after PCR purification. M. loreyi SFs were sequenced directly after purification using AccuPrep PCR Purification Kit reagents (Bioneer, Daejeon, Korea). The pGEM-T Easy vector (Promega, Madison, WI, USA) and HIT DH5a High 108 competent cells (Real Biotech Co., Banqiao City, Taiwan) were used for cloning. The resulting plasmid DNA was isolated using a Plasmid Mini Extraction Kit (Bioneer, Daejeon, Korea). All products were sequenced bidirectionally.

    Boundary delimitation and annotation

    Individual SF sequences were manually assembled into complete mitogenomes using SeqMan software (DNASTAR, Madison, WI, USA). The MITOS WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) was used for tRNA identification, boundary delimitation, and secondary structure folding with the search mode set to default, Mito/Chloroplast as the searching source, and the genetic code of invertebrate mitogenomes for tRNA isotype prediction (Lowe and Chan, 2016). To identify individual PCGs, the blastn program in BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used with the default settings. Gene delimitation and confirmation of start and stop codons were performed using MAFFT ver. 7 (Katoh and Standley, 2013) to align available PCGs with those of other Noctuoidea species. The two rRNAs and the A + T-rich region were identified and delimited using nucleotide blastn in BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi), and validated by the alignment of other Noctuoidea rRNA and A + T-rich region sequences using MAFFT ver. 7 (Katoh and Standley, 2013). M. loreyi sequence data have been deposited in the GenBank database under the accession number OQ536314.

    Genomic comparison between M. loreyi and M. separata

    Two M. loreyi mitogenome sequences and three M. separata sequences of were obtained from GenBank and compared with M. loreyi mitogenome sequences obtained in this investigation. Pairwise comparisons were used to evaluate the degree of sequence divergence of each of the 13 PCGs of M. loreyi and M. separata. When there were multiple mitogenome sequences from the same species, the average divergence of the species was used to calculate the sequence divergence of each gene within the genus. These values were then plotted using the boxplot in JMP software ver. 15.0.0 (SAS Institute, Cary, NC, USA) to show the minimum, maximum, and median values.

    Phylogenetic analysis

    Phylogenetic analysis was performed using 18 mitogenomes from the Noctuoidea, including those obtained in the present study (Fig. 1). The nucleotide sequence of each PCG was aligned based on codons using RevTrans ver. 2.0 (Wernersson and Pedersen, 2003). Each of the two rRNA genes was individually aligned using MAFFT ver. 7 (Katoh and Standley, 2013). The nucleotide sequences of all protein-coding genes (PCGs) and rRNAs were aligned, and well-aligned blocks were selected using GBlocks 0.91b software (Castresana, 2000), with the maximum number of contiguous non-conserved positions set to 15 and gap positions allowed. Subsequently, 13 PCGs and two rRNAs were concatenated in the alignment (13,376 bp, including gaps).

    Bayesian inference (BI) and maximum likelihood (ML) methods were applied using MrBayes version 3.2.6 (Ronquist et al., 2012) and RAxML-HPC2 version 8.0.24 (Stamatakis, 2014), respectively, and were incorporated into the CIPRES Portal version 3.1 (Miller et al., 2010). For the BI analysis, two independent runs of four incrementally heated Markov and Monte Carlo chains (one cold chain and three hot chains) were simultaneously run for 10 million generations, with tree sampling conducted every 100 generations. The first 25% of the trees were rejected as burn-ins. Partitioned analyses were performed, with each partition unlinked to each parameter (state freq, revmat, shape, pinvar, or tratio). To depict the convergence of two concurrent runs, an average split frequency of less than 0.01 was chosen. For ML analysis, we used the RAxML algorithm, which employs a “rapid” bootstrapping approach to find the best-scoring tree. The confidence values for the BI and ML trees were calculated using Bayesian posterior probabilities (BPP) and 1,000 bootstrap (BS) iterations. PartitionFinder 2 with a greedy algorithm was used to discover an optimal partitioning scheme (six partitions) and substitution model (GTR + Gamma + I) (Lanfear et al., 2014;2016). Conogethes pinicolalis (Jeong et al., 2021), Chilo suppressalis (Park et al., 2019), and Ostrinia kasmirica (Luo et al., 2021) which belong to the family Crambidae of the superfamily Pyraloidea, were used as outgroups. Phylogenetic trees were visualized using FigTree version 1.4.4 (http://tree.bio.ed.ac.uk/software/figtree/).

    Results

    Genome structure, organization, and composition

    The M. loreyi mitogenome was 15,314 bp long (Table 1), with typical gene sets (2 rRNAs, 22 tRNAs, and 13 PCGs) and a major non-coding A + T-rich region of 332 bp long (GenBank accession number OQ536314). Previous research has found that the shortest mitogenome is 15,312 bp long (MZ853169; unpublished) and the longest is 15,320 bp (MT506351; Nam et al., 2020). The length of M. loreyi was comparable to that of M. separata, ranging from 15,329 bp in KM099034 (unpublished data) to 15,332 bp in HG793808 (Yang and Kong, 2016) and KF730242 (Li et al., 2015). Each M. loreyi and M. separata mitogenome comprised 37 genes, including 13 PCGs, 22 tRNA genes, and two rRNA genes (Table 1), all of which are typically found in animals (Boore, 1999).

    The orientation and gene order of the M. loreyi and M. separata mitogenomes were identical to those of many other lepidopteran groups. They do, however, differ from the most common type (A + T-rich region-trnI-trnQ-trnM-ND2), which is thought to be ancestral to insects (Boore, 1999), as well as from the lepidopteran superfamilies Hepialoidea and Nepticuloidea. The only difference was that trnM was moved upstream of trnI, giving rise to the order trnM-trnI-trnQ in the A+T-rich region and ND2 junction (Table 1).

    Protein-coding genes

    Except for COI and ND1, M. loreyi and M. separata exhibited typical ATN codons that were identical in the remaining 11 PCGs. However, the start codons for ATP8, ND6, and ND1 differed between the two species, with ATA and ATT for ATP8 in M. loreyi and M. separata, ATT and ATC for ND3 in M. loreyi and M. separata, and ATA and TTG for ND1 in both species (Table 1). The ATN, GTG, TTG, and GTT start codons were those previously identified in animal mtDNA (Wolstenholme, 1992). Ten of the 13 PCGs in both M. loreyi and M. separata mitogenomes had a complete termination codon, TAA, while the remaining three PCGs (COI, COII, and ND4) had an incomplete termination codon, T (Table 1).

    Individual gene divergence

    The sequence divergence among the three M. loreyi mitogenomes ranged from 0% (COI, COII, ND2, and ND3) to 5.556% (ATP8), with 0% divergence in the DNA barcoding region (Fig. 1, Table 2). The sequence divergence among the three M. separata mitogenomes ranged from 0% (ATP6, COII, ND1, ND3, and ND4) to 5.556% (ATP8), with 0% divergence in the DNA barcoding region, indicating relatively low sequence divergence between the intra-specific genomic sequences (Fig. 1, Table 2).

    The divergence between M. loreyi and M. separata in the 658 bp DNA barcoding region was 6.535%, which was lower than the divergence in ATP8 (10.556%), CytB (7.928%), ND1 (8.733%), ND3 (7.123%), ND4L (7.616%), ND5 (7.009%), and ND6 (12.996%) (Fig. 1, Table 2). These findings suggest that genes with higher sequence divergence, rather than the DNA barcoding region, may be more useful for populationlevel studies, possibly by providing more variable nucleotide positions required for a comprehensive examination of the evolutionary history of the given populations.

    Phylogenetic analysis

    Phylogenetic analysis was performed on 18 mitogenome sequences, including the mitogenome of M. loreyi analyzed in this study, using concatenated 13 PCGs and two rRNAs. These were composed of five Noctuoidea families (Noctuidae, Euteliidae, Nolidae, Erebidae, and Notodontidae) (Fig. 2). The topologies of the PCG and rRNA datasets analyzed using the ML and BI algorithms were identical. The monophyly of each family was supported by the highest nodal support, revealing familial relationships of (((Noctuidae + Euteliidae) + Nolidae) + Erebidae)) + Nodontidae) in the superfamily Noctuoidea (Fig. 2). Furthermore, the greatest nodal support (BS = 94-100%, BPP = 1.0; Fig. 2) often confirmed the monophyly of each family. In both analyses, the sister relationship between M. loreyi and M. separata had the highest nodal support (BS = 100%, BPP = 1.0; Fig. 2).

    Discussion

    The current study indicates that M. loreyi and M. separata, which is morphologically difficult to distinguish are moleculary distinct by analyzing the newly entire mitogenomes of M. loreyi. M. loreyi and M. separata are distinct at the start codons of ATP8, ND6, and ND1.

    In addition, Individual gene divergence analyses clearly evidenced substantial divergence between these two species. Phylogenetic analysis showed a distinct separation between these two species. Collectively, our results confirmed that two species are molecularly distinct and mitochondrial genes with higher sequence divergence will be useful for population- level studies.

    Acknowledgments

    This study was supported by the National Institute of Agricultural Sciences (project No: RS-2022-RD009996), Korea.

    Statements for Authorship Position & Contribution

    • Jeong, N.R.: Gyeongsang National University, Student in Ph.D; Designed the research, wrote the manuscript, and conducted the experiments

    • Jeong, D.: National Institute of Agricultural Sciences, Researcher; Collected and examined specimens

    • Lee, G.-S.: National Institute of Agricultural Sciences, Researcher; Collected and examined specimens

    • Lee, W.: Gyeongsang National University, Professor, Ph.D; Examined specimens and designed the research

    All authors read and approved the manuscript.

    KJAE-62-4-347_F1.gif

    Boxplot distribution of interspecific and intraspecific genetic divergence for 13 protein coding genes in Mythimna loreyi and M. separata. Dots indicate the maximum and minimum divergence (%), respectively. Boxplots indicate range of the maximum and minimum divergence.

    KJAE-62-4-347_F2.gif

    Phylogenetic tree for the superfamily Noctuoidea. The tree was constructed using the concatenated 13 PCGs and 2 rRNAs via the maximum-likelihood (ML) and Bayesian Inference (BI) methods. The numbers at each node specify bootstrap percentages of 1000 pseudoreplicates by ML analysis and Bayesian posterior probabilities in percent by BI analysis. The scale bar indicates the number of substitutions per site. Three species of Crambidae in Pyraloidea were utilized as outgroups. GenBank accession numbers are as follows: Mythimna loreyi, MZ853169 (Unpublished); Mythimna loreyi, MT506351 (Nam et al., 2020); Mythimna separata, HG793808 (Yang and Kong, 2016); Mythimna separata, KF730242 (Li et al., 2015); Mythimna separata, KM099034 (Unpublished); Spodoptera litura, MZ618263 (Unpublished); Eutelia adulatricoides, KJ185131 (Yang et al., 2015); Odontodes seranensis, MW719565 (Unpublished); Camptoloma kishidai, MW435591 (Unpublished); Earias clorana, OK235312 (Unpublished); Risoba prominens, MZ618262 (Unpublished); Hydrillodes lentalis, MH013483 (Yang et al., 2019); Arctia plantagninis, MW394229 (Galarza and Mappes, 2021); Lymantria dispar, ON469817 (Jeong et al., 2021); Phalera flavescens, JF440342 (Sun et al., 2012); Thaumetopoea pityocampa, OM478592 (Unpublished); Clostera anastomosis, MH286069 (Zhu et al., 2018); Conogethes pinicolalis, MT674993 (Jeong et al., 2021); Ostrinia kasmirica, MT978075 (Park et al., 2019); Chilo suppressalis, MK207057 (Luo et al., 2021).

    Summaries of six mitochondrial genomes of Mythimna

    Estimates of intraspecific and interspecific genetic divergence for mitochondrial protein coding genes of Mythimna loreyi and M. separata

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    Vol. 40 No. 4 (2022.12)

    Journal Abbreviation Korean J. Appl. Entomol.
    Frequency Quarterly
    Doi Prefix 10.5656/KSAE
    Year of Launching 1962
    Publisher Korean Society of Applied Entomology
    Indexed/Tracked/Covered By