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Research Article
The complete mitochondrial genome of Aeschrocoris tuberculatus and A. ceylonicus (Hemiptera, Pentatomidae) and its phylogenetic implications
expand article infoWang Jia‡, Jiufeng Wei‡, Minmin Niu‡, Hufang Zhang§, Qing Zhao‡
‡ Shanxi Agricultural University, Taigu, China
§ Xinzhou Teachers University, Xinzhou, China

Corresponding author: Qing Zhao ( zhaoqing86623@163.com )

Academic editor: Wenjun Bu
© 2023 Wang Jia, Jiufeng Wei, Minmin Niu, Hufang Zhang, Qing Zhao.
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: Jia W, Wei J, Niu M, Zhang H, Zhao Q (2023) The complete mitochondrial genome of Aeschrocoris tuberculatus and A. ceylonicus (Hemiptera, Pentatomidae) and its phylogenetic implications. ZooKeys 1160: 145-167. https://doi.org/10.3897/zookeys.1160.100818
ZooBank: urn:lsid:zoobank.org:pub:CAF0F319-41E5-4B7F-8C4E-7DF79D2BBBB6
Open Access

Abstract

Aeschrocoris tuberculatus and A. ceylonicus (Hemiptera, Pentatomidae, Pentatominae) are mainly distributed in southern China, India, Myanmar, and Sri Lanka. Both species are also common agricultural pests. However, only the morphology of the genus Aeschrocoris has previously been studied, and molecular data have been lacking. In this study, the whole mitochondrial genomes of A. tuberculatus and A. ceylonicus are and annotated. The lengths of the complete mitochondrial genomes of the two species are 16,134 bp and 16,142 bp, respectively, and both contain 37 typical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. The mitochondrial genome structure, gene order, nucleotide composition, and codon usage of A. tuberculatus and A. ceylonicus are consistent with those of typical Pentatomidae. Most PCGs of both species use ATN as the start codon, except atp8, nad1, and cox1, which use TTG as the start codon. cox1, cox2, and atp6 use a single T, and nad1 use TAG as the stop codon; the remaining PCGs have TAA as the stop codon. The A+T contents of the two species are 73.86% and 74.08%, respectively. All tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. The phylogenetic tree is reconstructed using the maximum-likelihood method based on the newly obtained mitochondrial genome sequences and 87 existing mitochondrial genomes of Pentatomoidea from the NCBI database and two species of Lygaeoidea as outgroups. The phylogenetic trees strongly support the following relationships: (Urostylididae + ((Acanthosomatidae + ((Cydnidae + (Dinidoridae + Tessaratomidae)) + (Scutelleridae + Plataspidae))) + Pentatomidae). This study enriches the mitochondrial genome database of Pentatomoidea and provides a reference for further phylogenetic studies.

Keywords

Mitogenome, Pentatomoidea, phylogenetic analysis

Introduction

The insect mitochondrial genome is a circular double-stranded DNA molecule with a length of about 16–18 kb, which code 37 genes: 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes (Boore 1999). In addition, the mitochondrial genome usually includes a noncoding region of variable length that plays a regulatory role in transcription and replication, known as the mitochondrial control region (Cameron 2014). In recent years, with the development of sequencing technology and the amplification through universal primers for mitochondrial genes (Simon et al. 1994, 2006), the number of insect mitochondrial genomes has rapidly increased, and the characteristics and evolutionary patterns of insect mitochondrial genomes are becoming more and more clear; their applications in phylogenetic studies are gradually increasing. The mitochondrial genome contains important molecular evolutionary information such as base composition and codon usage (Yuan et al. 2022). It has been widely used in research on molecular evolution, phylogeny, genealogy, and population genetic structure because of its stable gene composition, relatively conserved order, matrilineal inheritance, and minimal recombination (Ballard and Whitlock 2004; Simon and Hadrys 2013; Cameron 2014).

Pentatomoidea (Hemiptera, Heteroptera, Pentatomomorpha) consists of more than 8,000 species in 18 families, of which Pentatomidae is the largest family containing 940 genera and about 5,000 species (Rider et al. 2018). Pentatomidae is a species-rich group, so it is difficult to propose defining characteristics that can be applied to all groups. All stinkbugs of Pentatomidae are terrestrial insects, most of which are phytophagous; only Asopinae are predatory species, and some are used as biological control agents (De Clercq et al. 2003).

The tribe Aeschrocorini was first proposed by Distant (1902) and included two genera, Aeschrocoris Bergroth, 1887 and Scylax Distant, 1887. It remained little known until Cachan (1952) added a new genus to the tribe. The Aeschrocorini is still relatively small, currently with only eight genera (Rider et al. 2018). Hassan et al. (2016) provided a brief record of Indian species of Aeschrocoris. Despite the complex taxonomic relationships within the Aeschrocorini, numerous scholars have consistently assigned the genus Aeschrocoris to Aeschrocorini (Rider et al. 2018). Aeschrocoris was reported to have five species in China and eight in the world. Aeschrocoris tuberculatus (Stål, 1865) and A. ceylonicus Distant, 1899 are mainly distributed in southern China, India, Myanmar, and Sri Lanka, and both are also common agricultural pests (Fan 2011). However, most studies of the genus Aeschrocoris have focused on morphological descriptions and lack molecular data.

In this study, we analyze the mitochondrial genomes of A. tuberculatus and A. ceylonicus in detail, including genome structure, nucleotide composition, and codon usage. Meanwhile, we also construct the genome structure of RNA. In addition, we analyze the phylogenetic relationship of eight families of Pentatomoidea and explore the phylogenetic location of these two species. The results of this study will provide a reference for phylogenetic analyses and identification of the Pentatomoidea.

Materials and methods

Sample collection

Adult specimens of Aeschrocoris tuberculatus and A. ceylonicus were collected from Baihua Ling (Baoshan City, Yunnan Province, China; 25°16'43"N, 98°48'12"E) on 13 August 2015 and from Guanlan Ting (Taohua Island, Zhoushan City, Zhejiang Province, China; 29°50'31"N, 122°14'13"E) on 4 August 2016. All samples were immediately placed in anhydrous ethanol and stored in a refrigerator at –25 °C until DNA was extracted. The species were identified by Qing Zhao.

DNA extraction and sequencing

Whole-genome DNA was extracted from the thoracic muscle of the samples using the Genomic DNA Extraction Kit (BGI, Wuhan, Hubei, China). Concentrations of samples were detected using Qubit Fluorometer and microplate reader (Mardis and McCombie 2017). The integrity of the samples was tested by agarose gel electrophoresis. High-throughput pair-ended sequencing (PE150) was performed on DNBSEQ platform for the complete mitochondrial genomes of the two species (Chen et al. 2018). All the above operations were carried out in the high-throughput laboratory at Wuhan BGI Technology Services Co., Ltd. (Wuhan, Hubei, China).

Genome annotation and sequence analysis

When the assembly was complete, the complete mitogenomes were manually annotated using Geneious v. 11.0 software (Kearse et al. 2012). Two reference sequences (Eurydema gebleri and Brachymna tenuis) for annotation were obtained from the Basic Local Alignment Search tool (BLAST) in the NCBI database. The boundaries of the PCGs were determined using Open Reading Frame Finder on the NCBI website (http://www.ncbi.nlm.nih.gov/gorf/gorf.html). MEGA v. 11.0 (Tamura et al. 2021) was used to translate the proteins to verify the start codons, stop codons, and amino acid sequences and to ensure the accuracy of the sequences. We annotated tRNA sequences using tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/; Lowe and Eddy 1997) or used automatic annotation done by MITOS (http://mitos.bioinf.uni-leipzig.de/index.py/; Bernt et al. 2013) with the invertebrate mitochondrial code. The boundaries of the rRNA genes were completed based on the positions of adjacent genes and published rRNA gene sequences (Boore 2006). The control region was identified through the boundary of the neighboring genes.

The base composition, codon usage (RSCU), and amino acid composition of the mitogenome were analyzed using MEGA v. 11.0. The skew of the nucleotide composition was calculated as follows: AT-skew = (A – T) / (A + T) and GC-skew = (G – C) / (G + C) (Perna and Kocher 1995; Hassanin et al. 2005; Bernt et al. 2013). DnaSP6 software (Rozas et al. 2017) was used to count the non-synonymous substitutions (Ka) and synonymous substitutions (Ks) of 13 PCGs of Pentatomoidea and to calculate the Ka/Ks values. The ratio Ka/Ks indicated the rate of evolution, the higher the ratio, and the faster the rate of evolution.

Phylogenetic analyses

In this study, we used the two newly sequenced species, 87 species from other eight families of Pentatomoidea, and two species (Geocoris pallidipennis and Kleidocerys resedae as the outgroup) from Lygaeoidea to analyze the phylogenetic position of A. tuberculatus and A. ceylonicus and the phylogenetic relationships within Pentatomoidea (Table 1). DNA alignment was inferred from the amino-acid alignment of the 13 PCGs using MUSCLE with default settings in MEGA v. 11 (Edgar 2004).

Table 1.
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List of species used to construct the phylogenetic tree.

Classification Family Species Accession number Reference
Outgroup
Lygaeoidea Lygaeidae Geocoris pallidipennis EU427336 Hua et al. 2008
Kleidocerys resedae KJ584365 Li et al. 2016
Ingroup
Pentatomoidea Acanthosomatidae Acanthosoma labiduroides JQ743670 Li et al. 2017
Anaxandra taurina NC042801 Liu et al. 2019
Sastragala edessoides JQ743676 Li et al. 2017
Sastragala esakii MW847247 Xu et al. 2021
Cydnidae Adrisa magna NC042429 Liu et al. 2019
Aethus nigritus MW847231 Xu et al. 2021
Macroscytus gibbulus EU427338 Hua et al. 2008
Macroscytus subaeneus MW847241 Xu et al. 2021
Scoparipes salvazai NC042800 Liu et al. 2019
Dinidoridae Coridius brunneus MW899158 Unpublished
Cyclopelta parva NC037739 Jiang 2017
Megymenum gracilicorne NC042810 Liu et al. 2019
Pentatomidae Aeschrocoris ceylonicus OP526368 This study
Aeschrocoris tuberculatus OP526367 This study
Arma custos NC051562 Wu et al. 2020
Anaxilaus musgravei NC061538 Unpublished
Brachymna tenuis NC042802 Liu et al. 2019
Carbula sinica NC037741 Jiang 2017
Catacanthus incarnatus NC042804 Liu et al. 2019
Caystrus obscurus NC042805 Liu et al. 2019
Cazira horvathi NC042817 Liu et al. 2019
Dalpada cinctipes NC058967 Xu et al. 2021
Dalsira scabrata NC037374 Jiang 2017
Deroploa parva NC063299 Unpublished
Dinorhynchus dybowskyi NC037724 Zhao et al. 2018
Dolycoris baccarum NC020373 Zhang et al. 2013
Eocanthecona furcellata MZ440302 Unpublished
Eocanthecona thomsoni NC042816 Liu et al. 2019
Eurydema dominulus NC044762 Zhao et al. 2019b
Pentatomoidea Pentatomidae Eurydema gebleri NC027489 Yuan et al. 2015
Eurydema liturifera NC044763 Zhao et al. 2019b
Eurydema maracandica NC037042 Zhao et al. 2017b
Eurydema oleracea NC044764 Zhao et al. 2019b
Eurydema qinlingensis NC044765 Unpublished
Eurydema ventralis MG584837 Unpublished
Erthesina fullo NC042202 Ji et al. 2019
Eysarcoris aeneus MK841489 Zhao et al. 2019a
Eysarcoris annamita MW852483 Li et al. 2021
Eysarcoris gibbosus MW846868 Li et al. 2021
Eysarcoris guttigerus NC047222 Chen et al. 2020
Eysarcoris montivagus MW846867 Li et al. 2021
Eysarcoris rosaceus MT165687 Li et al. 2021
Glaucias dorsalis NC058968 Xu et al. 2021
Gonopsis affinis NC036745 Chen et al. 2017
Graphosoma rubrolineatum NC033875 Wang et al. 2017
Halyomorpha halys NC013272 Lee et al. 2009
Hippotiscus dorsalis NC058969 Xu et al. 2021
Hoplistodera incisa NC042799 Liu et al. 2019
Menida violacea NC042818 Liu et al. 2019
Nezara viridula NC011755 Hua et al. 2008
Neojurtina typica NC058971 Xu et al. 2021
Palomena viridissima NC050166 Unpublished
Pentatoma metallifera NC058972 Xu et al. 2021
Pentatoma rufipes MT861131 Zhao et al. 2021
Pentatoma semiannulata NC053653 Unpublished
Picromerus griseus NC036418 Zhao et al. 2017a
Picromerus lewisi NC058610 Mu et al. 2022
Placosternum urus NC042812 Liu et al. 2019
Plautia crossota NC057080 Wang et al. 2019
Plautia fimbriata NC042813 Liu et al. 2019
Plautia lushanica NC058973 Xu et al. 2021
Priassus spiniger OK546352 Unpublished
Scotinophara lurida NC042815 Liu et al. 2019
Tholosanus proximus NC063300 Unpublished
Zicrona caerulea NC058303 Zhao et al. 2020
Plataspidae Brachyplatys subaeneus MW847232 Xu et al. 2021
Calacta lugubris MW847233 Xu et al. 2021
Coptosoma bifaria EU427334 Hua et al. 2008
Coptosoma variegatum OP123035 Zhu et al. 2022
Megacopta bituminata OP123020 Zhu et al. 2022
Megacopta caliginosa OP123022 Zhu et al. 2022
Megacopta centronubila OP123024 Zhu et al. 2022
Megacopta cribraria JF288758 Unpublished
Megacopta cribriella OP123025 Zhu et al. 2022
Megacopta distanti OP123028 Zhu et al. 2022
Megacopta horvathi OP123029 Zhu et al. 2022
Megacopta lobata OP123031 Zhu et al. 2022
Scutelleridae Cantao ocellatus MF497713 Liu et al. 2019
Chrysocoris stollii NC051942 Unpublished
Eurygaster testudinaria NC042808 Liu et al. 2019
Poecilocoris druraei MW847246 Xu et al. 2021
Tessaratomidae Dalcantha dilatata JQ910981 Li et al. 2017
Eusthenes cupreus NC022449 Song et al. 2013
Mattiphus splendidus NC053743 Xu et al. 2020
Pycanum ochraceum MW899159 Wang et al. 2021
Tessaratoma papillosa NC037742 Jiang 2017
Urostylididae Urostylis flavoannulata NC037747 Jiang 2017
Urolabida histrionica MW847249 Xu et al. 2021
Urochela quadrinotata NC020144 Li et al. 2012

To determine whether the sequences contained phylogenetic information, we tested nucleotide substitution saturation and plotted transition and transversion rates against the TN93 distances for two datasets: all codon positions of the 13 PCGs (PCG123) and first and second codon positions of PCGs (PCG12) using DAMBE to further validate the feasibility of constructing a phylogenetic tree (Xia and Xie 2001; Xia and Lemey 2009). Heterogeneity in sequence divergence in the two datasets was analyzed by using AliGROOVE with the default sliding window size (Kück et al. 2014). PartitionFinder was used to provide the best fit model (Kalyaanamoorthy et al. 2017). IQtree v. 1.6.12 was used to construct the ML tree (Nguyen et al. 2015), and node confidence was assessed with 500,000 replications for bootstrap (Hoang et al. 2018). The phylogenetic trees were constructed using two datasets, PCG123 and PCG12. Finally, the generated phylogenetic trees were visualized using the online editing tool Chipolt (https://www.chiplot.online).

Results

Genomic features

The complete mitogenomes of Aeschrocoris tuberculatus (16,134 bp, GenBank accession no. OP56367) and A. ceylonicus (14,142 bp, GenBank accession no. OP56368) were obtained (Fig. 1). The mitogenomes of the two species contain a control region and 37 genes (13 PCGs, 22 tRNA genes, and two rRNA genes). The composition of genes is similar to those described in other pentatomid insects (Lee et al. 2009; Zhao et al. 2017a, 2017b; Chen et al. 2019). In addition, the mitochondrial genomes of both species have similar overlapping regions and gene spacer regions. In A. tuberculatus, the intergenic overlap region is 34 bp in length and contains seven overlapping regions of 1–8 bp in length. The longest overlapping regions are located between trnW/trnC and nad6/cytb. The intergenic spacer is 127 bp in length and contains 17 spacers ranging from 1 to 25 bp in size. The longest spacer (25 bp) is located between trnS2 and nad1. In A. ceylonicus, seven intergenic overlapping regions were examined with varying lengths of 1–8 bp, and the longest overlapping region is at the same position (between trnW and trnC, nad6, and cytb) as in A. tuberculatus. The intergenic spacers are the same in A. ceylonicus as in A. tuberculatus, and the longest spacer (33 bp) region is also situated between trnS2 and nad1 (Table 2).

Table 2.
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Organization of the mitochondrial genomes of Aeschrocoris tuberculatus and A. ceylonicus.

A. tuberculatus A. ceylonicus
Gene Strand Anticodon Position Size (bp) Initiation codon Stop codon Intergenic nucleotide Position Size (bp) Initiation codon Stop codon Intergenic nucleotide
trnI J GAT 1–71 71 0 1–71 71 0
trnQ N TTG 80–148 69 8 79–147 69 7
trnM J CAT 154–224 71 5 152–222 71 4
nad2 J 225–1208 984 ATA TAA 0 226–1206 981 ATA TAA 3
trnW J TCA 1226–1292 67 17 1223–1290 68 16
trnC N GCA 1285–1352 68 –8 1283–1350 68 –8
trnY N GTA 1366–1434 69 13 1364–1429 66 13
cox1 J 1450–2986 1537 TTG T 15 1445–2981 1537 TTG T 15
trnL2 J TAA 2987–3053 67 0 2982–3048 67 0
cox2 J 3054–3732 679 ATA T 0 3049–3727 679 ATA T 0
trnK J CTT 3733–3804 72 0 3728–3799 72 0
trnD J GTC 3808–3873 66 3 3803–3869 67 3
atp8 J 3874–4035 162 TTG TAA 0 3870–4031 162 TTG TAA 0
atp6 J 4029–4701 673 ATG T –7 4025–4697 673 ATG T –7
cox3 J 4702–5490 789 ATG TAA 0 4698–5486 789 ATG TAA 0
trnG J TCC 5490–5555 66 –1 5486–5550 65 –1
nad3 J 5556–5909 354 ATT TAA 0 5551–5904 354 ATT TAA 0
trnA J TGC 5914–5982 69 4 5909–5977 69 4
trnR J TCG 5991–6058 68 8 5988–6056 69 10
trnN J GTT 6064–6131 68 5 6061–6128 68 4
trnS1 J GCT 6133–6202 70 1 6130–6199 70 1
trnE J TTC 6207–6275 69 4 6200–6269 70 0
trnF N GAA 6274–6341 68 –2 6268–6335 68 –2
nad5 N 6346–8052 1707 ATG TAA 4 6340–8046 1707 ATG TAA 4
trnH N GTG 8055–8123 69 2 8049–8117 69 2
nad4 N 8127–9455 1329 ATG TAA 3 8121–9449 1329 ATG TAA 3
nad4l N 9449–9736 288 ATT TAA –7 9443–9730 288 ATT TAA –7
trnT J TGT 9739–9807 69 2 9733–9801 69 2
trnP N TGG 9808–9871 64 0 9802–9865 64 0
nad6 J 9880–10353 474 ATA TAA 8 9868–10347 480 TTG TAA 2
cytb J 10346–11482 1137 ATG TAA –8 10340–11476 1137 ATG TAA –8
trnS2 J TGA 11482–11550 69 –1 11476–11534 68 –1
nad1 N 11576–12499 924 TTG TAG 25 11568–12491 924 TTG TAG 33
trnL1 N TAG 12500–12565 66 0 12492–12557 66 0
rrnL N 12566–13874 1309 0 12558–13859 1302 0
trnV N TAC 13875–13942 68 0 13860–13927 68 0
rrnS N 13943–14751 809 0 13928–14740 813 0
OH J 14752–16134 1383 0 14741–16142 1402 0
Figure 1. 

Mitochondrial genome structure of Aeschrocoris tuberculatus and A. ceylonicus. Arrows indicate the orientation of gene transcription. PCGs are shown as blue arrows; tRNAs are named using single-letter amino acid abbreviations.

Nucleotide composition and codon usage

The nucleotide composition of two species shows the predominance of A+T in the complete mitochondrial genome (Table 3). The order of base composition of the entire sequence in A. tuberculatus and A. ceylonicus is A (42.32%) > T (31.55%) > C (15.20%) > G (10.94%) and A (42.36%) > T (31.72%) > C (14.94%) > G (10.98%), respectively. This bias was observed in the complete mitochondrial genome. The A+T content of the two species is 73.09% and 72.79% in PCGs, 76.11% and 76.63% in tRNAs, 75.97% and 76.60% in rRNAs and 73.99% and 77.35% in the control region, respectively. The complete genomes of both also show a clear AC skew (GC skew = –0.16, AT skew = 0.15, GC skew = –0.15, and AT skew = 0.14), suggesting a greater abundance of A than T and a higher abundance of C than G.

Table 3.
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Nucleotide composition of the mitogenomes of Aeschrocoris tuberculatus and A. ceylonicus.

A. tuberculatus
Feature Length (bp) A% C% G% T% A+T% AT-skew GC-skew
Whole genome 16134 42.32 15.20 10.94 31.55 73.86 0.15 –0.16
PCGs 11036 32.63 13.54 13.37 40.46 73.09 –0.11 0.01
tRNA 1503 38.39 10.18 13.71 37.72 76.11 0.01 0.15
rRNA 2118 32.39 8.40 15.63 43.58 75.97 –0.15 0.30
Control region 1383 38.41 14.49 11.52 35.58 77.99 0.04 –0.11
A. ceylonicus
Feature Length (bp) A% C% G% T% A+T% AT-skew GC-skew
Whole genome 16142 42.36 14.94 10.98 31.72 74.08 0.14 –0.15
PCGs 11040 32.40 13.65 13.56 40.39 72.79 –0.11 0.00
tRNA 1502 38.08 9.85 13.52 38.55 76.63 –0.01 0.16
rRNA 2115 32.77 8.32 15.08 43.83 76.60 –0.14 0.29
Control region 1402 39.40 12.58 10.06 37.96 77.35 0.02 –0.11

The composition of nucleotides is also reflected in the use of codons. The RSCUs of the two species show some differences and are compared to each other in Fig. 2. The most frequently used codons are UUA (Leu2), and most of the codons with high frequency ended in A/T. These results indicate that in the codon composition of Aeschrocoris mitogenomes, AT was superior to GC.

Figure 2. 

Relative synonymous codon usage (RSCU) within Aeschrocoris tuberculatus and A. ceylonicus. Codon families are shown on the x-axis and the frequency of RSCU on the y-axis.

Protein-coding genes

The length of PCGs in A. tuberculatus and A. ceylonicus is 11,036 bp and 11,040 bp, respectively. For the 13 PCGs, nine (cox1, cox2, cox3, atp6, atp8, nad2, nad3, nad6, and cytb) are encoded on the major strand (J-strand), whereas the other four are encoded on the minor strand (N-strand). The typical ATN (five with ATG, three with ATA, and two with ATT) are used as the start codon in most PCGs of these species, except for the atp8, nad1, and cox1 genes, which use TTG as the start codon. cox1, cox2, and atp6 sequences terminate with a single T, the terminal codon of nad1 sequences is TAG, and the stop codon for the remaining genes was TAA.

In addition, we calculated non-synonymous substitutions (Ka), synonymous substitutions (Ks), and Ka/Ks ratios for the 13 PCGs of the Pentatomoidea (Fig. 3), and the evolutionary rates of the 13 PCGs are compared. The results clearly show that atp8 evolved at the fastest rate (Ka/Ks = 0.75), cox1 evolved at the slowest rate (Ka/Ks = 0.06), and the other genes evolved in the order of nad6 > nad2 > nad4 > nad5 > nad4l > atp6 > nad3 > nad1 > cox2 > cox3 > cytb. Furthermore, all 13 PCGs have Ks values greater than Ka values and Ka/Ks ratios less than 1, indicating that these genes are affected by purifying selection.

Figure 3. 

Evolutionary rates of 13 PCGs in Pentatomoidea. Rate of non-synonymous substitutions (Ka), rate of synonymous substitutions (Ks), and ratio of rate of non-synonymous substitutions to rate of synonymous substitutions (Ka/Ks) are calculated for each PCG.

Transfer and ribosomal RNAs

The total lengths of the tRNAs of A. tuberculatus and A. ceylonicus are 1,503 bp and 1,502 bp, respectively. And the length of tRNA genes are from 64 bp to 72 bp. Fourteen genes (trnA, trnE, trnD, trnG, trnK, trnI, trnL2, trnM, trnN, trnR, trnS1, trnS2, trnT, and trnW) are located on the J-strand, and other eight genes on the N-strand. Only trnS1 lacks a dihydrouridine (DHU) arm; the other tRNA genes all have the classic cloverleaf secondary structure. In addition to the typical base pairs (A-U and G-C), some wobble G-U pairs appear in these secondary structures, which can form stable chemical bonds between G and U (Fig. 4).

Figure 4. 

Predicted secondary structure of tRNA genes in Aeschrocoris tuberculatus. Conserved sites in Pentatomoidea are marked orange. Nonconserved sites in A. tuberculatus and A. ceylonicus are marked blue.

The rrnL and rrnS genes have the same situation in the two species. The rrnL gene is located between trnL1 (CUN) and trnV, and the rrnS gene is located between trnV and the control region; they are encoded on the N-strand. The lengths of the two genes in A. tuberculatus are 1,309 bp (rrnL) and 809 bp (rrnS); the complete secondary structures are shown in Figs 5, 6. In A. ceylonicus, the two genes are 1,302 bp (rrnL) and 813 bp (rrnS) in length. The order of the base content of the rRNA genes is T (43.58%) > A (32.39%) > G (15.63%) > C (8.40%) and T (43.83%) > A (32.77%) > G (15.08%) > C (8.32%), respectively. The AT-skews are negative, and the GC-skews are positive.

Figure 5. 

Predicted secondary structure of the rrnL in Aeschrocoris tuberculatus. Conserved sites in Pentatomoidea are marked orange. Nonconserved sites in A. tuberculatus and A. ceylonicus are marked blue.

Figure 6. 

Predicted secondary structure of the rrnS in Aeschrocoris tuberculatus. Conserved sites in Pentatomoidea are marked orange. Nonconserved sites in A. tuberculatus and A. ceylonicus are marked blue.

The control region

The control is the main regulatory region for replication and transcription of the mitochondrial genome (Taanman 1999; Stewart and Beckenbach 2006; Cameron 2014). The variation in length of the control region is mainly caused by the lengths and numbers of repeating units. In conclusion, the sequence and structure of the mitochondrial control region is highly variable in Hemiptera (Moreno et al. 2010). The control region of A. tuberculatus, located between rrnS and trnI genes, is 1,383 bp in length, and the A + T content is 73.99%. The length of the control region of A. ceylonicus, at 1,402 bp, is similar to A. tuberculatus, and the A + T content is 77.35%. Moreover, both species have a variety of different tandem repeat units (Fig. 7).

Figure 7. 

Organization of the control region in the mitochondrial genomes of Aeschrocoris tuberculatus and A. ceylonicus. The tandem repeats are shown by yellow ovals with repeat length inside. CR indicates the length of the sequence of the control region.

Tests of substitution saturation and heterogeneity

Before constructing the phylogenetic tree, we evaluated the substitution saturation of the PCG123 and PCG12 datasets. The results show that the Xia saturation index (Iss) is below the critical values for a symmetric (Iss.cSym) and asymmetric (Iss.cAsym) topology (Fig. 8). Meanwhile, the conversion rate and modified genetic distance both increase linearly, indicating that the nucleotide sequences of two datasets are not saturated.

Figure 8. 

The substitution saturation analysis of two datasets a PCG123 b PCG12.

Our analysis of the heterogeneity of the base composition in the two datasets show that the heterogeneity of PCG123 is higher than in PCG12, thus indicating a higher heterogeneity of the third site of the codon. The degree of heterogeneity between the two datasets is certainly consistent with the construction of a phylogenetic tree, which can be used for phylogenetic analysis (Fig. 9).

Figure 9. 

AliGROOVE analysis of 89 Pentatomoidea species a based on PCG123 b based on PCG12. The mean similarity score between sequences is represented by colored squares, based on AliGROOVE scores ranging from –1, which indicates a great difference in rates from the remainder of the data set (= heterogeneity, red color) to +1, which indicates rates that matched all other comparisons (blue color, as in this case).

Phylogenetic analyses

We constructed phylogenetic trees of Pentatomoidea based on the two datasets using the ML method (Figs 10, 11). The results show that the topological structure of the tree is reliable. The relationship is as follows: (Urostylididae + ((Acanthosomatidae + ((Cydnidae + (Dinidoridae + Tessaratomidae)) + (Scutelleridae + Plataspidae))) + Pentatomidae)). All analyses also show that A. tuberculatus and A. ceylonicus are the earliest diverging lineage within Pentatomidae and cluster as a sister group. The monophyly of Pentatominae and Podopinae is rejected, as both are scattered within the Pentatomidae clade. However, we recovered the monophyly of Asopinae and Phyllocephalinae with strong support values and high internal node support values. The two subfamilies are nested in one of the Pentatominae clades, so the subfamilies of Pentatomidae need further research.

Figure 10. 

Phylogenetic tree using ML analyses based on PCG123. Numbers at the node are bootstrap values.

Figure 11. 

Phylogenetic tree using ML analyses based on PCG12. Numbers at the node are bootstrap values.

Discussion and conclusions

In this study, we sequenced and annotated the complete mitogenomes of Aeschrocoris tuberculatus and A. ceylonicus using NGS technology and Geneious v. 11.0. Our analysis comparing of the mitochondrial genomes of the two species show that the gene arrangement is highly conserved, which is consistent with other published mitochondrial genomes of Hemiptera (Hua et al. 2008; Lee et al. 2009; Song et al. 2013). The lengths of the mitochondrial genomes of A. tuberculatus and A. ceylonicus are 16,134 bp and 16,142 bp, respectively. There were four overlapping regions in the mitochondrial genome of these two species. The positions of their overlapping regions re identical. One of the longest overlaps, located between trnW and trnC, is 8 bp in length, and the overlapping bases are AAGCTTTA, which is common in pentatomid species (Yuan et al. 2015; Zhao et al. 2019a). The other two pairs of genes, namely atp8/atp6 and nad4/nad4l, overlap by 7 bp, and both overlapping bases are ATGATAA. Specifically, an overlap of 8 bp between nad6 and cytb was also observed, and the overlapping bases are ATGAATAA. This is different from that found in previous studies on Pentatomidae. Between trnS2 and nad1, the longest spacer region appeared in both, which is consistent with the findings of other studies (Hua et al. 2008; Zhao et al. 2019a). The difference of mitogenome size between A. tuberculatus and A. ceylonicus is due to the length difference of the noncoding region.

In most Pentatomidae mitochondrial genomes, only cox1 has TTG as its start codon, and the remaining 12 PCGs use ATN as their start codon (Hua et al. 2008; Li et al. 2012). However, there is a difference between A. tuberculatus and A. ceylonicus in that nine PCGs have the same start codons ATN, and four PCGs (nad1, cox1, atp8, and nad6) use TTG as the start codon. Most PCGs use the TAA as the stop codon; nevertheless, in some insects, nad1, cox2, and some other genes use the single T or TAG as the stop codon (Liu et al. 2012; Song et al. 2013). In this study, our results show most PCGs stop with TAA, and three PCGs (cox1, cox2, and atp6) stop with a single T. However, one PCG (nad1) stops with TAG. In PCGs, cox1 is commonly used for barcode analysis and genus or species identification due to its slow rate of evolution (Hebert et al. 2004).

The composition of the four bases in A. tuberculatus and A. ceylonicus is A>T>C>G. There is a clear AT preference in nucleotide composition. Most tRNAs have the typical cloverleaf secondary structure as observed in Hemiptera. However, the lack of a DHU arm in the trnS1 is common in hemipteran mitogenomes (Wolstenholme 1992; Shi et al. 2012). rrnL and rrnS in A. tuberculatus and A. ceylonicus lie between trnL1 (CUN) and trnV, and between trnV and the control region, respectively. In Pentatomoidea, rrnS contains 19.37% conserved sites and included three domains. The rrnL contains 26.81% conserved sites and six domains (domain III is absent), and the IV and V domains are relatively conservative.

Through the topological structure of the trees, the clade including Urostylididae is found to be the earliest clade lineage. It forms a sister group to the other families. The relationship of (Cydnidae + (Dinidoridae + Tessaratomidae)) was recovered in our phylogenetic results with high support; these results are consistent with previous studies (Grazia et al. 2008; Yuan et al. 2015; Wu et al. 2018; Zhao et al. 2018; Xu et al. 2021). Xu et al. (2021) used PCGRNA and PCG12RNA data sets to recover the sister-group relationship of (Plataspidae + Scutelleridae) and (Dinidoridae + Tessaratomidae), and we also obtained this result. Of course, there are still other conclusions to be made based on the phylogenetic studies of Pentatomoidea. Previously, two sister groups (Plataspidae + Pentatomidae) and (Cydnidae + Scutelleridae) were recovered (Zhao et al. 2018; Liu et al. 2019). Possible reasons include, for example, the number of samples, the selection of outliers, the selection of data sets, and the influence of branches. In addition, the saturation and heterogeneity of the third site of PCG has little effect on the topological structure of the trees. In the study of Hemiptera insects, retention of the third site of PCG does not reduce the reliability of the phylogenetic results (Fenn et al. 2008). Although in many studies, the results obtained from different data sets and inference methods show that there are some contradictions among the relationships among families, our results based on more species have higher reliability. This study also confirms that adding more mitochondrial genome sequences is the key to solve the phylogenetic relationships of Pentatomoidea at various different taxonomic levels.

We studied the genus Aeschrocoris at a molecular level for the first time and preliminarily identified its taxonomic position and evolution in phylogenetic relationships. This study not only discusses the relationships among families, but it also adds new molecular data for Pentatomidae. These results demonstrate that mitochondrial genomes can effectively reveal the phylogenetic relationships among differing taxonomic hierarchies. We should sequence more mitochondrial genes to provide greater evidence for exploring the phylogenetic relationships among taxa.

Acknowledgements

This research was funded by the National Science Foundation Project of China (no. 31872272 and 32100370); the Research Project Supported by Shanxi Scholarship Council of China (no. 2020-064 and 2020-065), Natural Science Research General Project of Shanxi Province (No.202103021224331 and 202103021224132).

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