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ISSN : 1225-0171(Print)
ISSN : 2287-545X(Online)
Korean Journal of Applied Entomology Vol.64 No.4 pp.277-287
DOI : https://doi.org/10.5656/KSAE.2025.10.0.055

Genetic Characteristics of Mitochondrial Gene and Potential Invasive Pathway of the Oriental Fruit Fly, Bactrocera dorsalis, in Southeast Asia

Jiseok Kim1, Donghun Kim1,2*
1Department of Vector Biology, Kyungpook National University, Sangju 37224, Korea
2Research Institute of Invertebrate Vector, Kyungpook National University, Sangju 37224, Korea
*Corresponding author:dklome2018@knu.ac.kr
October 23, 2025 October 31, 2025 November 4, 2025

Abstract


The oriental fruit fly, Bactrocera dorsalis, is a major agricultural pest that infests over 400 plant species, including various crops and fruits. Originally endemic to Southeast Asia, it has recently spread in Japan and China, and its expansion has raised concerns about its potential spread to other regions. In this study, the mitochondrial cytochrome c oxidase subunit I (COI) gene was employed as a molecular marker to investigate the genetic diversity and dispersal dynamics of B. dorsalis. Specimens were collected from several Southeast Asian countries, namely, Thailand, Taiwan, Vietnam, Cambodia, and the Philippines. Mitochondrial COI sequences obtained from the GenBank database were incorporated to elucidate the regional genetic characteristics of B. dorsalis across Asia. A total of 753 haplotypes were identified across 13 Southeast Asian countries, and most populations exhibited a high haplotype diversity (Hd>0.8). Distinct genetic separations were observed in certain island populations, including those from the Philippines and Papua New Guinea. Notably, the major haplotype was shared among most continental populations except individuals from the Philippines and Papua New Guinea. These results provide valuable mitochondrial COI-based insights into the genetic structure of B. dorsalis in Southeast Asia, highlighting the geographic differentiation of island populations and extensive genetic connectivity among continental populations.


Oriental fruit fly , origin , epidemiological investigation , cytochrome c oxidase subunit I gene

동남아시아 오리엔탈과실파리(Bactrocera dorsalis) 미토콘드리아 유전자의 유전적 특성과 잠재적 침입 경로

김지석1, 김동흔1,2*
1경북대학교 질병매개곤충학과
2경북대학교 질병매개무척추동물연구소

초록


오리엔탈과실파리(Bactrocera dorsalis)는 400종 이상의 작물과 과일을 가해하는 주요 농업 해충이다. 동남아시아가 원산지로 알려져 있으나, 최근 일본과 중국에서의 확산이 보고되면서 인근 지역으로의 잠재적 확산 가능성이 우려되고 있다. 본 연구에서는 오리엔탈과실파리의 유전적 다양성과 분산 양상을 구명하기 위해 미토콘드리아 cytochrome c oxidase subunit I (COI) 유전자를 분자 마커로 활용하였다. 시료는 태국, 대만, 베트남, 캄보디아, 필리핀 등 동남아시아 여러 국가에서 채집하였으며, 아시아 지역의 지역별 유전적 특성을 비교하기 위해 유전자 데이터베이스에서 확보한 COI 염기서열을 분석에 활용하였다. 그 결과, 동남아시아 13개국에서 총 753개의 일배체형(haplotype)이 확인되었으며, 대부분의 동남 아시아 개체군에서 높은 일배체형 다양성(Hd>0.8)이 나타났다. 필리핀과 파푸아뉴기니 등 일부 섬 지역 개체군에서는 뚜렷한 유전적 분리가 관찰된 반면, 필리핀과 파푸아뉴기니를 제외한 대부분의 대륙 개체군은 주요 일배체형을 공유하였다. 본 연구 결과는 미토콘드리아 COI 유전자 기반 동남아시아 오리엔탈과실파리의 유전적 구조를 구명하였으며, 지리적 격리에 따른 섬 개체군의 비교적 안정된 유전형과 지리적 인접성과 이동성에 따른 대륙 개체군 간의 유전적 유사성을 시사한다.


오리엔탈과실파리 , 원산지 , 역학 조사 , cytochrome c oxidase subunit I gene

    Bactrocera dorsalis (Hendel, 1912) is one of the most detrimental pests affecting horticultural crops in tropical and subtropical regions (Akbar et al., 2020;Vargas and Carey, 1990). It is a highly polyphagous insect infesting more than 400 plant species, including economically important fruits such as mango, guava, citrus, and papaya (Clarke et al., 2005;Han et al., 2011;Kim and Kim, 2024). Initially documented in 1912 in Taiwan, its geographical range has progressively extended northward, extending in recent decades not only to Japan and China but also to several Southeast Asian countries (Christenson and Foote, 1960;Vargas et al., 2015;Zeng et al., 2019).

    Adult B. dorsalis engages in host-seeking behavior for feeding and oviposition (Christenson and Foote, 1960). Reproductively immature adults can fly and travel long distances of approximately 50 km to locate suitable food sources and breeding sites (Froerer et al., 2010;Iwahashi, 1972). Females subsequently oviposit in fruits, where larval development induces internal fruit decay, premature fruit drop, and considerable yield reductions (Akbar et al., 2020). In Wuhan, China, the species annually occurs in at least four generations, damaging various major crops such as pear, jujube, persimmon, and orange depending on the fruiting season (Han et al., 2011). In addition to causing direct damage, imposing strict quarantine restrictions on fruits infested with B. dorsalis individuals is warranted, resulting in considerable economic losses within fruit export industries (Clarke, 2019;Vargas et al., 2015).

    The morphological identification of B. dorsalis is frequently complicated by high intraspecific variation and morphological similarity to closely related species, such as B. correcta and B. carambolae (Leblanc et al., 2013). Consequently, DNA-based identification methods have been widely applied to improve taxonomic accuracy (Kim et al., 2021). For instance, the mitochondrial cytochrome c oxidase subunit I (COI) gene is a standard molecular marker for identifying species and assessing genetic variations to elucidate the origins of invasive species (Goldstein and DeSalle, 2011;Yan et al., 2021). It is characterized by high genetic divergence and conserved sequences among conspecifics (Hebert et al., 2003) because of its rapid mutation rate, absence of recombination, and maternal inheritance (Bergmann et al., 2013;Brown et al., 1979). For these reasons, COI-based approaches have been utilized to investigate the genetic diversity and population structure of B. dorsalis across various regions (Choudhary et al., 2016;Kim et al., 2019;Qin et al., 2018;Shi et al., 2012).

    Given the expanding distribution and invasive potential of B. dorsalis, understanding its population genetic structure is crucial for tracing invasive pathways and managing crossborder dispersion. This study analyzed the mitochondrial COI sequences from B. dorsalis collected from 13 Southeast Asian countries by integrating novel data with the sequences available in GenBank. Our findings provided molecular insights into the population dynamics of B. dorsalis and contributed to the development of effective regional monitoring and biosecurity strategies.

    Materials and Methods

    Sample collection and genomic DNA extraction

    A total of 347 flies were collected from Thailand, Taiwan, Vietnam, Cambodia, and the Philippines between 2022 and 2025 (Fig. 1 & Table 1). The flies were collected using a Lynfield trap with 70% alcohol. The collected B. dorsalis individuals were identified on the basis of their morphological characteristics (Fig. S1) and molecular biology by using mitochondrial COI sequences. Male and female individuals were collected.

    All specimens were individually stored in 2 ml tubes containing a DNA/RNA shield reagent (Zymo Research, Irvine, CA, USA) and maintained at -80°C until DNA extraction. Genomic DNA was extracted from whole-body homogenates by using a 2 ml FastPrep® tube (MP Biomedicals, USA) with four 2.8 mm stainless steel beads (Innogenetech, Gimpo, Korea) in a solid tissue buffer with proteinase K. A total of 200 μl of the homogenate was processed using the Quick-DNATM Miniprep Plus kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions. The DNA concentration and purity were measured using a nanophotometer (Implen, Germany), and the extracted genomic DNA was stored at – 20°C until mitochondrial gene amplification.

    Amplification and sequence analysis of mitochondrial COI genes

    Mitochondrial COI genes were amplified from B. dorsalis genomic DNA by using universal primers: LCO1490: 5'- GGTCAACAAATCATAAAGATATTGG-3' and HCO2198: 5'-TAAACTTCAGGGTGACCAAAAAATCA-3' (Folmer et al., 1994). PCR was conducted using 25 μl volumes containing the genomic DNA (up to 283 ng), 2.5 μl of 10x Standard Taq reaction buffer, 0.5 μl of 10 mM dNTP solution, 0.5 μl of each primer (10 μM), and 0.625 units of Taq DNA polymerase (New England Biolabs, Ipswich, MA, USA). PCR amplification was performed with an initial denaturation at 94°C for 30 s, followed by 35 cycles of denaturation at 94°C for 30 s, annealing at 54.8°C for 30 s, and extension at 72°C for 1 min, with a final extension step of 72°C for 5 min. PCR products were separated on a 1% agarose gel to confirm the successful DNA amplification and subsequently sequenced from the 5′ terminal of the amplicon by using an ABI 3730xl DNA analyzer (Macrogen, Daejeon, Korea). Sequence length and quality were determined in SeqBuilder (DNASTAR 7.1.0, Inc, Madison, Wi, USA), and low-quality sequences were excluded from further analysis.

    Analysis of the genetic characteristics of B. dorsalis individuals

    Mitochondrial COI sequences were translated into amino acid sequences to detect and remove the inclusion of pseudogene sequences or sequencing errors. Sequence alignment was performed using MUSCLE (Edgar, 2004) with the default parameters in MEGA X 10.2 (Kumar et al., 2018). The COI sequences were trimmed manually on the basis of the chromatogram, and a 615 bp segment (positions 35–649 bp of the amplicon) was selected. Furthermore, a dataset comprising 2,074 COI sequences of B. dorsalis originating from 12 Southeast Asian countries was obtained from the National Center for Biotechnology Information (NCBI) database (Qin et al., 2018;Thangaraj et al., 2019) and manually edited to match the 615 bp of the COI region.

    Genetic characteristics among populations categorized by geographical region or collection year was evaluated using DnaSP 6.12.03 (Rozas et al., 2017) to estimate the number of haplotypes (H), number of segregating sites (S), average number of nucleotide differences (k), haplotype diversity (Hd), and nucleotide diversity (Pi). The demographic history of these populations was assessed through selective neutrality tests by using Tajima’s D (Tajima, 1989) and Fu’s FS (Fu, 1997) in Arlequin 3.5 software (Excoffier and Lischer, 2010). These neutrality tests were conducted to infer historical demographic changes, including population expansion or contraction. Pairwise FST values were calculated to assess genetic differentiation among populations, and principal coordinate analysis (PCoA) was performed in GenAlex 6.51b2 (Peakall and Smouse, 2012) based on pairwise FST values. Haplotype networks were constructed using the Templeton, Crandall and Sing (TCS) method (Clement et al., 2002) and visualized with PopART 1.7 (Leigh and Bryant, 2015).

    Results

    B. dorsalis in Southeast Asia is undergoing genetic exchange among continental populations

    A total of 347 flies were collected between 2022 and 2025 (Fig. 1 & Table 1). Additionally, 2,074 mitochondrial COI sequences from 12 Southeast Asian countries were obtained from the NCBI database. A total of 2,421 mitochondrial COI sequences from 13 countries were categorized into 35 distinct geographic or temporal groups for subsequent analyses, and each group comprised between 18-238 individuals (Table 2). The mitochondrial COI sequences of B. dorsalis distributed in Southeast Asia exhibited a considerable intra-species genetic diversity. Overall, 753 haplotypes were detected from 2,421 COI sequences of B. dorsalis sampled across Southeast Asia, and 67.3% (507 out of 753) of these haplotypes were constructed by a single specimen (Table 2). Hd ranged from 0.417 to 0.982, and Pi varied between 0.00136 and 0.01230. Notably, high haplotype diversity values exceeding 0.8 were observed in most groups except Philippines_2015 (Hd=0.789) and Papua New Guinea_2015 (Hd=0.417) groups (Table 2).

    The genetic variation increased within most continental groups of B. dorsalis. Signals of genetic exchange among populations were detected in most continental groups, as indicated by significantly negative Fu’s FS values (Table 2). This finding was supported by haplotype network analysis (Fig. 3), which revealed that individuals from 32 continental groups shared a major haplotype (Hap3). Notably, this haplotype was absent in two Philippine groups (PHL_2024 and Philippines_2015) and Papua New Guinea_2015 group. Conversely, several island populations, including two groups from the Philippines (PHL_2024 and Philippines_2015) and the Papua New Guinea_2015 group, exhibited no significant Tajima’s D or Fu’s FS (Table 2). These results implied that these island populations were likely undergoing genetic bottlenecks or population contractions.

    Island individuals are genetically separated from continental groups in Southeast Asia

    PCoA was conducted on the basis of pairwise FST values to further clarify the genetic relationships among B. dorsalis populations (Table 3 & Fig. 2). Multiple island groups, including two groups from the Philippines (PHL_2024 and Philippines_ 2015), Indonesia_2015, and Papua New Guinea_2015, were genetically separated from the continental cluster (Fig. 2). Notably, pairwise FST values involving the Papua New Guinea_2015 group exceeded 0.25 compared with all the other groups except Indonesia_2015, indicating that this island group was genetically differentiated from the continental groups (Table 3). Conversely, 31 continental B. dorsalis groups, excluding certain island groups, were genetically clustered according to their geographical distributions (Fig. 2). Furthermore, pairwise comparisons among all Southeast Asian groups except Papua New Guinea were generally close to 0, indicating a high genetic similarity within these groups (Table 3).

    Among the 2,421 mitochondrial COI sequences of Southeast Asian B. dorsalis, 753 haplotypes were identified (Table 2). On the basis of TCS network analysis, these haplotypes were formed with a star-like cluster centered on a major haplotype (Hap3), which contained 12.7% of B. dorsalis individuals (307 out of 2,421) from 11 distinct countries (32 groups) except the Philippines (PHL_2024 and Philippines_2015) and Papua New Guinea_2015 (Fig. 3). Notably, Papua New Guinea was constructed by two haplotypes (Hap322 and Hap335) located in the central bottom; furthermore, these haplotypes commonly shared with 31.1% (14 out of 45) of individuals from the neighboring island country of Indonesia (Fig. 3).

    Discussion

    This study provided comprehensive insights into the genetic structure of B. dorsalis across Southeast Asia using mitochondrial COI sequences. The results revealed two primary genetic patterns: extensive genetic exchange among continental populations and distinct genetic separation in island populations, particularly those from the Philippines and Papua New Guinea.

    The identification of a shared major haplotype (Hap3) across 32 continental populations supported the hypothesis that B. dorsalis originated in Southeast Asia and maintains an ongoing genetic connectivity despite geographic distance. This finding was based on previous molecular-based studies suggesting that B. dorsalis is native to Southeast Asia or Southern China (Choudhary et al., 2016;Li et al., 2012;Shi et al., 2012), and it subsequently dispersed from this region to other parts of Asia (Qin et al., 2018;Zeng et al., 2019). Furthermore, the high haplotype diversity and significantly negative Fu’s FS values observed in continental groups further indicated active genetic exchange and recent population expansion. Thus, 753 haplotypes were observed; of these haplotypes, 507 were unique, indicating extensive polymorphism in the mitochondrial COI gene within B. dorsalis. These results were consistent with previous studies conducted in India and in Yunnan Province, China, which reported high levels of intraspecific polymorphism within the respective regions or countries (Choudhary et al., 2016;Shi et al., 2005;Shi et al., 2010). The genetic connectivity among continental populations is likely facilitated by natural and anthropogenic factors, including the strong flight capacity of B. dorsalis (Froerer et al., 2010;Iwahashi, 1972;Steiner, 1957) and the frequent cross-border movement of infested agricultural commodities (Clarke, 2019;Malacrida et al., 2007;Vargas et al., 2015).

    The island populations exhibited genetic separation from continental groups, as evidenced by distinct clustering in PCoA and high pairwise FST values. The Philippines and Papua New Guinea showed a reduced haplotype diversity and nonsignificant neutrality test results, indicating geographical isolation or limited genetic exchange with other populations. These results suggested that island populations are the results of single separate invasion by oceanic barriers, with minimal or no subsequent gene flow (Barr et al., 2014;Qin et al., 2018).

    The application of mitochondrial COI gene analysis is an effective approach for inferring the origins of B. dorsalis. The sequences of 10 quarantine specimens from the Republic of Korea (Accession Nos. MW322099, MW322100, MW322101, MW322102, MW322103, MW322106, MW322107, MW32 2118, MW322119, and MW322122), previously collected during quarantine inspections (Kim et al., 2021), were identical to the haplotypes identified in the current study. Among them, three specimens (Accession Nos. MW322099, MW322103, and MW322107) showed a complete sequence identity with the major haplotype (Hap3). Notably, these 10 individuals from Korea did not share any haplotypes with the samples from the Philippines or Papua New Guinea.

    Therefore, the utilization of the constructed mitochondrial COI database in population genetics not only provides an effective tool for predicting the potential origins and invasive pathways but also contributes to the establishment of sustainable quarantine systems of B. dorsalis detected in the Republic of Korea.

    Acknowledgements

    We are thankful to Dr. Deuk-Soo Choi of the Quarantine Technology Institute Inc., Republic of Korea, for his generous assistance in providing, identifying, and photographing the B. dorsalis specimens utilized in this research. This research was supported by a grant (Project Code No. PQ20234B015) from the Animal and Plant Quarantine Agency, Ministry of Agriculture, Food and Rural Affairs, Republic of Korea.

    Supplementary Information

    Supplementary data are available at Korean Journal of Applied Entomology online (http://www.entomology2.or.kr).

    Statements for Authorship Position & Contribution

    • Kim, J.: Kyungpook National University, Ph.D candidate; Conducted the experiment and wrote the draft of the manuscript

    • Kim, D: Kyungpook National University, Associate Professor; Designed the research and wrote and edited the manuscript

    All authors read and approved the manuscript.

    Figure

    KJAE-64-4-277_F1.jpg

    Map of B. dorsalis collection sites from different countries in Southeast Asia. The map illustrates the sampling locations of B. dorsalis. Detailed collection information is provided in Table 1. The colors on the map correspond to the years of collection from 2022 to 2025.

    KJAE-64-4-277_F2.jpg

    Nucleotide diversity of B. dorsalis in Southeast Asia. Principal coordinate analysis (PCoA) plot based on pairwise population FST values (Table 3). The colored dots indicate where the samples were collected. Green and yellow circles represent the continental group and the Philippine group, respectively. Abbreviations: Thailand (THA), Vietnam (VNM), Taiwan (TWA), Cambodia (KHM), Philippines (PHL), and China (CHN)

    KJAE-64-4-277_F3.jpg

    Haplotype network analysis for B. dorsalis in Southeast Asia. Mitochondrial DNA haplotype network derived from TCS analysis based on 2,421 COI sequences. The size of the circles is proportional to the abundance of the haplotype, and the colors in the circles represent the region. The horizontal line markers represent the number of sequence differences for each haplotype. Abbreviations: Thailand (THA), Vietnam (VNM), Taiwan (TWA), Cambodia (KHM), Philippines (PHL), and China (CHN).

    Table

    Number of collected B. dorsalis individuals in Southeast Asia. B. dorsalis individuals were collected from five countries in Southeast Asia. The table represents the global positioning system (GPS) coordinate information and the number of collected specimens

    DNA polymorphisms of B. dorsalis in Southeast Asia. Summary of the molecular diversity of B. dorsalis populations determined on the basis of DNA polymorphisms using the mitochondrial COI gene. Bold represents significance at P<0.05. Abbreviations: Thailand (THA), Vietnam (VNM), Taiwan (TWA), Cambodia (KHM), Philippines (PHL), and China (CHN)

    Bold represent significance at P<0.05

    Pairwise FST values among different groups of B. dorsalis based on the mitochondrial COI gene. Table presenting pairwise FST calculated among B. dorsalis populations. Bold represents pairwise FST values estimates exceeding 0.25. Abbreviations: Thailand (THA), Vietnam (VNM), Taiwan (TWA), Cambodia (KHM), Philippines (PHL), and China (CHN)

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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