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. 2026 Apr 10;11(5):599–603. doi: 10.1080/23802359.2026.2652762

The complete mitochondrial genome analysis of Elachiptera decipiens (Loew, 1863) (Diptera: Chloropidae)

Yong-Yue Gu a, Yue Guo a, Wan-Long Zhang a, Heng-Jia Zhang a, Ai-Mei Dai b, Hao Zhang a,✉
PMCID: PMC13072685  PMID: 41983030

Abstract

Elachiptera decipiens is cereal pest distributed in North America, Europe, and China. Its complete mitochondrial genome from Xinjiang, China was sequenced using next-generation sequencing technique. The 18,344 bp mitogenome contains 13 protein-coding gene sequences (PCGs), 22 tRNAs, and 2 rRNAs. Phylogenetic analysis based on 13 PCG sequences at family level and COI gene sequences at subfamily level. Phylogenetic analysis revealed that E. decipiens is closely related to E. insignis. The complete mitogenome of E. decipiens would help understand Chloropidae evolution and develop rapid identification methods based on mitochondrial genes.

Keywords: Mitogenome, Chloropidae, Oscinellinae, Elachiptera decipiens

Introduction

Elachiptera decipiens (Loew, 1863) (Diptera: Chloropidae: Oscinellinae) is mainly distributed in Canada, the United States, and some countries in Europe. In 2021, it was first discovered in Bole City of Xinjiang Uygur Autonomous Region, China, and since then it has become an important pest on common wheat (Triticum aestivum L.). The larva of E. decipiens feeds within the wheat stem, leading to stunting, distortion, and decreased tillering. The most evident symptom is the manifestation of the ‘white head’ condition. In this condition, the seed head undergoes necrosis and turns white, whereas the lower stem areas and leaves retain their green coloration. However, due to the strikingly similar morphological features and symptoms caused by the larvae, it is significantly challenging to identify E. decipiens from other Chloropids species in wheat fields, such as Meromyza saltatrix (L.) and Oscinella pusilla (Meigen) (Liu and Sun 1965; Wang and Yang 1990). E. decipiens also has the ability to damage maize (Zea mays L.) (Federal Research Centre for Cultivated Plants 2021).

Despite the fact that this pest has been widely distributed in North America and Europe for a long time, the studies on the biology, ecology, and genetics are still limited. In the present study, we sequenced the complete mitochondrial genome of E. decipiens for the first time and conducted the phylogenetic analysis.

Materials and methods

The larvae and pupae of E. decipiens were collected from Bole city (E 82.0046°, N 44.9255°), Xinjiang Uyghur Autonomous Region, China, in July 2021. All samples were live-collected and initially preserved in 5 ml centrifuge tubes in fields, and then were transferred to laboratory for rearing to adulthood (collected by Aimei Dai and Wanlong Zhang). The adult specimens have been deposited in the Insect Museum of College of Plant Protection, Northwest A&F University, and the certificate number is DI001 (contact person: Hao Zhang, email: zhh1972@nwsuaf.edu.cn).

The specimen was identified morphologically by Yue Guo by referencing Mlynarek and Wheeler (2018), and DNA sequencing. DNA samples were pooled using next-generation library construction following Gillett et al. (2014) on the Illumina NovaSeq 6000 platform by Personal Biotechnology Co., Ltd. (Shanghai, China). The raw reads were filtered and trimmed using Fastp (https://github.com/OpenGene/fastp) and Adapter Removal (version 2) following Schubert et al. (2016). De novo assemblies of high-quality reads were conducted using A5 miseq v20150522 (Coil et al. 2015) and SPAdes v3.9.0 (Bankevich et al. 2012). Following the completion of genome assembly using Bandage software (v0.8.1, https://github.com/rrwick/Bandage), a visualization analysis was conducted on the GFA format generated from the map file to confirm that the genomic DNA fragments formed complete circular molecules. Based on the connectivity and sequence information of each node in the graph, the complete genome sequence file was reconstructed through manual proofreading. Re-BLAST analysis revealed that sequencing depth was evenly distributed across most regions of the genome, thereby validating the completeness and accuracy of the assembly results. However, a reduction in sequencing depth was observed in AT-rich regions of the genome, likely due to amplification bias during PCR and bridge amplification, leading to decreased coverage in these areas. The gene annotation was performed using Mitos WebServer (http://mitos.bioinf.uni-leipzig.de/index.py) (Bernt et al. 2013), and the determination of the control region boundary was determined using the automatic annotation function of MitoS2. The circular map of the mitogenome was drawn using CGView Visualization software (Alikhan et al. 2011).

To determine the taxonomic position of E. decipiens, analyze the phylogenetic analysis was carried out using 13 protein-coding gene (PCG) sequences from 11 Chloropidae taxa, including E. decipiens, at family level with Mayetiola destructor (Say) (Diptera: Cecidomyiidae) and Drosophila busckii Coquillett (Diptera: Drosophilidae) as outgroups. Meanwhile, given the critical role of the COI gene in insect phylogeny and evolution, COI gene sequences from 10 species from Oscinellinae taxa were used for phylogenetic analysis at subfamily level with the two closely related species from subfamily Chloropinae, Meromyza saltatrix (L.) and Cetema elongatum (Meigen) as outgroup. All the 13 PCGs and COI gene sequences were downloaded from GenBank. All the sequences were concatenated and aligned in DNAman 6.0. The maximum-likelihood (ML) method was employed to analyze the phylogenetic tree. The ML analysis was performed by MEGA 11 with 1000 bootstrap replicates.

Results

The mitochondrial genome of E. decipiens (Figure 1), was assembled as a circular molecule measuring 18,344 bp (GenBank: PQ585796). It exhibited sequencing coverage depths varying from 59× to 1074×, with an average depth of 773.388× (Figure S1). The overall nucleotide composition was notably AT-rich, with A, T, C, and G contents of 42.89%, 39.59%, 10.10%, and 7.42%, respectively, showing in a total AT bias at 82.48%. This genome contained 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes (s-rRNA and l-rRNA), and a control region (A–T rich region/D-loop) (Figure 2). The combined length of all PCGs was 11,218 bp, representing 61.2% of the entire mitochondrial genome. The majority of PCGs started with standard ATN initiation codons, except for cox1 (TCG), nad1 (TTG), and nad5 (GTG). In terms of termination, eight PCGs ended with a complete TAA stop codon, while cob ended with TAG, and four genes—cox1, cox2, nad4, and nad5—used a single T as an incomplete stop codon. Gene overlaps were observed in 11 regions, totaling 21 bp, with the longest overlap (8 bp) occurring between trnW and trnC. Additionally, intergenic spacers spanned a total of 562 bp, ranging from 1 bp to 1070 bp. The longest spacer, measuring 1070 bp, was located between trnI and the D-loop region.

Figure 1.

Side-by-side images of two insect forms: a yellowish-brown larva on the left and a small black adult fly with transparent wings on the right, both shown at a 1mm scale.

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Elachiptera decipiens larva and adult. (a) Larva; (b) adult. Photos were taken and edited by Yue Guo.

Figure 2.

Circular genomic map of an 18,344 bp sequence, highlighting gene locations, GC content, and GC skew. This circular genomic map illustrates a DNA sequence of 18,344 base pairs. The outer ring features color-coded genomic elements: coding sequences (CDS) are in blue, tRNA in red, rRNA in orange, and the control region in gray. The second ring depicts GC content as green areas, while GC skew is shown with purple (negative) and green (positive) regions. Specific genes like nad and cox are labeled around the perimeter, including tRNA genes such as trnQ and trnM. A central scale marks the genome length, and a legend explains the color coding for clarity.

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Mitochondrial genome map of Elachiptera decipiens. From inside to outside, the first circle represents the scale; the second circle represents GC skew; the third circle represents GC content; the fourth and fifth circles represent the arrangement of protein coding, tRNA, and rRNA genes on the genome.

The phylogenetic tree of Chloropidae in this study based on 13 PCGs showed that the newly sequenced species E. decipiens was clustered in the subfamily Oscinellinae clade and had the closest relationships with E. insignis NC072208, but had a distant relationship with other species belonging to subfamily Siphonellopsinae, Rhodesiellinae, and Chloropinae (Figure 3). Based on COI gene sequences, the phylogenetic tree showed that the studied species was clustered together with Elachiptera decipiens JF874163 with a high bootstrap support values (BSV = 100), indicating that it is E. decipiens. Furthermore, E. decipiens was closely associated with E. insignis NC 072208 and E. cornuta HE614017, then with Anatrichus pygmaeus and Melanochaeta pubescens, but had a distant relationship with Oscinella pusilla, Cadrema minor, and Dicraeus orientalis, respectively (Figure 5). Interestingly, E. tuberculifera exhibits a greater genetic distance from the other Elachiptera species. Both the phylogenetic analyses showed that E. decipiens was closely related to E. insignis.

Figure 3.

Phylogenetic tree showing relationships among 12 insect species, highlighting Elachiptera decipiens and Elachiptera insignis. This phylogenetic tree illustrates the evolutionary relationships among 12 insect species divided into five colored subfamilies: Oscinellinae (light blue), Siphonellopsinae (pink), Rhodesiellinae (light orange), Chloropinae (light yellow), and an outgroup (light blue). Key species, including Elachiptera decipiens (marked with a red triangle) and Elachiptera insignis, are presented at the top, with corresponding bootstrap values indicating branch support. A scale bar reflects a genetic distance of 0.05, highlighting significant evolutionary connections among taxa.

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ML phylogenetic tree based on the 13 protein-coding genes (PCGs). The larger the number on the branch, the higher the proof reliability. Alphanumeric terms indicate the accession number of the GenBank. The following sequences were used: Elachiptera decipiens PQ585796 (this study); Elachiptera insignis OP612812 (Liu et al. 2024); Anatrichus pygmaeus OM214541 (Cai et al. 2022); Gampsocera sp. OR854638 (He et al. 2024); Oscinella pusilla OP612807 (Liu et al. 2024); Apotropina sp. OP612809 (Liu et al. 2024); Rhodesiella elegantula NC072206 (Liu et al. 2024); Rhodesiella sp. OP612804 (Liu et al. 2024); Cetema sp. OR522694 (Liu et al. 2024); Chlorops oryzae MW438309 (Wang et al. 2021); Pachylophus rufescens PP419106 (Liu et al. 2024); Drosophila busckii MT429169 (Zhang and Jin 2020); Mayetiola destructor GQ387648 (Beckenbach and Joy 2009).

Figure 4.

A phylogenetic tree illustrates relationships among 11 insect species in 7 color-coded genera. Bootstrap values indicate support, with a red triangle highlighting the study subject. Scale bar shows 0.02 genetic distance.

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ML phylogenetic tree based on the COI gene. The larger the number on the branch, the higher the proof reliability. Alphanumeric terms indicate the accession number of the GenBank. The following sequences were used: Elachiptera decipiens PQ585796 (this study); Elachiptera decipiens JF874163 (unpublished); Elachiptera insignis NC 072208 (unpublished); Elachiptera cornuta HE614017 (unpublished); Anatrichus pygmaeus NC063616 (unpublished); Melanochaeta pubescens MN868814 (Ferreira et al. 2020); Elachiptera tuberculifera MZ610071 (unpublished); Oscinella pusilla NC072205 (Liu et al. 2024); Cadrema minor NC072207 (unpublished); Dicraeus orientalis NC057210 (unpublished); Meromyza saltatrix NC072204 (Liu et al. 2024); Cetema elongatum MZ611060 (unpublished).

Discussion and conclusions

The mitochondrial genome size in Diptera insects varies from 11,339 bp to 19,517 bp (Zhang et al. 2013). In the present study, the complete mtDNA of E. decipiens was 18,344 bp in length, and the genomes exhibited a noticeable A + T bias (82.48%), which is consistent with the characteristics of insect mtDNA (Boore 1999) and Chloropidae species (Liu et al. 2024). Wang et al. (2021) reported that the complete mtDNA of Chlorops oryzae had an A + T value of 79.22%. Liu et al. (2024) reported that the A + T value of chloropid species ranged from 78.5% (Thaumatomyia glabra) to 80.9% (Elachiptera insignis). Compared with the two species, C. oryzae and E. insignis, E. decipiens has a slightly higher AT value. The sequencing results reveal that the COI promoter TCG of E. decipiens is the same as that of E. insignis determined by Liu et al. (2024).

Until now, the subfamily-level and genus-level relationships of Chloropidae have been a topic of debate. Mlynarek and Wheeler (2018) proposed that Elachiptera was closely related to Melanochaeta based on adult morphological characteristics including the cephalic bristling and the shape of the scutellum. Liu et al. (2024) suggested that Elachiptera was most closely related to Anatrichus based on the mitogenome sequences. In our studies, E. decipiens showed a close genetic relationship both to Anatrichus pygmaeus and Melanochaeta pubescens, which is in accordance with the previous research (Mlynarek and Wheeler 2018; Liu et al. 2024).

Regarding the lower bootstrap values observed in Figure 5, there are two primary reasons. First, the sequences are phylogenetically close and exhibit a high degree of similarity, which contributes to the lower bootstrap values. Second, during sequence alignment, we aligned and trimmed the sequences based on the shortest one, resulting in sequences approximately 300 bp in length, which is relatively short. The high similarity among the remaining parts further contributes to the lower bootstrap values. Additionally, due to data constraints, we are unable to obtain mitochondrial whole-genome data, as depicted in Figure 3, for analyzing the Oscinellinae subfamily in Figure 5. Consequently, our analysis of the Oscinellinae subfamily remains preliminary. Improved results are anticipated as more data become available in the future.

Mitogenome has been not only widely used for investigations into phylogeny, phylogeography, and population genetics (Cameron 2014; Lv et al. 2015; Du et al. 2019; Huang and Zhang 2020), but also to develop the rapid identifying method for invasive species, such as Daktulosphaira vitifoliae and Trogoderma granarium (Agarwal et al. 2020; Wu et al. 2023), and tissue of cattle origin (Kumari et al. 2019). E. decipiens is seen as an invasive pest in China, but difficulties remain in distinguishing this species from similar ones. The mitogenome sequence of E. decipiens would assist border ports and in fields in its effective rapid identification as well as pest control at the early stages of monitoring.

In conclusion, we sequenced mitochondrial genomes of E. decipiens, and suggested the phylogenetic relationships of the species with several other Elachiptera spp. This study may provide some valuable genetic resources to understand Oscinellinae subfamily evolution, and to develop rapid identification method for E. decipiens.

Supplementary Material

Supplemental Material
TMDN_A_2652762_SM5216.tif (204.7KB, tif)

Acknowledgments

The authors are grateful to Dr. Xiangshun Hu for his advice during the revision of the manuscript.

Funding Statement

This work was supported by the Natural Science Foundation of Xinjiang (2022D01A06), Ministry of Science and Technology Assistance Program for Developing Countries of China (KY202002018), and National Modern Agricultural Industry Technology System Project of China (CARS-03-37).

Ethical approval

This study was permitted and ethically approved by the College of Plant Protection, Northwest A&F University. The study was supported and assisted by the Agricultural Technology Promotion Center of Bole Mongol Autonomous Prefecture.

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 number PQ585796. Raw sequencing reads used here have been deposited in the SRA database of NCBI under accession number SRR31912344. The associated ‘BioProject’ and ‘Bio-Sample’ numbers are PRJNA1202719 and SAMN45963734, respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Supplemental Material
TMDN_A_2652762_SM5216.tif (204.7KB, tif)

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 number PQ585796. Raw sequencing reads used here have been deposited in the SRA database of NCBI under accession number SRR31912344. The associated ‘BioProject’ and ‘Bio-Sample’ numbers are PRJNA1202719 and SAMN45963734, respectively.

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