Research Article |
Corresponding author: Hufang Zhang ( zh_hufang@sohu.com ) Academic editor: Mariusz Kanturski
© 2023 Shijun Wang, Xiaofei Ding, Wenbo Yi, Wanqing Zhao, Qing Zhao, Hufang Zhang.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Wang S, Ding X, Yi W, Zhao W, Zhao Q, Zhang H (2023) Comparative mitogenomic analysis of three bugs of the genus Hygia Uhler, 1861 (Hemiptera, Coreidae) and their phylogenetic position. ZooKeys 1179: 123-138. https://doi.org/10.3897/zookeys.1179.100006
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Hygia Uhler, 1861 is the largest genus in the bug family Coreidae. Even though many species of this genus are economically important, the complete mitogenomes of Hygia species have not yet been reported. Therefore, in the present study, the complete mitogenomes of three Hygia species, H. lativentris (Motschulsky, 1866), H. bidentata Ren, 1987, and H. opaca (Uhler, 1860), are sequenced and characterized, and submitted in a phylogenetic analysis of the Coreidae. The results show that mitogenomes of the three species are highly conserved, typically with 37 genes plus its control region. The lengths are 16,313 bp, 17,023 bp, and 17,022 bp, respectively. Most protein-coding genes (PCGs) in all species start with the standard codon ATN and terminate with one of three stop codons: TAA, TAG, or T. The tRNAs secondary structures of all species have a typical clover structure, except for the trnS1 (AGC) in H. bidentata, which lacks dihydrouridine (DHU) arm that forms a simple loop. Variation in the length of the control region led to differences in mitochondrial genome sizes. The maximum-likelihood (ML) and Bayesian-inference (BI) phylogenetic analyses strongly supported the monophyly of Hygia and its position within Coreidae, and the relationships are ((H. bidentata + (H. opaca + (H. lativentris + Hygia sp.))). The results provide further understanding for future phylogenetic studies of Coreidae.
Coreoidea, evolutionary relationships, mitogenome, phylogeny
The mitogenome of insects usually comprises a double-stranded circular DNA molecule ranging from 14 to 18 kb in size, containing 37 genes (22 transfer RNAs, 13 protein-coding genes, 2 ribosomal RNAs) and a control region, which is consistent with the most typical insect mitochondrial genome, namely Drosophila yakuba Burla (
Coreidae
, well known for its odious defensive or alarm pheromones, is the largest family of Coreoidea, including 481 genera and 2,584 species. It is widely distributed worldwide (
Hygia
Uhler, 1861 is a larger genus in the family Coreidae. It is widely distributed in the Oriental and Palearctic regions. The genus includes 10 subgenera and 118 known species worldwide. At present, 26 species in three subgenera are known to be distributed in China (
In the present study, we newly sequenced, annotated, characterized, and compared the complete mitogenomes of H. lativentris (Motschulsky, 1866), H. bidentata Ren, 1987, and H. opaca (Uhler, 1860) in detail to reveal the mitogenomic characteristics of the genus Hygia and reconstruct the phylogenetic relationships of Hygia within the Coreidae with the existing data. Furthermore, we provide more taxon sampling data from the perspective of mitogenomes, which can be used to infer a higher level of evolutionary history later.
Chinese Hygia specimens of H. lativentris, H. bidentata, and H. opaca were collected by sweeping in July 2021 from Kuankuoshui National Natural Reserves in Guizhou Province, Zilinshan National Forest Park, Qiannan Autonomous Prefecture, and Jinxiu County in Guangxi Province, respectively. All specimens were placed in ethanol (95%) and stored in −20 °C freezers at the Shanxi Agricultural University (SAU), Shanxi, China. The DNA was extracted from the thorax or leg tissues of individual adults using the Genomic DNA Extraction Kit (Sangon Biotech, Shanghai, China) following the manufacturer’s protocol.
The whole mitogenomes of the three species were sequenced separately using the Illumina NovaSeq platform (Personalbio, Shanghai, China) using a 400-bp insert size and paired-end 150-bp sequencing strategy. Each species’ assembled full-length mitochondrial genome features were annotated using Geneious v. 8.1.4 software (
The phylogenetic relationships within Coreidae were analyzed using the three newly sequenced Hygia mitogenomes and another 21 mitogenomes of Coreidae. Dicranocephalus agilis (Scopoli, 1763) was used as an outgroup (Table
Family | Subfamily | Species | GenBank No. | References |
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Stenocephalidae | Dicranocephalus agilis | JQ910990 |
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Coreidae | Pseudophloeinae | Gralliclava horrens | MW619671 |
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Coreidae | Hydarinae | Hydarella orientalis | MW619672 |
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Hydaropsis longirostris | NC_012456 |
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Coreidae | Coreinae | Cloresmus pulchellus | NC_042806 |
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Enoplops sibiricus | MW619678 |
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Derepteryx lunata | NC_042807 |
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Mictis tenebrosa | NC_042811 |
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Anoplocnemis curvipes | NC_035509 | Unpublished | ||
Cletus punctiger | NC_050997 |
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Notopteryx soror | NC_037376 |
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Pseudomictis brevicornis | NC_042814 |
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Cletomorpha raja | NC_063143 |
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Leptoglossus membranaceus | NC_042809 |
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Helcomeria spinosa | MW619674 |
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Homoeocerus unipunctatus | MW619675 |
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Hygia sp. | MW619679 |
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Manocoreus sp. | MW619724 |
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Petillopsis calcar | MW619673 |
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Physomerus sp. | MW619681 |
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Sinodasynus sp. | MW619676 |
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Notobitus montanus | NC_065112 | Unpublished | ||
Hygia lativentris | OP837484 | This study | ||
Hygia bidentata | OP837485 | This study | ||
Hygia opaca | OP837486 | This study |
The mitogenomes lengths of H. lativentris, H. bidentata, and H. opaca were 16,313 bp, 17,023 bp, and 17,022 bp, respectively (Fig.
The complete mitogenomes of these three Hygia species had a strong A+T base composition bias relative to G+C (76.1–77.3%; mean = 76.73%). The A+T base compositions of H. lativentris, H. bidentata, and H. opaca were 76.8% (A: 42.9%, T: 33.9%, G: 9.7%, C: 13.4%), 77.3% (A: 44.1%, T: 33.2%, G: 9.2%, C: 13.5%), and 76.1% (A: 43.6%, T: 32.5%, G: 9.6%, C: 14.3%), respectively. All three species had positive AT skew values (ranging from 0.117 to 0.146, mean = 0.134) and negative GC-skew values (ranging from −0.197 to −0.159, mean = −0.182) (Suppl. material
The 13 PCGs of H. lativentris, H. bidentata, and H. opaca were 11,043 bp, 11,046 bp, and 11,043 bp long, accounting for 67.7%, 64.9%, and 64.9% of the total sequences, respectively (Suppl. material
The three mitogenomes of Hygia encoded 5,437, 5,674, and 5,674 amino acids, respectively (Suppl. material
The ratios of the nonsynonymous (Ka)/synonymous (Ks) substitution rates (Ka/Ks) for the 13 PCGs from the three Hygia species were calculated and used to estimate the evolutionary rate (
The complete mitogenomes of the three Hygia species contained 22 tRNA genes. Fourteen tRNA genes (trnI, trnM, trnW, trnL2, trnK, trnD, trnG, trnA, trnR, trnN, trnS1, trnE, trnT, and trnS2) were located on the J-strand, and eight tRNA genes (trnQ, trnC, trnY, trnF, trnH, trnP, trnL1, and trnV) were located on the N-strand. The 22 tRNA gene sequences were 62–74 bp in length. The entire tRNA region was 1,453 bp, 1,459 bp, and 1,455 bp, respectively (Suppl. material
Similar to the published pentatomid mitogenomes, two ribosomal RNA genes (rrnL and rrnS) were encoded on the N‐strand in the mitogenomes. The lengths of rrnL in H. lativentris, H. bidentata, and H. opaca were 1,277 bp, 1,272 bp, and 1,275 bp, respectively, all located between tRNA‐Leu (TAG) and tRNA‐Val (Suppl. material
The control region is related to the origin of transcription and replication (
We performed the phylogenetic analyses using 25 mitochondrial genomes to reconstruct the relationships among the genus Hygia and other genera in Coreidae, which included species from three subfamilies (Figs
In this study, we first described the newly sequenced mitogenomes of three Hygia species, H. bidentata, H. lativentris, and H. opaca, and found that Hygia mitogenome arrangements are highly conserved. The results are consistent with other published mitochondrial genomes of Hemiptera (
The protein-coding genes started with the standard codon ATN, except for the cox1, which starts with a non-traditional start codon TTG. Moreover, except for cox1, cox2, and cox3, which used T codons—a common feature in insects—the other PCGs finish with a complete TAN codon. The stop codon TAA is more frequent than TAG in all three mitogenomes. (
The tRNAs secondary structures in Hygia had a typical clover structure, except for the trnS1 (AGC) of H. bidentata, which had a reduced dihydrouridine (DHU) arm that formed a simple loop. This reduced DHU arm in trnS1 is common in most metazoans (
We performed the phylogenetic analyses based on BI and ML using a dataset with the 13 PCGs, our results are generally consistent with some studies on phylogenetic analysis of the bug subfamily Coreinae (
In conclusion, three new mitogenomes of the genus Hygia were sequenced and compared in this study. The results show the monophyly of Hygia and the relationships within Coreidae. The genus Hygia is very diverse, but only a few species of the group were used in this analysis. Therefore, we need to analyze more groups and add more mitogenome sequences to better reconstruct and evaluate the phylogeny at different levels, including family and subfamily level relationships within the superfamily Coreoidea, by combining morphological and molecular data.
The authors have declared that no competing interests exist.
No ethical statement was reported.
This study was supported by the National Natural Science Foundation of China (no. 31872272), Shanxi Graduate Innovation Project of Shanxi Province (no. 2020BY059), Natural Science Research General project of Shanxi Province (no. 202103021224331), and the Scientific Research Project of Xinzhou Teachers University (no. 2019KY11).
Hufang Zhang and Qing Zhao: conceived and designed the experiments; Shijun Wang: performed the experiments; Shijun Wang and Xiaofei Ding: analyzed the data; Wenbo Yi and Wanqing Zhao: provided specimen/contributed analysis tools; Shijun Wang: wrote the paper. All authors have read and agreed to the published version of the manuscript.
Shijun Wang https://orcid.org/0000-0002-2673-9677
Xiaofei Ding https://orcid.org/0009-0000-5519-1316
Wenbo Yi https://orcid.org/0000-0002-0963-8364
Qing Zhao https://orcid.org/0000-0003-2744-1239
Hufang Zhang https://orcid.org/0000-0003-4279-9597
All of the data that support the findings of this study are available in the main text or Supplementary Information.
Supplementary information
Data type: docx
Explanation note: table S1. Mitogenomic organization of H. lativentris, H. bidentata, and H. opaca; table S2. Nucleotide composition and skewness of different elements of mitogenomes of H. lativentris, H. bidentata, and H. opaca; figures S1–S3. Predicted secondary cloverleaf structure of tRNA of H. lativentris, H. bidentata, and H. opaca, respectively.