Complete Mitochondrial Genome of the Backswimmer: Notonecta triguttata Motschulsky, 1861 (Hemiptera: Notonectidae): Sequence, Structure, and Phylogenetic Analysis
College of Biological Science and Technology, Taiyuan Normal University, Jinzhong 030619, China
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Authors to whom correspondence should be addressed.
Diversity 2024, 16(1), 16; https://doi.org/10.3390/d16010016
Submission received: 8 November 2023
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Revised: 22 December 2023
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Accepted: 23 December 2023
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Published: 25 December 2023
(This article belongs to the Special Issue Heteroptera: Biodiversity, Evolution, Taxonomy and Conservation, 2nd Edition)
Abstract
:Notonecta triguttata Motschulsky, 1861 (Hemiptera, Notonectidae) is distributed in China, Japan, and South Korea. It is the dominant hexapod predator in aquatic ecosystems and can control harmful insects, such as mosquitoes and parasites. This study presents the first determination of the complete mitochondrial genome of N. triguttata. The mitogenome was 15,156 base pairs in length and was made up of 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs, and one non-coding control region. All genes were arranged in the same order as most other known heteropteran mitogenomes. All PCGs started with the ATN codon except COX1 (TTG) and NAD2 (GTG) and ended with TAA, TAG, or the partial stop codon T. The tRNAs had a typical cloverleaf secondary structure, except tRNA-Ser (GCT). The A + T content (75.96%) was relatively high across the entire mitogenome. The optimal phylogenetic trees were inferred through the Bayesian inference and maximum likelihood methods. The trees suggested a topology of (Corixoidea + ((Nepoidea + Ochteroidea) + (Naucoroidea + (Pleoidea + Notonectoidea)))) and identified that N. triguttata belongs to Notonectoidea. The complete mitogenome of N. triguttata provides a potentially useful resource for further exploration of the taxonomic status and phylogenetic history of the Notonecta species.
1. Introduction
The mitochondrial genomes (mitogenomes) of sequenced heteropteran insects in GenBank are generally circular molecules of 14–20 kilobases (14,540 bp and 19,587 bp for Phaenacantha marcida Horváth and Picromerus lewisi Scott, respectively). They are usually composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a 558 bp non-coding control region (D-loop) with a highly variable length. Mitogenome data have been widely used as molecular markers for phylogeny, molecular evolution, population genetics, and phylogeographic analyses, as they have a rapid evolutionary rate and are easy to sequence with a low recombination rate and conserved gene content [1,2]. Moreover, rearrangements of the mitogenome and aberrant genomic systems (such as gene truncations and genome fragmentation) are also reliable phylogenetic markers [3]. More than 300 mitogenomes have been sequenced in Heteroptera, but only 4 definite species from the family Notonectidae, including Enithares tibialis Liu & Zheng, Notonecta amplifica Kiritshenko, N. chinensis Fallou, and N. montandoni Motschulsky, are publicly available in GenBank.
The backswimmers, Notonectidae (Hemiptera: Heteroptera: Nepomorpha), embrace aquatic forms differing from all others in the persistent habit of swimming on their backs [4]. They have long, tiny hairs covering the hind legs that help them swim on the surface of the water. Since this family was first established by Latreille (1802) based on Notonecta Linnaeus, 1758 as the genus type, many species have been described [5]. This family contains more than 400 species in two subfamilies (Notonectinae and Anisopinae). Notonectinae contains seven genera, of which Notonecta is the most diverse in the New World; Enithares occurs in the Old World. The remaining genera contain very few species. Anisopinae contains four genera: Anisops from the Old World, Buenoa from the New World, Paranisops and Walambianisops from Australia [6,7]. All of the species belonging to 11 genera in this family are predaceous and are natural enemies that help reduce the proliferations of medically important mosquitoes, such as Culex pipiens Linnaeus, C. quinquefasciatus Say, Anopheles stephensi Liston, and Aedes togoi Theobald [4,8,9,10,11].
The genus of Notonecta was divided into five subgenera (Bichromonecta, Enitharonecta, Erythronecta, Notonecta and Paranecta), of which two (Erythronecta and Notonecta) are found in the Oriental Region [12]. As one member of the genus Notonecta, Notonecta triguttata is mainly distributed in China, Japan, and South Korea [13]. Its body is primarily black, with a few bright flavous portions. They prefer stagnant water and mainly inhabit freshwater ponds. Adults normally range in size from 13 to 14 mm long. The females appear to be larger than the males. Current knowledge of N. triguttata is very scanty, only involving some studies on their feeding ecology and toxicology. Two studies by Ohba suggest that the larvae of Cybister brevis Aubé and Cybister japonicus Sharp mainly feed on N. triguttata nymphs [14,15]. Hirayama and Kasuya reported that N. triguttata only preys on adult Aquarius paludum Fabricius, and not the eggs or early instars of A. paludum [16]. Kobashi et al. showed that the number of N. triguttata was high from the start but later declined under imidacloprid treatment, suggesting delayed chronic toxicity, while dinotefuran did not decrease the population of N. triguttata [17]. No mitogenome sequences of N. triguttata have been reported, which hinders the exploration of its phylogenetic status and phylogeography study.
In the present study, we sequenced and characterized the complete mitogenome sequence of N. triguttata using next-generation sequencing technology. We analyzed the nucleotide composition, strand asymmetry, codon usage pattern, and tRNA secondary structure. Additionally, we constructed phylogenetic trees to confirm the phylogenetic position of N. triguttata and to provide insight into the family-level phylogenetic relationships within Nepomorpha.
2. Materials and Methods
2.1. Sample Collection, DNA Extraction, and Sequencing
Adult specimens of N. triguttata were collected from roadside puddles between Lushuihe Town and Dongsheng Village, Fusong County, Jilin Province, China (42°31′9″ N, 127°44′11″ E) on 8 August 2017. The sampling sites were not privately owned or safeguarded, and no protected or endangered species were affected by the field collections. No specific field ethics approval was required for collecting wild backswimmers in this area. All samples were placed in sterile tubes with anhydrous ethanol. The anhydrous ethanol was replaced three times every 12 h and the tubes were stored at −20 °C for later use. Voucher specimens were deposited at the Insect Molecular Systematics Laboratory, College of Biological Science and Technology, Taiyuan Normal University, Jinzhong, China.
We extracted total genomic DNA from thoracic muscle tissue from one individual of N. triguttata, according to the manufacturer’s instructions for the Universal Genomic DNA Kit (CWBIO, Beijing, China). The yield of the DNA was detected using 1% agarose gel electrophoresis and an Invitrogen Qubit Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). After the DNA sample was examined, it was randomly fragmented using a Covaris ultrasonic disruptor. Following this, terminus repair, A-tail addition, sequencing adaptor ligation, purification, PCR amplification, and other steps were performed to complete the DNA library preparation process. A DNA library of 350 bp insert size was constructed and sequenced on an Illumina HiSeq 2000 platform using a pair-end 150 bp sequencing strategy from Novogene Bioinformatics Technology Co., Ltd. (Tianjin, China). All raw reads were assessed for quality using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, accessed on 19 March 2018) and cleaned using Trimmomatic [18] to trim adapters and low-quality reads.
2.2. Sequence Assembly, Annotation, and Analysis
Whole genomic clean sequenced data were assembled using A5-miseq [19] and SPAdes v3.9.0 [20]. The accuracy and completeness of the assemblies were assessed by MUMmer4 [21] and Pilon v1.18 [22].
The tRNA genes were initially identified using a MITOS WebServer [23] and invertebrate mitochondrial genetic codes. After identifying the tRNAs, the PCGs were initially identified using the ORF finder on the NCBI website (https://www.ncbi.nlm.nih.gov/orffinder/, accessed on 5 October 2021) with invertebrate mitochondrial genetic codes. Then, an NCBI BLAST tool was used to further verify the correctness of the identified PCGs. The rRNA boundaries were predicted by alignment with other available nepomorphan mitogenomes. The secondary structures of the tRNA genes were predicted with MITOS and manually curated in Adobe Illustrator 2022. The complete mitochondrial genome was circularized and visualized in CGView server (https://proksee.ca/, accessed on 5 October 2021) [24].
The nucleotide composition, amino acid composition, and relative synonymous codon usage (RSCU) were calculated in MEGA 11 [24,25]. The RSCU stacked barplot was drawn in PhyloSuite v1.2.3 [26]. Strand asymmetry was calculated by the formulas “AT skew = (A − T)/(A + T)” and “GC skew = (G − C)/(G + C)” [27]. The complete annotated mitogenome was submitted to GenBank using a Bankit tool (https://submit.ncbi.nlm.nih.gov/about/bankit/, accessed on 10 February 2020).
2.3. Gene Arrangement and Phylogenetic Analysis
The N. triguttata PCGs were aligned with the mitogenomes of other heteropteran species based on their amino acid sequences utilizing ClustalW implemented in MEGA 11. The rRNA and tRNA sequences were aligned using MEGA 11 [25]. A total of 15 nepomorphan mitogenomes available in GenBank were included in the gene rearrangement and phylogenetic analyses. Leptopus sp. NKMT019, Valentia hoffmanni China, and Stictopleurus subviridis Hsiao were used as outgroups (Table 1). Subsequently, the gene order was mapped based on coding genes from the mitogenomes of the 19 analyzed species in PhyloSuite [26]. All individual genes were concatenated into a combined matrix. Because saturation in substitutions could lead to incorrect phylogenetic inferences, the PCG12 matrix (including the first and second codon positions of 13 PCGs) and the PCG12RT matrix (including the first and second codon positions of 13 PCGs, rRNA genes, and tRNA genes) were used to perform the analysis [28].
The phylogenetic trees were inferred utilizing the Bayesian inference (BI) and maximum likelihood (ML) methods. MrBayes v3.2.7 [29] was used to construct the phylogenetic tree for the BI analysis. A PartitionFinder v2.1.1 program [30] was selected to infer the best substituted evolutionary model under the Akaike Information Criterion, and GTR + G + I was selected. A total of 10,000,000 generations were executed, with a sampling frequency of 10,000. The first 25% of the samples was discarded, and the remaining samples were used to summarize the phylogenetic trees.
ML analyses were performed using the IQ-TREE v1.6.12 [31] automatically chosen substitution model GTR + F + R3, and bootstrap resampling with 1000 replicates was conducted to assess the node support values. Figtree v1.4.4 (https://github.com/rambaut/figtree/releases, accessed on 9 March 2023) was used to display the results of the phylogenetic trees.
3. Results and Discussion
3.1. Genome Organization
The complete mitochondrial genome of N. triguttata was a typical double-stranded circular molecule of 15,156 bp in length (Figure 1, Table 2). It was made up of 37 genes, consisting of 13 PCGs, 22 tRNA genes, 2 rRNA genes, and a control region. Among the 37 genes, the N strand encoded 4 protein genes (ND1, ND4, ND4L, and ND5), 2 rRNA genes (16S rRNA and 12S rRNA), and 8 tRNA genes (tRNA-Gin, tRNA-Cys, tRNA-Tyr, tRNA-Phe, tRNA-His, tRNA-Val, tRNA-Leu1, and tRNA-Ser2), while the J strand encoded 9 other protein genes and 14 tRNA genes. A total of 14 gene junctions in the genome exhibited overlapping regions, totaling 47 base pairs, which may be related to the compactness of the genome. In addition to the control region, there were 71 nucleotides scattered across 11 intergenic spacers, ranging in size from 1 to 32 bp. The ATGATAA sequence was present in the ATPase8-ATPase6 and ND4L-ND4 segments of the N. triguttata mitogenome, aligning with the commonly reported ATGATAA sequence in other heteropteran mitogenomes [32,33,34,35]. The complete mitochondrial genome of N. triguttata was submitted to GenBank, with the accession number MT043157.
3.2. Nucleotide Composition and Codon Usage
The statistical analysis of the content of four nucleotides (A, T, C, and G) in the N. triguttata mitochondrial genome indicated significant A + T bias (Table 3). The total nucleotide composition of the entire genome was biased toward A + T (75.96%). The PCG-N exhibited the highest proportion of A + T content (78.28%), while the control region exhibited the lowest proportion (67.74%). The statistics of nucleotide skew [36] for the mitogenome of N. triguttata revealed that the entire genome, PCGs-J, tRNA genes, tRNA genes-J, tRNA genes-N, and rRNA genes exhibited AT-skewness. Additionally, GC-skewness was observed in the PCGs, PCG-N, and tRNA genes-J. Such skewness in the nucleotide composition may be related to the asymmetrical process of mutation during replication [37].
The RSCU in the N. triguttata mitogenome is counted in Table 4 and Figure 2. The 13 PCGs contained 3,698 codons. Four commonly used codons (UUU-Phe, UUA-Leu2, AUU-Ile, and AUA-Met) were composed entirely of A or T, which may play an important role in the A + T bias of the whole mitogenome. The most commonly used codons in the J strand were UUA-Leu2 and AUU-Ile, while the N strand codons were UUU-Phe and UUA-Leu2. The most frequently used codons for each amino acid were NNA and NNU, which reflect the AT preference of the entire mitogenome nucleotide composition and the higher content of AT in the third codon than in the first and second codons. The most frequently used amino acids in the N. triguttata PCGs were Leu2 (426), Ile (363), and Phe (345), which did not correspond exactly to the tRNA anticodon [38].
3.3. Protein-Coding Genes
The total length of the 13 PCGs in the N. triguttata mitogenome was 11,125 bp, of which the total length of 9 PCGs in the J strand was 6835 bp, and the length of 4 PCGs in the N strand was 4290 bp (Table 2). The start codon of the PCGs was ATN, except for NAD2 and COX1, which used GTG and TTG as start codons, respectively. Nine PCGs were terminated using TAN termination (seven with TAA, two with TAG). Four PCGs of COX2, ATPase6, COX3, and NAD3 used the partial stop codon T, and it has been verified that post-transcriptional polyadenylation produces the complete stop codon TAA [39].
3.4. Transfer, Ribosomal RNA Genes and Control Regions
All 22 tRNAs encoding all 20 amino acids in metazoan mitogenomes were present in the mitogenome of N. triguttata (Table 2, Figure 3). The total length of the tRNA genes was 1465 bp, with 14 genes containing 934 bp in the J strand and 8 genes containing 531 bp in the N strand. The tRNAs were folded into a nearly perfect secondary cloverleaf structure, except for tRNA-Ser (GCT), which lacked a dihydrouridine arm. Leucine and serine tRNA acceptors contained two kinds of anticodons, such as TAA/TAG and GCT/TGA, respectively. In addition to the traditional A-U and G-C base pairs, 23 G-U base pairs that form stable chemical bonds were observed.
The total length of the two rRNAs was 1785 bp, and both were encoded in the N-strand. The 16S rRNA was located between leucine (UAG) and valine with a length of 1019 bp, while the 12S rRNA was situated between valine and the control region with a length of 766 bp. The A + T content of the rRNA genes was 76.30%, which was slightly higher than that of the entire genome (75.96%), suggesting a preference for A + T in the rRNA genes.
The length of the control region between 12S rRNA and isoleucine was 558 bp. The nucleotide composition of this region was T (37.99%), A (29.75%), C (25.09%), and G (7.17%), and the AT-skew and GC-skew were −0.12 and −0.56, respectively. No tandem repeat sequences were predicted in this region.
3.5. Gene Arrangement and Phylogenetic Analysis
The order of the mitochondrial genes from N. triguttata is presented in Figure 4. The gene order in the 19 species remained consistent, and no gene rearrangement was observed. This result indicates that the mitochondrial gene order is highly conserved in Nepomorpha. This will provide some information for future study of the Nepomorpha evolution [35,40,41].
Phylogenetic trees were constructed using the ML and BI methods based on two matrices (PCG12 and PCG12RT) in Figure 5. The resulting trees have identical topological structures with relatively high nodal support. The monophyly of each superfamily within Nepomorpha was well supported. The topological structures (Corixoidea + (Nepoidea + (Ochteroidea + (Naucoroidea + (Notonectoidea + Pleoidea))))) are consistent with previous studies on evolutionary relationships [42]. These results show that N. triguttata and E. tibialis are sister species in Notonectoidea. Although the relationships among the superfamilies are generally consistent in most studies, there is still controversy about whether Corixoidea or Nepoidea is the sister group to all other Nepomorpha as well as whether the Nepomorpha is the sister group to all other Heteroptera or a member of Panheteroptera nested within Nepomorpha [43,44,45]. More morphological, molecular, and biological data for Nepomorpha or better algorithms are needed to further confirm the phylogenetic position of Corixoidea and Nepoidea, and even Nepomorpha.
4. Conclusions
In this study, we first determined the complete mitogenome of N. triguttata, with a total length of 15,156 bp. It included 13 PGCs, 22 tRNA genes, and a 558 bp non-coding control region, which had the same gene order as most other known heteropteran mitogenomes. We determined that the N. triguttata belonged to Notonectoidea by constructing a phylogenetic tree. We did not observe gene rearrangement in the N. triguttata mitogenome. We obtained the same result when we compared the gene order with the other 18 species, which suggests that the nepomorphan mitogenomes are extremely highly conserved. Previous studies have paid more attention to the relationships of higher-level taxa. The complete mitogenome of N. triguttata provides a potentially valuable resource for further exploration of the taxonomic status and phylogenetic history of the Notonecta species.
We performed a phylogenetic analysis based on PCG12 and PCG12RT. Our results strongly support the sister relationship between N. triguttata and E. tibialis. The phylogenetic trees show strong support for the monophyly of the six superfamilies and the basal position of Corixoidea. More mitochondrial genomes and nuclear genes need to be sequenced to reveal the mitochondrial genome evolution and phylogenetic relationships within Nepomorpha or Notonectidae more comprehensively.
Author Contributions
Conceptualization, M.L. and D.Z.; methodology, M.L. and G.W.; software, G.W. and C.S.; validation, G.W., M.L. and C.S.; formal analysis, M.L. and G.W.; investigation, G.W. and C.S.; resources, M.L.; data curation, G.W. and H.H.; writing—original draft preparation, G.W. and H.H.; writing—review and editing, M.L. and D.Z; visualization, G.W. and H.H.; supervision, M.L. and D.Z.; project administration, M.L.; funding acquisition, M.L. and D.Z. All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by the National Natural Science Foundation of China, grant numbers 31501840 and 32300377, and the Basic Research Program of Shanxi Province, grant number 20210302123318.
Institutional Review Board Statement
Not applicable.
Data Availability Statement
The mitogenome sequence of Notonecta triguttata is available at GenBank with accession number: MT043157.
Acknowledgments
The authors acknowledge any support given that is not covered by the author contributions or by funding.
Conflicts of Interest
The authors declare no conflict of interest.
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Figure 1.
The structure of the Notonecta triguttata mitogenome. Blue arrows denote protein-coding genes (PCGs), while purple and red arrows represent the rRNA and tRNA genes, respectively. The control region is indicated by a grey arrow. The tRNA genes are labeled using single-letter amino acid abbreviations. Sequence length is noted by ticks on the inner circle.
Figure 1.
The structure of the Notonecta triguttata mitogenome. Blue arrows denote protein-coding genes (PCGs), while purple and red arrows represent the rRNA and tRNA genes, respectively. The control region is indicated by a grey arrow. The tRNA genes are labeled using single-letter amino acid abbreviations. Sequence length is noted by ticks on the inner circle.
Figure 2.
The relative synonymous codon usage (RSCU) in the N. triguttata mitogenome.
Figure 3.
Secondary cloverleaf structures of the 22 N. triguttata tRNAs. The green gene name indicates its location in the forward strand, while blue is for the reverse strand. Watson−Crick base pairs are represented by a hyphen (-), while GU bases pairs are denoted by a red dot.
Figure 3.
Secondary cloverleaf structures of the 22 N. triguttata tRNAs. The green gene name indicates its location in the forward strand, while blue is for the reverse strand. Watson−Crick base pairs are represented by a hyphen (-), while GU bases pairs are denoted by a red dot.
Figure 4.
The arrangement patter of mitochondrial genes N triguttata. Green circles denote tRNA genes, while blue and pink arrows represent protein-coding genes and rRNA genes, respectively. The “+” and “−” represent heavy and light strands, respectively.
Figure 4.
The arrangement patter of mitochondrial genes N triguttata. Green circles denote tRNA genes, while blue and pink arrows represent protein-coding genes and rRNA genes, respectively. The “+” and “−” represent heavy and light strands, respectively.
Figure 5.
Phylogenetic trees were constructed from two matrices (PCG12 on the left and PCG12RT on the right) using the maximum likelihood and Bayesian inference methods. Node numbers show bootstrap support values on the left and Bayesian posterior probability support values on the right. Dashed lines indicate posterior probabilities less than 0.5. Different branches of the superfamily are represented by different colors.
Figure 5.
Phylogenetic trees were constructed from two matrices (PCG12 on the left and PCG12RT on the right) using the maximum likelihood and Bayesian inference methods. Node numbers show bootstrap support values on the left and Bayesian posterior probability support values on the right. Dashed lines indicate posterior probabilities less than 0.5. Different branches of the superfamily are represented by different colors.
Table 1.
GenBank accession numbers for the mitogenomes of the studied species.
| Infraorder | Superfamily | Family | Species | Accession Number |
|---|---|---|---|---|
| Leptopodomorpha | Leptopodoidea | Leptopodidae | Leptopus sp. NKMT019 | FJ456946 |
| Cimicomorpha | Reduvioidea | Reduviidae | Valentia hoffmanni | FJ456952 |
| Pentatomomorpha | Coreoidea | Rhopalidae | Stictopleurus subviridis | EU826088 |
| Nepomorpha | Nepoidea | Belostomatidae | Diplonychus esakii | MK251109 |
| Diplonychus rusticus | FJ456940 | |||
| Lethocerus deyrollei | KU237288 | |||
| Lethocerus indicus | NC_027194 | |||
| Nepidae | Nepa hoffmanni | NC_028084 | ||
| Laccotrephes robustus | FJ456948 | |||
| Corixoidea | Corixidae | Sigara septemlineata | FJ456941 | |
| Micronectidae | Micronecta sahlbergii | NC_039588 | ||
| Ochteroidea | Gelastocoridae | Nerthra indica | NC_012838 | |
| Ochteridae | Ochterus marginatus | FJ456950 | ||
| Pleoidea | Pleidae | Paraplea frontalis | NC_028629 | |
| Helotrephidae | Helotrephes sp. NKMT027 | NC_012822 | ||
| Notonectoidea | Notonectidae | Enithares tibialis | NC_012819 | |
| Notonecta triguttata | MT043157 | |||
| Naucoroidea | Naucoridae | Ilyocoris cimicoides | NC_012845 | |
| Aphelocheiridae | Aphelocheirus ellipsoideus | FJ456939 |
Table 2.
Complete mitochondrial genome composition of Notonecta triguttata.
| Gene | Strand | Position | Anticodon | Site (bp) | Start Codon | Stop Codon | Intergenic Nucleotides |
|---|---|---|---|---|---|---|---|
| tRNA-Ile | J | 1–65 | GAT | 65 | |||
| tRNA-Gln | N | 63–131 | TTG | 69 | −3 | ||
| tRNA-Met | J | 131–199 | CAT | 69 | −1 | ||
| NAD2 | J | 200–1210 | 1011 | GTG | TAA | 0 | |
| tRNA-Trp | J | 1209–1279 | TCA | 71 | −2 | ||
| tRNA-Cys | N | 1272–1335 | GCA | 64 | −8 | ||
| tRNA-Tyr | N | 1340–1405 | GTA | 66 | 4 | ||
| COX1 | J | 1407–2945 | 1539 | TTG | TAA | 1 | |
| tRNA-Leu2 | J | 2941–3005 | TAA | 65 | −5 | ||
| COX2 | J | 3006–3684 | 679 | ATA | T- | 0 | |
| tRNA-Lys | J | 3685–3756 | CTT | 72 | 0 | ||
| tRNA-Asp | J | 3757–3821 | GTC | 65 | 0 | ||
| ATPase8 | J | 3822–3980 | 159 | ATA | TAA | 0 | |
| ATPase6 | J | 3974–4643 | 670 | ATG | T- | −7 | |
| COX3 | J | 4644–5430 | 787 | ATG | T- | 0 | |
| tRNA-Gly | J | 5431–5492 | TCC | 62 | 0 | ||
| NAD3 | J | 5493–5844 | 352 | ATT | T- | 0 | |
| tRNA-Ala | J | 5845–5909 | TGC | 65 | 0 | ||
| tRNA-Arg | J | 5910–5975 | TGC | 66 | 0 | ||
| tRNA-Asn | J | 5982–6050 | GTT | 69 | 6 | ||
| tRNA-Ser1 | J | 6050–6118 | GCT | 69 | −1 | ||
| tRNA-Glu | J | 6118–6181 | TTC | 64 | −1 | ||
| tRNA-Phe | N | 6180–6245 | GAA | 66 | −2 | ||
| NAD5 | N | 6246–7955 | 1710 | ATG | TAA | 1 | |
| tRNA-His | N | 7957–8021 | GTG | 65 | 1 | ||
| NAD4 | N | 8021–9352 | 1332 | ATG | TAG | −1 | |
| NAD4L | N | 9346–9660 | 315 | ATG | TAA | −7 | |
| tRNA-Thr | J | 9663–9726 | TGT | 64 | 2 | ||
| tRNA-Pro | N | 9727–9792 | TGG | 66 | 0 | ||
| NAD6 | J | 9795–10,295 | 501 | ATT | TAA | 2 | |
| CYTB | J | 10,295–11,431 | 1137 | ATG | TAG | −1 | |
| tRNA-Ser2 | J | 11,430–11,497 | TGA | 68 | −2 | ||
| NAD1 | N | 11,515–12,447 | 933 | ATA | TAA | 17 | |
| tRNA-Leu1 | N | 12,442–12,506 | TAG | 65 | −6 | ||
| 16S rRNA | N | 12,539–13,557 | 1019 | 32 | |||
| tRNA-Val | N | 13,761–13,830 | TAC | 70 | 3 | ||
| 12S rRNA | N | 13,833–14,598 | 766 | 2 | |||
| CR | 14,599–15,156 | 558 | 0 |
Table 3.
Nucleotide composition and skewness of the N. triguttata mitochondrial genome.
| Feature | Length (bp) | A% | G% | C% | T% | A + T (%) | AT-Skew | GC-Skew |
|---|---|---|---|---|---|---|---|---|
| Whole genome | 15,156 | 42.93 | 10.40 | 13.64 | 33.03 | 75.96 | 0.13 | −0.14 |
| PCGs | 11,125 | 33.67 | 12.40 | 11.60 | 42.33 | 76.00 | −0.11 | 0.03 |
| PCGs-J | 6835 | 38.22 | 12.07 | 13.36 | 36.36 | 74.57 | 0.02 | −0.05 |
| PCGs-N | 4290 | 26.43 | 12.91 | 8.81 | 51.84 | 78.28 | −0.32 | 0.19 |
| tRNA genes | 1465 | 40.89 | 10.92 | 12.76 | 35.43 | 76.32 | 0.07 | −0.08 |
| tRNA genes-J | 934 | 41.33 | 12.63 | 11.13 | 34.90 | 76.23 | 0.08 | 0.06 |
| tRNA genes-N | 531 | 40.11 | 7.91 | 15.63 | 36.35 | 76.46 | 0.05 | −0.33 |
| rRNA genes | 1785 | 43.47 | 9.41 | 14.29 | 32.83 | 76.30 | 0.14 | −0.20 |
| Control region | 558 | 29.75 | 7.17 | 25.09 | 37.99 | 67.74 | −0.12 | −0.56 |
Table 4.
Codon usage and relative synonymous codon usage (RSCU) in the mitochondrial 13 PCGs of N. triguttata. JN denotes a double strand, while J and N refer to the J strand and N strand, respectively. Bold values represent the most utilized amino acid codons, while underlined codons signify the cognate tRNA codon for each amino acid.
Table 4.
Codon usage and relative synonymous codon usage (RSCU) in the mitochondrial 13 PCGs of N. triguttata. JN denotes a double strand, while J and N refer to the J strand and N strand, respectively. Bold values represent the most utilized amino acid codons, while underlined codons signify the cognate tRNA codon for each amino acid.
| Amino Acid | Codon | JN | RSCU | J | RSCU+ | N | RSCU- |
|---|---|---|---|---|---|---|---|
| Phe | UUU(F) | 284 | 1.65 | 123 | 1.46 | 161 | 1.83 |
| UUC(F) | 60 | 0.35 | 45 | 0.54 | 15 | 0.17 | |
| Leu2 | UUA(L) | 402 | 4.66 | 220 | 4.57 | 182 | 4.77 |
| UUG(L) | 24 | 0.28 | 4 | 0.08 | 20 | 0.52 | |
| Leu1 | CUU(L) | 41 | 0.47 | 17 | 0.35 | 24 | 0.63 |
| CUC(L) | 1 | 0.01 | 0 | 0 | 1 | 0.03 | |
| CUA(L) | 49 | 0.57 | 47 | 0.98 | 2 | 0.05 | |
| CUG(L) | 1 | 0.01 | 1 | 0.02 | 0 | 0 | |
| Ile | AUU(I) | 339 | 1.87 | 214 | 1.84 | 125 | 1.92 |
| AUC(I) | 24 | 0.13 | 19 | 0.16 | 5 | 0.08 | |
| Met | AUA(M) | 287 | 1.88 | 199 | 1.9 | 88 | 1.85 |
| AUG(M) | 18 | 0.12 | 11 | 0.1 | 7 | 0.15 | |
| Val | GUU(V) | 76 | 1.55 | 30 | 1 | 46 | 2.42 |
| GUC(V) | 4 | 0.08 | 2 | 0.07 | 2 | 0.11 | |
| GUA(V) | 109 | 2.24 | 82 | 2.77 | 27 | 1.42 | |
| GUG(V) | 6 | 0.12 | 5 | 0.17 | 1 | 0.05 | |
| Ser1 | UCU(S) | 119 | 2.57 | 26 | 1.07 | 93 | 4.23 |
| UCC(S) | 5 | 0.11 | 1 | 0.04 | 4 | 0.18 | |
| UCA(S) | 107 | 2.31 | 91 | 3.73 | 16 | 0.73 | |
| UCG(S) | 3 | 0.06 | 2 | 0.08 | 1 | 0.05 | |
| Pro | CCU(P) | 59 | 1.8 | 34 | 1.39 | 25 | 3.03 |
| CCC(P) | 7 | 0.21 | 6 | 0.24 | 1 | 0.12 | |
| CCA(P) | 63 | 1.92 | 57 | 2.33 | 6 | 0.73 | |
| CCG(P) | 2 | 0.06 | 1 | 0.04 | 1 | 0.12 | |
| Thr | ACU(T) | 75 | 1.6 | 41 | 1.12 | 34 | 3.32 |
| ACC(T) | 5 | 0.11 | 3 | 0.08 | 2 | 0.2 | |
| ACA(T) | 106 | 2.27 | 101 | 2.77 | 5 | 0.49 | |
| ACG(T) | 1 | 0.02 | 1 | 0.03 | 0 | 0 | |
| Ala | GCU(A) | 63 | 1.7 | 25 | 0.97 | 38 | 3.38 |
| GCC(A) | 7 | 0.19 | 7 | 0.27 | 0 | 0 | |
| GCA(A) | 76 | 2.05 | 70 | 2.72 | 6 | 0.53 | |
| GCG(A) | 2 | 0.05 | 1 | 0.04 | 1 | 0.09 | |
| Tyr | UAU(Y) | 145 | 1.81 | 58 | 1.59 | 87 | 2 |
| UAC(Y) | 15 | 0.19 | 15 | 0.41 | 0 | 0 | |
| His | CAU(H) | 50 | 1.39 | 34 | 1.21 | 16 | 2 |
| CAC(H) | 22 | 0.61 | 22 | 0.79 | 0 | 0 | |
| Gin | CAA(Q) | 56 | 1.87 | 44 | 1.96 | 12 | 1.6 |
| CAG(Q) | 4 | 0.13 | 1 | 0.04 | 3 | 0.4 | |
| Asn | AAU(N) | 154 | 1.79 | 96 | 1.7 | 58 | 1.97 |
| AAC(N) | 18 | 0.21 | 17 | 0.3 | 1 | 0.03 | |
| Lys | AAA(K) | 83 | 1.68 | 63 | 1.83 | 20 | 1.33 |
| AAG(K) | 16 | 0.32 | 6 | 0.17 | 10 | 0.67 | |
| Asp | GAU(D) | 59 | 1.71 | 35 | 1.59 | 24 | 1.92 |
| GAC(D) | 10 | 0.29 | 9 | 0.41 | 1 | 0.08 | |
| Glu | GAA(E) | 78 | 1.75 | 60 | 1.97 | 18 | 1.29 |
| GAG(E) | 11 | 0.25 | 1 | 0.03 | 10 | 0.71 | |
| Cys | UGU(C) | 49 | 2 | 13 | 2 | 36 | 2 |
| UGC(C) | 0 | 0 | 0 | 0 | 0 | 0 | |
| Trp | UGA(W) | 91 | 1.84 | 69 | 2 | 22 | 1.47 |
| UGG(W) | 8 | 0.16 | 0 | 0 | 8 | 0.53 | |
| Arg | CGU(R) | 18 | 1.33 | 5 | 0.57 | 13 | 2.74 |
| CGC(R) | 0 | 0 | 0 | 0 | 0 | 0 | |
| CGA(R) | 31 | 2.3 | 29 | 3.31 | 2 | 0.42 | |
| CGG(R) | 5 | 0.37 | 1 | 0.11 | 4 | 0.84 | |
| Ser2 | AGU(S) | 43 | 0.93 | 12 | 0.49 | 31 | 1.41 |
| AGC(S) | 1 | 0.02 | 0 | 0 | 1 | 0.05 | |
| AGA(S) | 91 | 1.96 | 63 | 2.58 | 28 | 1.27 | |
| AGG(S) | 2 | 0.04 | 0 | 0 | 2 | 0.09 | |
| Gly | GGU(G) | 81 | 1.54 | 24 | 0.73 | 57 | 2.89 |
| GGC(G) | 2 | 0.04 | 0 | 0 | 2 | 0.1 | |
| GGA(G) | 114 | 2.17 | 100 | 3.05 | 14 | 0.71 | |
| GGG(G) | 13 | 0.25 | 7 | 0.21 | 6 | 0.3 |
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Wang, G.; Sun, C.; Hu, H.; Zhang, D.; Li, M. Complete Mitochondrial Genome of the Backswimmer: Notonecta triguttata Motschulsky, 1861 (Hemiptera: Notonectidae): Sequence, Structure, and Phylogenetic Analysis. Diversity 2024, 16, 16. https://doi.org/10.3390/d16010016
AMA Style
Wang G, Sun C, Hu H, Zhang D, Li M. Complete Mitochondrial Genome of the Backswimmer: Notonecta triguttata Motschulsky, 1861 (Hemiptera: Notonectidae): Sequence, Structure, and Phylogenetic Analysis. Diversity. 2024; 16(1):16. https://doi.org/10.3390/d16010016
Chicago/Turabian StyleWang, Guobin, Chengze Sun, Huijun Hu, Danli Zhang, and Min Li. 2024. "Complete Mitochondrial Genome of the Backswimmer: Notonecta triguttata Motschulsky, 1861 (Hemiptera: Notonectidae): Sequence, Structure, and Phylogenetic Analysis" Diversity 16, no. 1: 16. https://doi.org/10.3390/d16010016
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