Complete mitochondrial genome of the clearwing moth Synanthedon namdoelegans Kim, Kim and Choi, 2025 (Lepidoptera: Sesiidae)

Abstract

The clearwing moth Synanthedon namdoelegans Kim, Kim and Choi, 2025 (Lepidoptera: Sesiidae) was newly discovered in South Korea in 2024. We sequenced 15,578 bp-long complete mitochondrial genome of the species. It contained the trnQ–trnS2–trnM–trnI arrangement at the A + T-rich region and ND2 junction (the underline indicates counterclockwise direction) unique to tribe Synanthedonini. Phylogenetic analyses of 18 Cossoidea species supported the monophyly of each Synanthedonini and Synanthedon, and revealed a sister relationship between S. namdoelegans and Synanthedon bicingulata (Staudinger 1887). These data will be useful in taxonomic, molecular ecological, and pest management research.

Introduction

The genus Synanthedon Hübner, 1819 (Lepidoptera: Sesiidae) comprises 234 species and nine subspecies (Pühringer and Kallies 2024), with eight species in South Korea (Arita et al. 2004). In 2023 and 2024, we performed field surveys in the southern part of South Korea assessing the seasonal abundance of Synanthedon bicingulata (Staudinger 1887), which causes significant damage to urban trees, especially the cherry trees commonly found in city forests and parks. During this survey, a new species of Synanthedon was discovered on a cherry tree (Kim et al. 2025). Morphological analysis, along with the DNA barcoding sequences from four individuals, supported the novelty of this species, which was named Synanthedon namdoelegans Kim, Kim and Choi, 2025 (Kim et al. 2025).

To supplement this finding, extended molecular data could be essential. Notably, mitochondrial genome (mitogenome) sequences are available for only five Synanthedon species. Thus, additional species’ genomes will be required for the further exploration of evolutionary and phylogenetic relationships within this genus.

In this study, we sequenced the complete mitogenome of S. namdoelegans and compared it with the mitogenomes of other Cossoidea superfamily members to understand its baseline genomic features and phylogenetic relationships.

Materials and methods

An adult male S. namdoelegans individual collected in Suncheon-si, Jeollanam-do, South Korea (34°57′37.8ʺ N, 127°29′20.8ʺ E) was used for molecular analysis. The specimen was captured using an S. bicingulata-specific pheromone lure in a funnel-trap (170 × 250 mm; Green Agrotech, Gyeongsan, South Korea) installed on the branches of a cherry tree (Prunus × yedoensis Matsumura 1901) on 26 April 2023 (Figure 1). Species identification was made by one of the authors (Iksoo Kim) based on morphological characteristics, described in Kim et al. (2025) and the DNA barcode sequences reported in Kim et al. (2025).

Figure 1.

Images of Synanthedon namdoelegans Kim, Kim and Choi, 2025 and the pheromone traps used in the survey: (A) dorsal and (B) ventral views of an S. namdoelegans adult and (C, D) pheromone traps installed on a cherry tree (Prunus × yedoensis Matsumura 1901). The photos were taken by the authors, Jee-Young Pyo and Woo Jin Kim.

Genomic DNA was extracted from two hind legs using the Wizard™ Genomic DNA Purification Kit (Promega, Madison, WI). A specimen and leftover DNA were deposited at the Chonnam National University, Gwangju, South Korea (https://www.jnu.ac.kr/, Iksoo Kim, ikkim81@chonnam.ac.kr) under the voucher number CNU17887. Using the genomic DNA as a template, three long-overlapping fragments (COX1–ND4, ND5–16S rRNA, and 16S rRNA–COX1) were amplified using primers described in a previous study (Kim et al. 2012) along with a few primers newly designed for this study (Table S1). Subsequently, 26 short overlapping fragments were amplified using the long fragments as templates (Figure S1). Bidirectional sequencing was conducted using the Sanger method, and the SeqMan tool from the DNASTAR software package (SeqMan NGen^® v13.0, DNASTAR, Madison, WI) was used to assemble the 26 overlapping fragments into a complete mitogenome. Individual genes and the A + T-rich region were annotated by aligning their sequences with homologous sequences from known full-length lepidopteran mitogenomes using MAFFT v7 (Katoh et al. 2002). The nucleotide sequences of protein-coding genes (PCGs) were aligned based on codons using RevTrans v2.0 (Wernersson and Pedersen 2003), and tRNA genes were identified using tRNAscan-SE v2.0 (Lowe and Eddy 1997).

The baseline mitogenome information of 17 mitogenomes from species in the Cossoidea superfamily was downloaded from GenBank (as of 10 October 2025). Using these mitogenomes, along with that of S. namdoelegans, phylogenetic analyses were conducted based on 13 PCGs and two rRNAs (13,732 bp, including gaps). Leguminivora glycinivorella (Matsumura 1898) (unpublished) and Grapholita funebrana (Treitschke, 1835) (unpublished), belonging to the Tortricoidea superfamily, were used as the outgroups. Phylogenetic analyses were performed using MrBayes for Bayesian inference tree (Ronquist et al. 2012) and IQ-TREE for maximum-likelihood tree (Nguyen et al. 2015), implemented in PhyloSuite v1.2.3 (Xiang et al. 2023). The optimal partitioning scheme (four for MrBayes and nine partitions for IQ-TREE) and corresponding substitution models (Table S2) were determined using PartitionFinder 2 with the greedy algorithm (Lanfear et al. 2017). The genetic distance within the Synanthedonini tribe, to which current S. namdoelegans is included, was calculated using all 37 genes to know the sequence divergence of S. namdoelegans from other Synanthedon species. The calculation was performed using unrooted pairwise distances estimated with PAUP ver. 4.01b10 (Swofford 2002).

Results

The 15,578-bp long complete mitogenome of S. namdoelegans contained two rRNAs, 22 tRNAs, 13 PCGs, and an A + T-rich region (Figure 2). Eleven PCGs started with typical ATN codons, whereas COX1 and ATP8 used atypical start codons, CGA and TTG, respectively (Table 1). The PCGs COX1, ND5, and ND4 had the incomplete stop codon T, whereas the remaining PCGs terminated with TAA or TAG (Table 1). The S. namdoelegans mitogenome had a rearranged gene block (trnQ–trnS₂–trnM–trnI (the underline indicates a counterclockwise transcriptional direction)) between the A + T-rich region and ND2, which differs from the typical gene arrangement seen in Lepidoptera, trnM–trnI–trnQ (Figure S2). The A/T content was highest in the A + T-rich region (91.29%), followed by the 12S rRNA gene (85.82%), 16S rRNA gene (85.10%), 22 tRNA genes (83.46%), whole genome (79.18%), and 13 PCGs (76.50%) (Table S3).

Figure 2.

Circular map of the mitochondrial genome of Synanthedon namdoelegans obtained using the GenomeVx tool (http://wolfe.ucd.ie/GenomeVx/). The tRNA abbreviations follow the IUPAC-IUB one-letter code, with trnL₁, trnL₂, trnS₁, and trnS₂ denoting tRNA^Leu(CUN), tRNA^Leu(UUR), tRNA^Ser(AGN), and tRNA^Ser(UCN), respectively. Genes with names outside the circular map are transcribed in the clockwise direction (excluding the A + T-rich region), while those with names inside the map are transcribed in the counterclockwise direction.

Table 1.

Summary of Synanthedon namdoelegans’ mitochondrial genome.

Gene	Nucleotide range	Size (bp)	Anticodon	Codon		O/S
				Start	Stop
trnQ	1–68	68	TTG	–	–
trnS2	78–139	62	TGA	–	–	−9
trnM	142–208	67	CAT	–	–	−2
trnI	218–281	64	GAT	–	–	−9
ND2	312–1304	993	–	ATA	TAA	−30
trnW	1306–1372	67	TCA	–	–	−1
trnC	1365–1436	72	GCA	–	–	+8
trnY	1437–1503	67	GTA	–	–
COX1	1507–3037	1531	–	CGA	T-tRNA	−3
trnL2	3038–3101	64	TAA	–	–
COX2	3102–3782	681	–	ATA	TAA
trnK	3784–3854	71	CTT	–	–	−1
trnD	3854–3925	72	GTC	–	–	+1
ATP8	3926–4087	162	–	TTG	TAA
ATP6	4081–4758	678	–	ATG	TAA	+7
COX3	4763–5557	795	–	ATG	TAA	−4
trnG	5562–5625	64	TCC	–	–	−4
ND3	5626–5979	354	–	ATT	TAA
trnA	5981–6046	66	TGC	–	–	−1
trnR	6068–6133	66	TCG	–	–	−21
trnN	6141–6205	65	GTT	–	–	−7
trnS1	6208–6266	59	GCT	–	–	−2
trnE	6267–6332	66	TTC	–	–
trnF	6335–6398	64	GAA	–	–	−2
ND5	6399–8133	1735	–	ATT	T-tRNA
trnH	8134–8199	66	GTG	–	–
ND4	8200–9538	1339	–	ATG	T-tRNA
ND4L	9539–9823	285	–	ATG	TAG
trnT	9829–9897	69	TGT	–	–	−5
trnP	9897–9962	66	TGG	–	–	+1
ND6	10,009–10,494	486	–	ATA	TAA	−46
CytB	10,525–11,676	1152	–	ATG	TAA	−30
ND1	11,696–12,631	936	–	ATG	TAG	−19
trnL 1	12,633–12,700	68	TAG	–	–	−1
16S rRNA	12,734–14,015	1282	–	–	–	−33
trnV	14,016–14,079	64	TAC	–	–
12S rRNA	14,080–14,855	776	–	–	–
A + T-rich region	14,856–15,578	723	–	–	–

Genes with non-underlined names (excluding the A + T-rich region) are transcribed in the clockwise direction, whereas those with underlined names are transcribed in the counterclockwise direction. The tRNA abbreviations follow the IUPAC-IUB one-letter code, with trnL₁, trnL₂, trnS₁, and trnS₂ denoting tRNA^Leu(CUN), tRNA^Leu(UUR), tRNA^Ser(AGN), and tRNA^Ser(UCN), respectively. The O/S column quantifies the number of overlapping (+)/intergenic spacer (−) sequences.

The genetic distance of S. namdoelegans to other Synanthedon species ranged from 7.54% (1115 bp, S. bicingulata) to 9.57% (1416 bp, Synanthedon myopaeformis (Borkhausen, 1789) and Synanthedon vespiformis (Linnaeus 1761)) in the range from 8.79% (1301 bp) to 10.26% (1518 bp) within Synanthedon (Table S4). Phylogenetic analysis showed that the Synanthedon genus, Synanthedonini tribe, and Sesiinae subfamily, to which S. namdoelegans belongs, are monophyletic groups with the highest nodal supports (Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-aLRT) = 100, ultrafast bootstrap (UFBoot) = 100, Bayesian posterior probabilities (BPPs) = 1) (Figure 3). S. namdoelegans was placed as the sister taxon to the S. bicingulata, with a relatively high nodal support (SH-aLRT = 100, UFBoot = 99, BPP = 1) (Figure 3).

Figure 3.

Phylogeny of 18 mitochondrial genomes from members of the families Sesiidae and Cossidae, which constitute the Cossoidea superfamily, including Synanthedon namdoelegans (in bold). The tree was derived using maximum-likelihood and Bayesian inference methods. The numbers at each node are Shimodaira–Hasegawa-like approximate likelihood ratio test (SH-aLRT) support values, ultrafast bootstrap (UFBoot) support values, and Bayesian posterior probabilities (BPPs), respectively (SH-aLRT/UFBoot/BPP). The scale bar indicates the number of substitutions per site. Grapholita funebrana and Leguminivora glycinivorella, belonging to the Tortricoidea superfamily, were used as the outgroups. The analyzed sequences include Eogystia hippophaecolus (KC831443; Gong et al. 2014), Paracossulus thrips (PQ668644 and PQ668645; Jordán et al. 2025), Chalcidica minea (KX364097; Li et al. 2018), Endoxyla cinereus (OK644702; unpublished), Endoxyla cinereus (OR637448; Cameron 2023), Zeuzera multistrigata (MF491642; Kim et al. 2017), Zeuzera multistrigata (KX364098; Li et al. 2018), Zeuzera pyrina (OP379744; Cheng et al. 2022), Sesia bembeciformis (OX031055; Boyes et al. 2023b), Sesia siningensis (MN708363; Yan et al. 2019), Bembecia ichneumoniformis (OU342551; Boyes et al. 2023a), Synanthedon andrenaeformis (OW387807; Boyes et al. 2024), Synanthedon bicingulata (PP622747; Kim et al. 2024), Synanthedon formicaeformis (OX243984; Langdon and Fagan 2023), Synanthedon myopaeformis (OX122944; Langdon and Holland 2024), Synanthedon namdoelegans (PV762247; this study), Synanthedon vespiformis (OU906976; Boyes et al. 2022), Grapholita funebrana (PP776023; unpublished), and Leguminivora glycinivorella (MZ506769; unpublished).

Discussion and conclusions

In this study, we sequenced the complete mitogenome of S. namdoelegans, a newly discovered Synanthedon species from South Korea. The relative A/T contents among the whole mitogenome, genes, and the A + T-rich region in S. namdoelegans were largely consistent with those of other Cossoidea species, though a few species differed in the relative A/T contents of their 12S rRNA gene, 16S rRNA gene, and 22 tRNA genes (Table S3), indicating that relative A/T content is a conserved mitogenome characteristic in the Cossoidea superfamily. Although the start codons for COX1 (CGA) and ATP8 (TTG) are not canonical, the CGA codon for COX1 is a highly conserved feature in Lepidoptera, and TTG is common in insect PCGs, including those of lepidopterans (Kim et al. 2009; Zhao et al. 2011; Jeong et al. 2022). The gene rearrangement identified in S. namdoelegans’ mitogenome (trnQ–trnS₂–trnM–trnI) is seen in all species in the Synanthedonini tribe at the same junction, but differs from the typical trnM–trnI–trnQ arrangement found in Lepidoptera, with a few exceptions (Figure S2; Cao et al. 2012; Timmermans et al. 2014). This consistency suggests it is a synapomorphic trait for the tribe. However, additional research is necessary to validate this hypothesis. The observed rearrangement may have resulted from the tandem duplication–random loss model, which can generate new arrangements (Moritz et al. 1987; Cameron 2014).

From the taxonomic perspective, our findings are consistent with the previous study (Kim et al. 2025), which demonstrated the distinctiveness of S. namdoelegans based on both morphological traits and mitochondrial gene sequences (the partial sequence of COX1 and ND1). In that study, S. namdoelegans was closely related to Synanthedon soffneri Špatenka, 1983, Synanthedon bastak Gorbunov & Koshkin, 2023, and Synanthedon velox (Fixsen, 1887), in some morphological characters, but was distinguished by differences in the forewing’s black band, the hindwing’s discoidal vein spot, and male genitalia (Kim et al. 2025). The present mitogenome analysis further supports this conclusion, showing that S. namdoelegans is robustly separated from its congeners in mitogenome sequences (Table S4). As S. namdoelegans is a newly discovered species (Kim et al. 2025), the addition of its mitogenome sequence could facilitate a variety of applications, including species identification, molecular ecology, pest management, and phylogenetic studies. In particular, the robustness of the sister relationship between S. namdoelegans and S. bicingulata could be further tested by incorporating mitogenome sequences from other Synanthedon species and nuclear DNA fragments into future phylogenetic analyses.

Funding Statement

No funding was received.

Ethical approval

This study did not involve experiments requiring ethical approval. The studied species is not endangered and was not collected from nature reserves. Therefore, no specific permits were required. All sample collection and sequencing procedures were conducted in strict compliance with local regulations and laboratory guidelines to ensure the preservation of wild resources.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov under the accession no. PV762247. The chromatography files are available in Mendeley Data (https://doi.org/10.17632/jmwsgx59m9.1).