Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

Xiaoke Tian; Yongqin Li; Qin Chen; Qianquan Chen

doi:10.1371/journal.pone.0281597

. 2023 Feb 10;18(2):e0281597. doi: 10.1371/journal.pone.0281597

Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

Xiaoke Tian ¹, Yongqin Li ¹, Qin Chen ¹, Qianquan Chen ^1,^*

Editor: Neelesh Dahanukar²

PMCID: PMC9916562 PMID: 36763628

Abstract

Notobitus montanus Hsiao, 1963 is a major pest of bamboos. The mitogenome of N. montanus (ON052831) was decoded using next-generation sequencing. The mitogenome, with 42.26% A, 30.54% T, 16.54% C, and 10.65% G, is 16,209 bp in size. Codon usage analysis indicated that high frequently used codons used either A or T at the third position of the codon. Amino acid usage analysis showed that leucine 2, phenylalanine, isoleucine and tyrosine were the most abundant in 31 Coreoidea species. Thirteen protein-coding genes (PCGs) were evolving under purifying selection, nad5 and cox1 had the lowest and strongest purifying selection stress, respectively. Correlation analysis showed that evolutionary rate had positive correlation with A+T content. No tandem repeat was detected in the non-coding region of N. montanus. The phylogenetic tree showed that Alydidae and Coreidae were not monophyletic. However, the topology of phylogenetic trees, based on 13 PCGs, was in accordance with that of tree based on both mitochondrial and nuclear genes but not ultraconserved element loci or combination of 13 PCGs and two rRNAs. It seems that their relationships are complex, which need revaluation and revision. The mitogenomic information of N. montanus could shed light on the evolution of Coreoidea.

Introduction

Leaf-footed bugs, hemipteran superfamily Coreoidea, are phytophagous insects which consist of several forest and agricultural pests [1, 2]. For example, Notobitus montanus Hsiao, 1963 is a major pest of bamboos, which not only supply human with foods, building materials, crafts, and high-quality paper, but also are involved in landscaping and soil conservation [3]. It distributes in many southern provinces of China, such as Zhejiang, Sichuan, Yunnan, Guizhou, which serves as the pest of serval species of bamboo, including, Phyllostachys sulphurea var. Viridis, Phyllostachys glauca, Phyllostachys heteroclada, Phyllostachys bambusoides f. shouzhu, Phyllostachys heteroclada var. pubescens, Pleioblastus amzrus, Phyllostachys praecox f. provernalis [4]. The adults and nymphs of N. montanus feed on the sap of bamboo shoot and young bamboo, making bamboo falls into a decline and even dead. A female can lay 20–70 eggs, and the egg hatchability is high. Eggs take up 15–20 days to develop as nymphs, and then nymphs take up 30–50 days to develop as adult, which can live for 330–350 days [4]. Due to its high reproduction, strong ability of flying and gregariousness, N. montanus can cause serious economic loss of bamboo [5]. For example, in 1973, 90% of bamboo shoots were attacked by it in Liangping count, Sichuan province, leading 16.4% bamboo shoots dead [4]. Currently, approximately 30 Coreoidea species are recorded as the pest of bamboo.

In addition to two extinct families (Trisegmentatidae and Yruipopovinidae), Coreoidea consists of five families: Coreidae (2571 species), Alydidae (282 species), Rhopalidae (224 species), Stenocephalidae (30 species) and Hyocephalidae (three species) [1, 6, 7]. The Coreidae is divided into four subfamilies: Coreinae, Hydarinae, Meropachyinae, and Pseudophloeinae [6, 7]. Coreinae, with 2,320 (90%) species (372 genera), is the largest subfamily of Coreidae. In the past, the taxonomic classification of Coreidae was mainly based on morphological traits such as apical spine or tooth on the hind tibiae, hind femora, and metathoracic scent gland orifices [8]. The phylogenetic relationships among the tribal rank taxa of Coreidae have not been investigated comprehensively since 1997 [8, 9]. However, some studies indicated that these morphological traits exhibited homoplasy [1, 9], which might explain contradictory results from different studies [1]. Phylogenomic trees constructed with ultraconserved element loci and mitogenome showed that both Coreidae and Alydidae were not monophyly [1, 6]. Furthermore, the phylogenomic analysis showed that several genera, and subfamilies of Coreidae were para- and polyphyly, which suggested that the taxonomic classification of Coreidae need revaluation and revision [9]. In short, leaf-footed bugs’ phylogenetic relationships have remained far from solved [1].

Animal mitochondrial genome (mitogenome) is a circular double-stranded DNA molecule. Generally, it encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), and 22 transfer RNA (tRNAs) [10]. In addition, it contains a non-coding control region (A+T-rich region, D-loop), which contains essential regulatory elements for replication and transcription [11]. Owing to the lack of protection of histones, mitogenomic DNA has a much higher mutation frequency than nuclear DNA. As a result, mitogenomes are widely used in phylogenetics, phylogeography, population genetics, and evolutionary biology [12, 13]. With the development of next-generation sequencing (high-throughput sequencing), many mitogenomes have been decoded using this technique.

In this work, the mitogenome of N. montanus has been decoded. The characteristics of the mitogenome, including nucleotide composition, codon usage, tRNA secondary structure, and the evolutionary pattern of 13 PCGs, were systematically analyzed. The phylogenetic tree of Coreoidea was constructed with the new mitogenome and 30 mitogenomes extracted from NCBI (S1 Table). The mitogenome could shed light on the evolution of Coreoidea.

Materials and methods

Samples and identification

Notobitus montanus is a common pest of bamboos in China as well as not recorded in the species list-of-ethics committees for research involving animals of the Guizhou Normal University. Therefore, no ethical approval or other relevant permission can be provided for the study. Specimens of N. montanus were collected from the campus of Guizhou Normal University (26°22′50.30″N, 106°38′11.72″E) in July 2021. All specimens were identified from their morphological characteristics. Total DNA was then extracted from the muscle tissue of an adult specimen with the phenol-chloroform extracting method [14, 15]. The fragment of mitochondrial cytochrome c oxidase subunit I gene (cox1) was amplificated with primers (LCO1490 and HCO2198) [16]. The PCR productions were checked by agarose gel electrophoresis and sequenced by sanger sequencing. The sequence was submitted to BOLD systems v4 (http://www.boldsystems.org/) as a query for species identification. The similarity between the query sequence and reference sequence of N. montanus in the BOLD was 99.77%. The specimens (specimen ID: GZNU-cqq-136) were soaked in absolute alcohol and then stored at 4°C in the Museum of Guizhou Normal University.

Next-generation sequencing, annotation, and bioinformatics analysis

Total DNA was isolated from the muscle tissue of an adult specimen with ONE-4-ALL Genomic DNA Mini-Prep Kit (BS88504, Sangon, Shanghai, China). DNA was fragmented, then ~500 bp DNA was recycled. Paired-end libraries were constructed with the Illumina platform. The DNA was sequenced using the Illumina Hiseq X Ten at the Sangon Biotechnology Company (Shanghai, China). The adapter sequences were removed, and low-quality reads were trimmed with Trimmomatic version 0.36 [17]. The mitogenome of Cloresmus pulchellus (NC_042806) was used as reference, and clean reads were assembled with SOAPdenovo2 (version 2.04) [18]. PCGs were identified by BLAST comparison with C. pulchellus mitogenome [19]. The secondary structures of tRNAs were predicted with MITOS2 and tRNAscan-SE 2.0 [20, 21], rRNAs and non-coding control region were determined by the boundary of tRNAs. Nucleotide composition was calculated with MEGA X [22]. The AT-skew values were calculated by the following formula: AT-skew = (A—T)/(A + T). Similarly, GC-skew values were calculated by GC-skew = (G—C)/(G + C). Codon usage indexes, including codons counts, and relative synonymous codon usage (RSCU), were calculated with MEGA X [22]. The number of nonsynonymous substitutions per nonsynonymous site (Ka), and the number of synonymous substitutions per synonymous site (Ks) were calculated with DnaSP 6 [23]. Tandem repeats in the non-coding control region were identified using tandem repeats online finder server [24]. Circular map of the N. montanus mitogenome was generated with CGView server [25]. Heatmap of codon and amino acid usage was generate with ggplot2 as implemented in R v4.1.2. Figures were edited with Adobe Illustrator CS5.

Phylogenetic analysis

The mitogenomes of N. montanus and 30 available complete mitogenomes of Coreoidea in NCBI were used to construct the phylogenetic tree of Coreoidea (S1 Table). Malcus inconspicuus (Hemiptera: Malcidae), Physopelta gutta (Hemiptera: Largidae), and Nezara viridula (Hemiptera: Pentatomidae) were selected as representative of the outgroups. These mitogenomes were imported into PhyloSuite V1.2.2 [26]. Then the nucleic acid sequences of 13 PCGs were extracted from these mitogenomes. Codon-based multiple alignments were carried out with MAFFT as implemented in PhyloSuite [26]. Then alignments of 13 PCGs were concatenated. PartitionFinder2 was used to select the best-fit partitioning strategy and models for the concatenated sequences. Phylogenetic trees were reconstructed by the Bayesian (Mrbayes v 3.2.6) and maximum likelihood (IQ-TREE v1.6.8) method as implemented in PhyloSuite [26]. The number of generations was 10, 000, 000 and Partition Models were selected as models. The phylogenetic tree was visualized with Figtree v1.4.4 and Adobe Illustrator CS5.

Results

Genomic structure and nucleotide composition

The complete mitogenome of N. montanus (ON052831) was 16209 bp, which encoded 13 PCGs, 22 tRNAs, two rRNAs, and a non-coding control region (D-loop) (Fig 1 and S2 Table). Fourteen genes, including four PCGs, eight tRNAs, and two rRNAs, were encoded by the minority strand (N strand), and the remaining genes were encoded by the majority strand (J strand). The gene arrangement of N. montanus was in accordance with that of other Coreoidea species [19, 27]. A total of 39 bp intergenic spacers were distributed across eight locations. The shortest intergenic spacers were one bp, and the longest intergenic spacer which was located between trnS2 and nad1, was 21 bp. A total of 28 bp overlaps were distributed across seven locations. The shortest overlaps were one bp, and the longest overlap was eight bp which was located between trnW and trnC. two seven bp overlaps were located between atp8 and atp6, between nad4 and nad4L.

The mitogenome consisted of 42.26% A, 30.54% T, 16.54% C and 10.65% G (S3 Table). The A+T content of the whole genome, PCGs, tRNAs, rRNAs and non-coding control region was 72.81%, 72.79%, 75.35%, 75.59% and 67.17%, respectively. It seemed that the name of A-T rich region was not suitable for non-coding control region. The AT-skew value was 0.161, and the GC-skew value was -0.220, which indicated that the mitogenome had a preference to A and C. The AT-skew of Coreidae species ranged from 0.097 (Leptoglossus membranaceus) to 0.176 (Acanthocoris sp. FS-2019), and GC-skew ranged from -0.253 (Hydaropsis longirostris) to -0.187 (Clavigralla tomentosicollis), which indicated A and C were more abundant than T and G in Coreidae species, respectively.

Protein-coding genes

The total length of 13 PCGs of N. montanus was 11047 bp (S2 Table), accounting for 72.79% of the whole genome, which was medium size in Coreidae species (from 11020 bp to 11110 bp). For all Coreidae species, all AT-skew values were positive, and GC-skew values were positive except for Leptoglossus membranaceus (-0.008) and Notopteryx soror (-0.001). Four PCGs, including nad1, nad4, nad4L, and nad5, were encoded by the N strand, and the remaining nine PCGs were encoded by the J strand (Fig 1 and S2 Table). In N. montanus, cox1 used TTG as start codon, however, the remaining 12 PCGs used ATN as start codon (ATA for atp8, nad3, and nad6; ATC for cox2; ATG for atp6, cox1, cox3, nad2, nad4, nad5, and cytb; ATT for nad1, and nad4L). Five PCGs, including atp8, atp6, nad5, nad4, and nad4L, used TAA as stop codon; however, two PCGs (nad3, and nad6) and six PCGs (cox1, cox2, cox3, cytb, nad1, and nad2) used TA and T as incomplete stop codon, respectively (S2 Table).

Relative synonymous codon usage (RSCU) analysis of N. montanus showed that a total of 62 codons were used, except for two stop codons (UAA and UAG) (S4 Table). The highest frequent four codons were UUA (264), UUU (251), AAU (243), and AUA (204), which accounted for 26.13% total number of codons. These codons were composed of either A or U. On the contrary, high G+C contents codons, including GCG (2), CGC (3), and CGG (4), were the lowest frequent codons. For codons with RSCU values more than one, they were more likely to use either A or T rather than either G or C at the third position of the codon (Fig 2A and 2B). The heatmap of codon usage for 31 Coreoidea species showed that codons used either A or T at the third position of the codon which were more frequently used than these used either G or C.

Fig 2 — (A) Relative synonymous codon usage (RSCU) of N. *montanus*. (B) Heatmap indicates codon usage in 31 Coreoidea species. (C) Heatmap indicates amino acid usage in 31 Coreoidea species.

For amino acids, leucine 2, phenylalanine, isoleucine, methionine, tyrosine, and asparagine, were the most abundant in N. montanus, which accounted for 9.92%, 8.92%, 8.86%, 7.52%, 6.96% and 6.15% the total number of amino acids, respectively (Fig 2C). The heatmap of amino acid usage for 31 Coreoidea species showed that leucine 2, phenylalanine, isoleucine and tyrosine were the most abundant, and the abundance variation was small. However, the abundance of methionine and asparagine had larger variation among species than that of leucine 2, phenylalanine, isoleucine and tyrosine. Furtherly, there was a linear correlation between the effective number of codons (ENc) and the G+C content of 13 PCGs (S1 Fig). Specifically, ENc had a better linear correlation with the G+C content of the third position of the codon than the remaining positions.

Nad5 and cytb had the lowest and highest Ks values, respectively (Fig 3). Cox1 had the lowest value of Ka and Ka/Ks, atp8 had the highest value of Ka, and nad5 the highest value of Ka/Ks (Fig 3). The value of Ka/Ks for 13 PCGs was less than 1, which indicated that all PCGs were evolving under purifying selection. There were negative correlations between the value of Ka/Ks and G+C contents (S2 Fig).

Transfer RNA and ribosomal RNA genes

The total length of 22 tRNAs of N. montanus was 1444 bp. The shortest tRNAs were 63 bp (trnI, trnC, trnY, trnD, trnG, trnA, trnT and trnP), while the longest tRNA was 75 bp (trnK). The total A+T content of tRNAs was 75.35%. The AT-skew value was 0.079, and the GC-skew value was -0.096. Eight tRNAs (trnQ, trnC, trnY, trnF, trnH, trnP, trnL, and trnV) were encoded by the N strand, and the remaining tRNAs were encoded by the J strand (Fig 1 and S2 Table). The distribution pattern of tRNAs in the mitogenome was in accordance with that of other Coreidae species.

For secondary structure, trnS1 lacked a dihydrouridine (DHU) arm (Fig 4). The remaining tRNAs had a typical cloverleaf secondary structure. Non-Watson-Crick base pairing (G-U pairing) appeared in the acceptor stem of trnA, trnH and trnV. G-U pairing also appeared in the anticodon arm of trnV, and the TΨC arm of trnS1 and trnV. Four tRNAs (trnC, trnH, trnT, and trnS2) used U as the discriminator nucleotide, and the remaining 18 tRNAs used A as the discriminator nucleotide.

The mitogenome of N. montanus encoded two rRNAs. RrnL (16s rRNA) was 1281 bp which was located between trnL1 and trnV, and rrnS (12s rRNA) was 784 bp which was located between trnV and the non-coding control region. Both were encoded by the N strand (S2 Table). The A+T content of rRNAs was 75.59%, the AT-skew value was 0.213, and the GC-skew value was -0.310 (S3 Table).

Non-coding control region

The non-coding control region (D-loop) of N. montanus, located between 12s rRNA and trnI, was 1642 bp (Fig 5). Its position in the mitogenome was accordance with that of other Coreidae species [6]. The A+T content of D-loop was 67.17%. AT-skew value was 0.081, and GC-skew value was -0.328 (S3 Table). Among the 15 Coreidae species, the length of D-loop ranged from 794 bp (Cletus rubidiventris) to 3441 bp (C. pulchellus), which made significant contribution to the size variation of mitogenome (Fig 5) [28]. No tandem repeat was detected in the non-coding region of N. montanus (Fig 5). Similar phenomenon was occurred in Hydaropsis longirostris, Pseudomictis tenebrosa, Manocoreus sp. However, most Coreidae species had tandem repeats in their non-coding control region. For Coreidae species, the shortest tandem repeat unit in D-loop was seven bp (Molipteryx lunata), and the longest tandem repeat unit was 369 bp (C. pulchellus) (Fig 5).

Phylogenetic relationship

Phylogenetic analyses were carried out with nucleotide sequences of 13 PCGs extracted from 31 mitogenomes of Coreoidea (S1 Table). The topologies of Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees, with high support scores at most nodes, were identical except for Alydinae (Fig 6 and S3 Fig). Bayesian tree showed that five Alydinae species’ relationship was (((Megalotomus costalis + Riptortus pedestris) + Camptopus lateralis) + (Daclera levana + Melanacanthus marginatus)). However, maximum likelihood tree showed that their relationship was ((((Camptopus lateralis + Riptortus pedestris) + Melanacanthus marginatus) + Daclera levana) + Megalotomus costalis). Compared with maximum likelihood tree, Bayesian tree had higher support scores.

Fig 6 — The tree is constructed with nucleotide sequences of 13 mitochondrial PCGs. For family, Black, red, orange, purple and dark blue represents outgroup, Stenocephalidae, Rhopalidae, Alydidae and Coreidae, respectively. For subfamily, orange, bright red, wathet blue, green, bright green, and bright blue represents Rhopalinae, Micrelytrinae, Hydarinae, Pseudophloeinae, Alydinae, and Coreinae, respectively. The posterior probabilities were labeled at each node.

Stenocephalidae had a sister group relationship with the remaining families of Coreoidea (PP = 1, BS = 98.60). Stenocephalidae and Rhopalidae, were monophyly; however, Alydidae and Coreidae were not monophyly (Fig 6). At subfamily level, Alydinae and Coreinae showed monophyly with high support (PP = 1, BS>97). Their relationship was (((((Alydinae + Pseudophloeinae) + Hydarinae) + Micrelytrinae) + Coreinae) + Rhopalinae). At present, Coreinae have 13 genera with complete mitogenomic information, their relationship was (Manocoreus + (Enoplops + Cletus)) + (((Acanthocoris + (Notobitus + Cloresmus)) + (Leptoglossus + (Mictis + (Pseudomictis + (Anoplocnemis + (Molipteryx + (Notopteryx + Cletomorpha))))))).

Discussion

Two seven bp overlaps were detected in PCGs, including between atp8 and atp6, between nad4 and nad4L. These two overlaps are popular in arthropods [14, 15, 29]. The A+T content of PCGs was 75.79%, the AT-skew value was -0.116, and the GC-skew value was -0.004 (S3 Table). It seemed that PCGs had a preference to T than A, and no obvious preference between G and C. In N. montanus, only cox1 used TTG as start codon, and the remaining 12 PCGs used ATN as start codon. Our results are in accordance with that most PCGs use ATN as start codon in metazoan [10]. TTG is usually used as start codon for cox1 in animals [30, 31]. Eight PCGs used TA (nad3 and nad6) or T (cox1, cox2, cox3, cytb, nad1, and nad2) as incomplete stop codon. Incomplete stop codons are usually used in metazoan, which can be added with either A or AA by post-transcriptional polyadenylation [10, 13]. Relative synonymous codon usage (RSCU) analysis of N. montanus showed that they were more likely to use either A or T rather than either G or C at the third position of the codon. For 31 Coreoidea species, they preferred to use codons which used either A or T at the third position of the codon than codons which used either G or C at the third position of the codon. Furtherly, there was a positive correlation between the effective number of codons (ENc) and the G+C content of 13 PCGs (S1 Fig). Taken together, G+C content could influence codon usage [32, 33]. The value of Ka/Ks for 13 PCGs was less than 1, which indicated that all PCGs were evolving under purifying selection. As a result, all PCGs could be used to construct phylogenetic tree. Nad5 had the highest value of Ka/Ks, which suggested that nad5 had the fastest evolutionary rate in all PCGs. Cox1, with the lowest value of Ka/Ks, had the strongest purifying selection stress. Cox1 is suitable for barcoding marker. Correlation analysis indicated that the value of Ka/Ks had a negative correlation with G+C content (S2 Fig). In short, G+C content not only influences codon usage but also evolutionary rate.

The AT-skew value was 0.079, and the GC-skew value was -0.096, which indicated that tRNAs had a weak preference to A and C. Most tRNAs had the typical cloverleaf secondary structure, but trnS1 lacked a dihydrouridine (DHU) arm. Previous studies reveal that the phenomenon of trnS1 lacking DHU arm is popular in insects [34]. Four tRNAs (trnC, trnH, trnT, and trnS2) used U as the discriminator nucleotide, and the remaining 18 tRNAs used A as the discriminator nucleotide. This phenomenon occurs in other insects, such as Dinorhynchus dybowskyi (NC_037724) [29]. Non-Watson-Crick base pairing (G-U pairing) appeared in the acceptor stem, anticodon arm and TΨC arm of tRNAs. Non-Watson-Crick base pairing in tRNA could increase the stability of tRNAs, which is popular in insects [13]. The A+T content of rRNAs was 75.59%, the AT-skew value was 0.213, and the GC-skew value was -0.310 (S3 Table). It seemed that rRNAs had similar A+T content with tRNAs, however, rRNAs had stronger preference to A and C than tRNAs.

The position of non-coding control region (D-loop) in N. montanus was accordance with that of other Coreidae species [6]. The A+T content of D-loop was 67.17%, which was lower than PCGs, tRNAs and rRNAs. It seems that the name of A-T rich region is not suitable for non-coding control region. AT-skew value was 0.081, and GC-skew value was -0.328 (S3 Table), which suggested that non-coding control region had a weak preference to A but had a strong preference to C. The length of non-coding control region ranged from 794 bp (Cletus rubidiventris) to 3441 bp (C. pulchellus) in 15 Coreidae species, which made significant contribution to the size variation of mitogenome (Fig 5) [28]. No tandem repeat was detected in the non-coding region of N. montanus (Fig 5). Similar phenomenon was occurred in Hydaropsis longirostris, Pseudomictis tenebrosa, Manocoreus sp [34]. Most Coreidae species had tandem repeats in their non-coding control region. For Coreidae species, the shortest tandem repeat unit was seven bp (Molipteryx lunata), and the longest tandem repeat unit was 369 bp (C. pulchellus) (Fig 5), which might influence mitochondrial replication and post-transcriptional modifications [10, 13]. High frequent mutations were occurred in the D-loop, making region was variable in both size and nucleotide sequence [28].

Coreoidea consists of five extant families: Coreidae, Alydidae, Rhopalidae, Stenocephalidae and Hyocephalidae [1, 6, 7]. Currently, no mitogenome of Hyocephalidae species is available in NCBI, as a result, only four families were analyzed in the study. Stenocephalidae had a sister group relationship with the remaining families of Coreoidea (PP = 1, BS = 98.60), which was consistent with the previous study [6]. Stenocephalidae and Rhopalidae, were monophyly; however, Alydidae and Coreidae were not monophyly (Fig 6), which was in accordance with previous studies [1, 6].

At subfamily level, Alydinae and Coreinae showed monophyly with high support (PP = 1, BS>97). Our phylogenetic tree, based on 13 PCGs, showed that their relationship was (((((Alydinae + Pseudophloeinae) + Hydarinae) + Micrelytrinae) + Coreinae) + Rhopalinae). One study, based on 13 PCGs and 2 rRNAs showed their relationship was ((((Coreinae + Hydarinae) + Micrelytrinae) + (Alydinae + Pseudophloeinae)) + Rhopalinae) [6]. Another study, based on ultraconserved element loci showed their relationship was ((((Micrelytrinae + Hydarinae) + (Alydinae + Pseudophloeinae)) + Coreinae) + Rhopalinae) [1]. Rhopalinae was a sister group of the remaining five subfamilies in common. In addition, Alydinae had a closer relationship with Pseudophloeinae than the remaining subfamilies. Our tree showed that Coreinae was a sister group of the remaining four subfamilies, including Alydinae, Pseudophloeinae, Hydarinae, Micrelytrinae, which was consistent with the tree based on ultraconserved element loci but not the tree based on 13 PCGs and 2 rRNAs. Previous study indicated that the sequence of rRNAs was not suitable for phylogenetic tree reconstruction [34]. However, the topology of our tree was in accordance with that of tree based on both mitochondrial and nuclear genes [35] but not ultraconserved element loci [1]. It seems that their relationships are complex, and their relationships need revaluation and revision [9].

At present, Coreinae have 13 genera with complete mitogenomic information, their relationship was (Manocoreus + (Enoplops + Cletus)) + (((Acanthocoris + (Notobitus + Cloresmus)) + (Leptoglossus + (Mictis + (Pseudomictis + (Anoplocnemis + (Molipteryx + (Notopteryx + Cletomorpha))))))). Coreinae, with 372 genera, is the largest subfamily of Coreidae. The mitogenome of most genera remains unknown. Owing to a large number of species belonging to Coreinae (2320 species), phylogenetic analysis with ultraconserved elements showed that some genera were not monophyletic [9], which suggested that the relationships among Coreinae species were complex, and need further study. The mitogenomic information of N. montanus could shed light on the evolution of Coreoidea.

Conclusions

This study has decoded the complete mitogenome of N. montanus. Codon usage analysis indicated that high frequently used codons used either A or T at the third position of the codon. Amino acid usage analysis showed that leucine 2, phenylalanine, isoleucine and tyrosine were the most abundant in 31 Coreoidea species. The value of Ka/Ks for 13 PCGs was less than one, which suggested that all PCGs were evolving under purifying selection, Nad5 and Cox1 had the lowest and strongest purifying selection stress, respectively. Correlation analysis showed that A+T content could influence codon usage and evolutionary rate. The phylogenetic tree showed that Alydidae and Coreidae were not monophyletic. However, the topology of phylogenetic trees, based on 13 PCGs, was in accordance that of tree based on both mitochondrial and nuclear genes but not ultraconserved element loci or combination of 13 PCGs and two rRNAs. It seems that their relationships are complex, and their relationships need revaluation and revision. The mitogenomic information of N. montanus could shed light on the evolution of Coreoidea.

Supporting information

S1 Fig. Effective numbers of codons have a positive correlation with the G+C content of codons.

(A) total GC content of codons; (B) GC content of the first position of the codon; (C) GC content of the second position of the codon; (D) GC content of the third position of the codon.

(EPS)

Click here for additional data file.^{(802.7KB, eps)}

S2 Fig. The Ka/Ks has a negative correlation with the G+C content of codons.

(A) total GC content of codons; (B) GC content of the first position of the codon; (C) GC content of the second position of the codon; (D) GC content of the third position of the codon.

(EPS)

Click here for additional data file.^{(828KB, eps)}

S3 Fig. Maximum likelihood phylogenetic tree of 31 Coreoidea species.

The tree is constructed with nucleotide sequences of 13 mitochondrial PCGs. For family, Black, red, orange, purple and dark blue represents outgroup, Stenocephalidae, Rhopalidae, Alydidae and Coreidae, respectively. For subfamily, orange, bright red, wathet blue, green, bright green, and bright blue represents Rhopalinae, Micrelytrinae, Hydarinae, Pseudophloeinae, Alydinae, and Coreinae, respectively. The bootstrap values were labeled at each node.

(EPS)

Click here for additional data file.^{(909.2KB, eps)}

S1 Table. List of species for phylogenetic analysis.

(DOCX)

Click here for additional data file.^{(18.4KB, docx)}

S2 Table. Annotation of the Notobitus montanus mitogenome.

(DOCX)

Click here for additional data file.^{(20.2KB, docx)}

S3 Table. Nucleotide composition of Notobitus montanus (%).

(DOCX)

Click here for additional data file.^{(22.5KB, docx)}

S4 Table. Codon usage in the mitochondrial genome of Notobitus montanus.

(DOCX)

Click here for additional data file.^{(18.2KB, docx)}

Data Availability

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. ON052831.

Funding Statement

This research was funded by National Natural Science Foundation of China, grant number 32060124; Guizhou Normal University, grant number Qianshixinmiao[2021]A11 The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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PLoS One. doi: 10.1371/journal.pone.0281597.r001

Decision Letter 0

Neelesh Dahanukar

28 Sep 2022

PONE-D-22-21262Mitogenome of Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of CoreoideaPLOS ONE

Dear Dr. Chen,

Both the reviewer and the academic editor have found your manuscript interesting. However, both have comments on manuscript preparation and authors will have to revise the manuscript substantially based on the comments provided at the bottom of this email.

Please submit your revised manuscript by Nov 12 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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We look forward to receiving your revised manuscript.

Kind regards,

Neelesh Dahanukar, Ph.D.

Academic Editor

PLOS ONE

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Additional Editor Comments:

Authors have provided complete mitogenome of the Leaf-footed bug Notobitus montanus and its analysis. Apart from routine analysis, authors have also provided some comparative genomics and phylogenetics. Although the study is interesting and the analysis is performed appropriately, the manuscript is not presented well and authors will have to revise it carefully before a final decision can be made. I have made the concerns clear below.

Major comment

In several cases authors draw major conclusions without providing data or analysis. Most of this conclusion could also be because authors are not aware of several basic concepts in molecular genetics of mitochondria. Authors should know that, while making any big statement they should provide evidence or arguments based on earlier studies to support the claims.

The first claim authors make is that “Most amino acids preferred to use tRNAs encoded by nuclear genome.” It is unclear how authors came to this conclusion. The tRNAs for all 20 amino acids (including the two separate starting codons for leucine and serine) are present in the mitochondrial genome so why do authors mention that the mitochondria is using nuclear tRNAs. If this conclusion is drawn based on the mismatch between the third codon position in the CDS and tRNA anticodon arm, then authors should know that the third codon position is a wobble position.

The second claim authors make is regarding the overlap between the genes. Authors mention, “The presence of polycistron might contribute to generating overlaps between PCGs.” Authors cite reference [32] for this statement; however, the reference does not make any such claim. This statement is an ignorance of basic molecular biology of mitochondrial genome. First, polycistron has nothing to do with overlap in the genes. Most polycistron exists without overlap in the genes. In the case of mitochondria, the mitochondrial genes are generally transcribed as two large precursor polycistronic transcripts. These transcripts are subsequently cleaved to generate individual mRNAs, tRNAs and rRNAs. So polycistron does not explain the overlapping genes because even the genes that do not have overlap are transcribed from polycistronic transcripts.

Minor comments: Authors will need to improve manuscript writing substantially.

(1) Authors can add the common name “Leaf-footed bug” before Notobitus montanus to make it more accessible to non technical readers. Suggested title: Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

(2) As per the zoological nomenclatural rules, authority of scientific names that are written as per their original combination are not in parenthesis. Notobitus montanus is the original combination in which the species was described. So the authority and year cannot be in parenthesis. This should be - Notobitus montanus Hsiao, 1963. Make this change in abstract and remaining text.

(3) Abstract is not drafted properly. Authors unnecessarily provide details on the start and stop codons of coding genes when most of this is common in other organisms as well. In the manuscript authors talk about RSCU, compare codon usage with other species, they also provide comparison of D-loop of several species but none of this analysis is mentioned in the abstract. An abstract is a vital part of the manuscript and should be presented properly with a proper flow. There should be one or two lines providing the background of the study and its importance. One or two lines describing the methods use (also mention you determined secondary structure of tRNAs, compared genomes for codon usage and performed phylogeny). Important results in a few lines and implications of this study in understanding ecology and evolution of the species as a conclusion.

(4) The word “taxology” is normally not used in the field. What authors are referring to is called “taxonomy”.

(5) Introduction does not provide any information on the taxa under study Notobitus montanus and why it is important to study its mitogenome.

(6) As a rule, authors should use present tense when they are referring to established facts published earlier or any other facts. For example, second last line in first paragraph of results and discussion, “These two overlaps were popular in arthropods [19, 20]” should be “……. overlaps are popular in arthropods…”. Last line in third paragraph of results and discussion, “Incomplete stop codons were usually used in metazoan [18]” should be “Incomplete stop codons are usually used in metazoan [18]”. Similarly, in figure caption of figure 6, “The posterior probabilities were labeled at each node” should be “The posterior probabilities are labeled at each node”.

(7) The results are not stated properly and discussed at length. It is actually better to separate results and discussions. Authors can explain all the results in the results section and in the discussion discuss the results with respect to other mitogenomes and also discuss the implications of the results with respect to understanding ecology and evolution of the focal taxa. Authors have provided some analysis with respect to the published genomes of related taxa but the implications of the results are not clear.

(8) Figure legends should be self-explanatory and readers should understand the figure from figure legends without referring to the main text. For example, authors use several colours, numbers, etc. in figure 5 but the figure legend does not explain any of these. Similarly, for figure 6, there are two classification schemes shown in the figure but these are not explained in the figure legend. Figure legend of figure 6 also does not explain what data was used for the phylogenetic analysis, both coding and non-coding genes or just the coding genes. Although this is mentioned in the main text, as stated earlier, figure legends should be in details and self-explanatory.

(9) Supplementary information should be referred to as Fig. S1, Fig. S2, Table S1, etc. and not S1 Fig., S2 Fig., S1 Table, etc. Also, revise the figure captions to make them self-explanatory.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Dear Editor,

This manuscript focuses on sequencing a mitogenome of Notobitus montanus (Hemiptera: Coreidae) - the first mitogenome of Notobitus to investigate the mitogenome structure and phylogeny analysis. Their results were consistent with Dong et al. 2022 and didn't get any innovative results but one mitogenome of a species. I have some key points that I will address here if you think it was deserved to publication.

Reference

Dong X, Wang K, Tang Z, Zhang Y, Yi W, Xue H, et al. Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae. Archives of Insect Biochemistry and Physiology. 2022;110(1):e21878.

Comments to Author:

Major questions:

Q1: Coreoidea consists of five extant families, but mitochondrial genomes in your manuscript only covered four families (Hyocephalidae not included). You should state clearly the group used for phylogeny reconstruction in all related description. Such as this sentence “The phylogenetic tree of Coreoidea was constructed with the new mitogenome and 30 mitogenomes extracted from NCBI.”

Q2: The methods for genome extraction, sequencing and mitochondrial genome assembly are inaccurate in materials and methods. “DNA was isolated from…. Mitogenomic DNA was fragmented, then ~500 bp DNA was recycled. Paired-end libraries were constructed with the Illumina platform. The mitogenome was sequenced using the…”. It confused me for obtaining the mitogenome between genomic DNA extraction and sequencing or assembly. There is more than one way to get to the mitogenome (sequence genomic DNA and then to isolate mitogenome after sequencing; enrich the mitogenome prior to sequencing and other approach).

Q3. In the Transfer RNA and ribosomal RNA genes results, you described the amino acid preferences about the use of tRNAs. “…….preferred to use tRNAs encoded by the mitogenome or nuclear genome”. How do you determine the use in the nuclear genome? And you operate only for Notobitus montanus, cannot represent the whole large group, whether there are relevant references to justify?

Q4: I think that authors should give a detailed and accurate description in results and discussion part about phylogenetic relationship. For example, you cited the reference but inaccurate. “However, based on nucleotide sequences of 13 PCGs and two rRNAs, some studies considered Alydidae and Coreidae were monophyletic [40].” It clarified the sister group of Rhopalidae with Alydidae + Coreidae but not revealed the monophyly of Alydidae and Coreidae because one subfamily of Alydidae were not covered.

Minor comments:

Q1. You used many analyses software in materials and methods, but not all of them has corresponding version number. Determine the software version you are using.

Q2. In phylogenetic analysis part, I don’t understand the operation for PCGs in Phylosuite. “These mitogenomes were imported into PhyloSuite. After standardization of sequences, the nucleic acid sequences of 13 PCGs were extracted from these mitogenomes.” I wonder what’s meaning and how to standardize in Phylosuite. That is, what is being done to the sequences.

**********

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Reviewer #1: No

**********

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PLoS One. 2023 Feb 10;18(2):e0281597. doi: 10.1371/journal.pone.0281597.r002

Author response to Decision Letter 0

13 Nov 2022

We have carefully read the comments from the editors and reviewers. The comments and suggestions are very valuable for us to improve this manuscript. Please see manuscript and Response to Reviewers for specific revision!

Attachment

Submitted filename: Response to Reviewers.docx

Click here for additional data file.^{(36.7KB, docx)}

PLoS One. doi: 10.1371/journal.pone.0281597.r003

Decision Letter 1

Neelesh Dahanukar

22 Dec 2022

PONE-D-22-21262R1Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of CoreoideaPLOS ONE

Dear Dr. Chen,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Revised manuscript is a substantial improvement over the earlier draft. However, there are some minor issues that authors will have to resolve before the manuscript can be finally accepted. Specific comments are made in the attached manuscript file.

Please submit your revised manuscript by Feb 05 2023 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

We look forward to receiving your revised manuscript.

Kind regards,

Neelesh Dahanukar, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Revised manuscript is a substantial improvement over the earlier draft. However, there are some minor issues that authors will have to resolve before the manuscript can be finally accepted. Specific comments are made in the attached manuscript file.

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Attachment

Submitted filename: Manuscript with comments.docx

Click here for additional data file.^{(46.9KB, docx)}

PLoS One. 2023 Feb 10;18(2):e0281597. doi: 10.1371/journal.pone.0281597.r004

Author response to Decision Letter 1

9 Jan 2023

We have carefully read the comments from the editor and revised the manuscript according to the comments.

Attachment

Submitted filename: Response to Reviewers.docx

Click here for additional data file.^{(17.7KB, docx)}

PLoS One. doi: 10.1371/journal.pone.0281597.r005

Decision Letter 2

Neelesh Dahanukar

27 Jan 2023

Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

PONE-D-22-21262R2

Dear Dr. Chen,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Neelesh Dahanukar, Ph.D.

Academic Editor

PLOS ONE

PLoS One. doi: 10.1371/journal.pone.0281597.r006

Acceptance letter

Neelesh Dahanukar

1 Feb 2023

PONE-D-22-21262R2

Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

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Associated Data

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

Supplementary Materials

S1 Fig. Effective numbers of codons have a positive correlation with the G+C content of codons.

(A) total GC content of codons; (B) GC content of the first position of the codon; (C) GC content of the second position of the codon; (D) GC content of the third position of the codon.

(EPS)

Click here for additional data file.^{(802.7KB, eps)}

S2 Fig. The Ka/Ks has a negative correlation with the G+C content of codons.

(A) total GC content of codons; (B) GC content of the first position of the codon; (C) GC content of the second position of the codon; (D) GC content of the third position of the codon.

(EPS)

Click here for additional data file.^{(828KB, eps)}

S3 Fig. Maximum likelihood phylogenetic tree of 31 Coreoidea species.

(EPS)

Click here for additional data file.^{(909.2KB, eps)}

S1 Table. List of species for phylogenetic analysis.

(DOCX)

Click here for additional data file.^{(18.4KB, docx)}

S2 Table. Annotation of the Notobitus montanus mitogenome.

(DOCX)

Click here for additional data file.^{(20.2KB, docx)}

S3 Table. Nucleotide composition of Notobitus montanus (%).

(DOCX)

Click here for additional data file.^{(22.5KB, docx)}

S4 Table. Codon usage in the mitochondrial genome of Notobitus montanus.

(DOCX)

Click here for additional data file.^{(18.2KB, docx)}

Attachment

Submitted filename: Response to Reviewers.docx

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Attachment

Submitted filename: Manuscript with comments.docx

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Attachment

Submitted filename: Response to Reviewers.docx

Click here for additional data file.^{(17.7KB, docx)}

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. ON052831.

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PERMALINK

Mitogenome of the leaf-footed bug Notobitus montanus (Hemiptera: Coreidae) and a phylogenetic analysis of Coreoidea

Xiaoke Tian

Yongqin Li

Qin Chen

Qianquan Chen

Roles

Abstract

Introduction

Materials and methods

Samples and identification

Next-generation sequencing, annotation, and bioinformatics analysis

Phylogenetic analysis

Results

Genomic structure and nucleotide composition

Fig 1. Mitogenome map of Notobitus montanus.

Protein-coding genes

Fig 2. Codon and amino acid usage.

Fig 3. Evolutionary rates of 13 protein-coding genes in the mitogenome of 31 Coreoidea.

Transfer RNA and ribosomal RNA genes

Fig 4. Predicted secondary structure of 22 tRNAs of N. montanus.

Non-coding control region

Fig 5. Tandem repeat sequences in the non-coding control region.

Phylogenetic relationship

Fig 6. Bayesian phylogenetic tree of 31 Coreoidea species.

Discussion

Conclusions

Supporting information

Data Availability

Funding Statement

References

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Neelesh Dahanukar

Roles

Author response to Decision Letter 0

Decision Letter 1

Neelesh Dahanukar

Roles

Author response to Decision Letter 1

Decision Letter 2

Neelesh Dahanukar

Roles

Acceptance letter

Neelesh Dahanukar

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Associated Data

Supplementary Materials

Data Availability Statement

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