Research Article |
Corresponding author: Hufang Zhang ( zh_hufang@sohu.com ) Academic editor: Laurence Livermore
© 2021 Wanqing Zhao, Dajun Liu, Qian Jia, Xin Wu, Hufang Zhang.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Zhao W, Liu D, Jia Q, Wu X, Zhang H (2021) Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses. ZooKeys 1070: 13-30. https://doi.org/10.3897/zookeys.1070.72742
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Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.
Mitogenome, next-generation sequencing, phylogeny, scentless plant bugs
Mitochondria are important cytoplasmic organelles in eukaryotic cells, playing a critical role in cell metabolism, disease, apoptosis, and senescence. Mitochondrial genomes are characterized by a simple structure, stable composition, conserved arrangement, maternal inheritance, and rapid evolutionary rate (
Rhopalidae, commonly known as scentless plant bugs, is a family of Pentatomomorpha insects in the superfamily Coreoidea (
Myrmus lateralis Hsiao, 1964 is an endemic species of China (Beijing, Hebei, eastern Inner Mongolia), Korea, Mongolia, and Russia (Far East) (Liu et al. 1994; Aukema and Rieger 2006;
Family | Species | Accession number | |
---|---|---|---|
Outgroup | Nabidae | Himacerus nodipes | JF927832 |
Ingroup | Aradidae | Aradacanthia heissi | HQ441233 |
Aradus compar | NC_030362 | ||
Aneurus similis | NC_030360 | ||
Cydnidae | Macroscytus gibbulus | NC_012457 | |
Adrisa magna | NC_042429 | ||
Scoparipes salvazai | MF614955 | ||
Pentatomidae | Eurydema dominulus | NC_044762 | |
Palomena viridissima | NC_050166 | ||
Eysarcoris guttigerus | MN831205 | ||
Arma custos | MT535604 | ||
Pentatoma semiannulata | MT985377 | ||
Colobathristidae | Phaenacantha marcida | EU427342 | |
Rhyparochromidae | Panaorus albomaculatus | NC_031364 | |
Malcidae | Malcus inconspicuus | EU427339 | |
Lygaeidae | Kleidocerys resedae | KJ584365 | |
Pyrrhocoridae | Dindymus rubiginosus | NC_042439 | |
Euscopus rufipes | NC_042436 | ||
Melamphaus faber | NC_042435 | ||
Dysdercus decussatus | NC_042438 | ||
Antilochus coquebertii | NC_042441 | ||
Rhopalidae | Stictopleurus subviridis | EU826088 | |
Myrmus lateralis | MN412595 | ||
Chorosoma macilentum | MN412594 | ||
Aeschyntelus notatus | EU427333 | ||
Corizus sp. | KM983397 | ||
Alydidae | Riptortus pedestris | EU427344 | |
Neomegalotomus parvus | MG253274 | ||
Coreidae | Hydaropsis longirostris | EU427337 | |
Clavigralla tomentosicollis | KY274846 | ||
Acanthocoris sp. | MF497707 | ||
Enoplops potanini | MF497720 | ||
Leptoglossus membranaceus | MF497724 | ||
Anoplocnemis curvipes | KY906099 | ||
Mictis tenebrosa | MF497729 | ||
Pseudomictis brevicornis | MF497732 | ||
Molipteryx lunata | MF497721 | ||
Notopteryx soror | KX505857 |
In this study, we sequenced and annotated the complete mitogenome of M. lateralis. We examined the genomic features, nucleotide composition, codon usage, RNA secondary structure, evolutionary pattern of 13 PCGs and characteristics of the control region. Finally, we evaluated the phylogenetic relationship of the mitochondrial sequence data at different taxonomic levels.
Adult specimens of Myrmus lateralis were collected from Jincheng City, Shanxi Province, China on 20 July 2014. Specimens were preserved in 100% ethanol and stored at –20 °C. The genomic DNA was extracted from leg muscles using a ONE-4-ALL Genomic DNA Mini-Prep Kit (BS88504; Sangon, Shanghai, China) according to the manufacturer’s protocols. The mitogenome was sequenced using the whole-genome shotgun method on an Illumina Miseq platform (Personalbio, Shanghai, China). After filtering low-quality and adapter contaminated reads, A5-miseq version 20150522 (Coil et al. 2015) was used for contig assembly.
Sequence annotation was performed using Geneious 10.1.3 (
The base compositions, codon usages, and relative synonymous codon usage (RSCU) values were calculated by MEGA 6.0. AT and GC skew were calculated by the following formulae: AT skew = (A–T)/(A+T) and GC skew=(G–C)/(G+C). To analyse the evolutionary patterns of the 13 PCGs, the rates of nonsynonymous substitution (Ka), the rates of synonymous substitution (Ks), and the ratio of Ka/Ks for each gene were calculated by the software DnaSP 5.0 (
In addition to the mitogenome newly sequenced here, 37 other mitogenomes were taken from Genbank for the phylogenetic analyses (Table
The dataset was used to reconstruct phylogenetic trees under Bayesian inference (BI) and maximum likelihood (ML) using MrBayes 3.2.6 (
The 17,309 bp mitochondrial genome of Myrmus lateralis was determined to be a typical circular nucleotide molecule, consisting of 13 PCGs, 22 tRNA genes, two rRNA genes, and a putative control region (Table
Gene | Strand | Size(bp) | Position | Intergenicnucleotides(IGN) | Anticodon | Codons | ||
---|---|---|---|---|---|---|---|---|
Start | Stop | Start | Stop | |||||
trnI | J | 66 | 1 | 66 | 0 | GAU | — | — |
trnQ | N | 69 | 64 | 132 | 2 | UUG | — | — |
trnM | J | 69 | 137 | 205 | 4 | CAU | — | — |
nad2 | J | 985 | 207 | 1191 | 1 | — | ATG | T |
trnW | J | 63 | 1204 | 1266 | 12 | UCA | — | — |
trnC | N | 62 | 1259 | 1320 | −8 | GCA | — | — |
trnY | N | 64 | 1321 | 1384 | 0 | GUA | — | — |
cox1 | J | 1539 | 1387 | 2925 | 2 | — | TTG | TAA |
trnL2UUR | J | 66 | 2921 | 2986 | −5 | UAA | — | — |
cox2 | J | 676 | 2987 | 3662 | 0 | — | ATT | T |
trnK | J | 72 | 3663 | 3734 | 0 | CUU | — | — |
trnD | J | 65 | 3738 | 3802 | 3 | GUC | — | — |
atp8 | J | 162 | 3803 | 3964 | 0 | — | ATA | TAA |
atp6 | J | 669 | 3958 | 4626 | −7 | — | ATG | TAA |
cox3 | J | 790 | 4626 | 5415 | −1 | — | ATG | T |
trnG | J | 63 | 5413 | 5475 | −3 | UCC | — | — |
nad3 | J | 349 | 5476 | 5824 | 0 | — | ATA | T |
trnA | J | 63 | 5825 | 5887 | 9 | UGC | — | — |
trnR | J | 64 | 5891 | 5954 | 3 | UCG | — | — |
trnN | J | 66 | 5954 | 6019 | −1 | GUU | — | — |
trnS1AGN | J | 69 | 6023 | 6091 | 3 | GCU | — | — |
trnE | J | 64 | 6091 | 6154 | −1 | UUC | — | — |
trnF | N | 66 | 6154 | 6219 | −1 | GAA | — | — |
nad5 | N | 1702 | 6220 | 7921 | 0 | — | ATA | T |
trnH | N | 63 | 7931 | 7993 | 9 | GUG | — | — |
nad4 | N | 1317 | 7994 | 9310 | 0 | — | ATG | TAA |
nad4L | N | 288 | 9304 | 9591 | −7 | — | ATT | TAA |
trnT | J | 62 | 9594 | 9655 | 3 | UGU | — | — |
trnP | N | 64 | 9656 | 9719 | 0 | UGG | — | — |
nad6 | J | 483 | 9728 | 10210 | 8 | — | ATA | TAA |
cytB | J | 1137 | 10210 | 11346 | −1 | — | ATG | TAG |
trnS2UCN | J | 69 | 11345 | 11413 | −2 | UGA | — | — |
nad1 | N | 927 | 11432 | 12358 | 18 | — | ATT | TAA |
trnL1CUN | N | 67 | 12359 | 12425 | 0 | UAG | — | — |
rrnL | N | 1261 | 12426 | 13686 | 0 | — | — | — |
trnV | N | 69 | 13687 | 13755 | 0 | UAC | — | — |
rrnS | N | 967 | 13756 | 14722 | 0 | — | — | — |
Control region | 2587 | 14723 | 17309 | 0 | — | — | — |
The mitochondrial genome of M. lateralis was strongly biased toward A+T (75.8%) in nucleotide composition, with 75.5%, 75.7%, 71.3%, and 74.8% A+T content in PCGs, rRNAs, tRNAs, and control regions, respectively. The nucleotide composition and skewness of the mitogenome is shown in Table
Nucleotide composition and skewness of the Myrmus lateralis mitochondrial genome.
Feature | T% | C% | A% | G% | A+T% | AT-skew | GC-skew |
Whole genome | 34.4 | 14.1 | 41.4 | 10.1 | 75.8 | 0.092 | −0.165 |
PCGs | 42.2 | 11.8 | 33.3 | 12.6 | 75.5 | −0.118 | 0.033 |
PCGs-1st | 44 | 14.1 | 28.5 | 13.6 | 72.5 | −0.214 | −0.018 |
PCGs-2nd | 39 | 11 | 35.3 | 14.2 | 74.3 | −0.05 | 0.127 |
PCGs-3rd | 44 | 10.4 | 36.1 | 10 | 80.1 | −0.099 | −0.02 |
tRNAs | 40 | 8.6 | 35.7 | 15.7 | 75.7 | −0.057 | 0.292 |
rRNAs | 35.7 | 14.1 | 35.6 | 14.7 | 71.3 | −0.001 | 0.019 |
Control region | 35 | 15.9 | 39.8 | 9.4 | 74.8 | 0.064 | −0.257 |
Relative synonymous codon usage (RSCU) values of the 13 PCGs were calculated based on 3633 codons (Fig.
In the M. lateralis mitogenome, nine PCGs were located on the J-strand (majority strand) and four PCGs were located on the N-strand (minority strand). The PCGs had a total length of 11,024 bp that accounted for 63.69% of the complete mitogenome. Among the mitochondrial proteins, Leu (16.67%), Phe (11.02%), and Tyr (9.58%) were the most frequent amino acids.
Most PCGs started with a typical ATN codon; five started with ATG (nad2, atp6, cox3, nad4, and cytb), four with ATA (atp8, nad3, nad5, and nad6), and three with ATT (cox2, nad4L, and nad1). The only unusual initiation codon was TTG in cox1. Among the 13 PCGs, seven genes ended with the complete stop codon TAA (cox1, atp8, atp6, nad1, nad4, and nad4L) or TAG (cytb), whereas five genes ended with the partial termination codon T (nad2, cox2, cox3, nad3, and nad5).
The evolutionary patterns of the 13 PCGs were analyzed and shown in Figure
A total of 22 tRNA genes were encoded by the M. lateralis mitogenome, ranging from 62 bp (trnC and trnT) to 72 bp (trnK) in length (Table
The large 1,261 bp rrnL gene was located between trnL1 (CUN) and trnV, and the small 967 bp rrnS gene was located between trnV and the control region. The secondary structures of both the rrnL and rrnS genes are shown in Figures
The 2587 bp mitochondrial control region of M. lateralis was located between the rrnS gene and trnI. The A+T content (74.76%) was higher than the G+C content (25.24%), with a positive AT-skew and a negative GC-skew. In the control region, tandem repeat sequences, polyT stretch, polyA stretch, stem-loop structure, tandem repeats, and G(A)n motif were commonly found. Based on these features, we identified the following important elements: a 13 bp polyT stretch, a G(A)9T sequence, an ATAGA motif, and a 9 bp polyA stretch. In addition, a stem-loop structure was observed at the end of the control region (Fig.
We conducted phylogenetic analyses based on the nucleotide sequences of the PCG+rRNA from eleven families within five superfamilies; one species from the Nabidae (damsel bugs) was used as an outgroup. The dataset contained 14,128 nucleotide sites from these 38 taxa. The BI and ML analyses generated identical phylogenetic results with most posterior probabilities (PP) of one and bootstrap pseudoreplicates (BP) of 100 (Fig.
In this study, we sequenced the mitogenome of Myrmus lateralis and built the molecular phylogenetic relationships with 37 other heteropteran taxa. The mitogenome was found to be 17,309 bp long, with 37 genes arranged consistent with other species of Hemiptera (
The present study analyzed the initiation and termination codons of the 13 PCGs. The majority of PCGs used common start codons (ATN), except for cox1, which was initiated with TTG, a frequently used start codon in heteropteran mitogenomes (
Although many studies have reconstructed phylogenetic relationships among members of Pentatomomorpha, the relationships of different levels are still ambiguous (
At the family level, Rhopalidae was found to be a sister group to Alydidae + Coreidae. This relationship, based on mitogenomes, was consistent with that based on cladistic analysis by
Previous studies on the classification of Rhopalinae came to a variety of conclusions and the positions of some species were not clear (
The complete mitogenome of the scentless plant bug Myrmus lateralis was sequenced using next-generation sequencing technologies, providing the fifth mitogenome sequence from approximately 230 species of Rhopalidae. The nucleotide composition, codon usage, RNA structures, and protein-coding genes evolution were analyzed in our paper. The mitogenome of M. lateralis revealed the phylogenetic position of Myrmus. However, more mitogenomes should be sequenced to investigate the mitogenomic evolution and phylogenetic relationships of Rhopalidae.
This project was supported by the National Science Foundation Project of China (no. 31501876, 31872272) and supported by Scientific Research Project of Xinzhou Teachers University (2018KY04).