Abstract
The complete mitochondrial genome (mitogenome) of Tropidothorax sinensis (Reuter, 1888) was determined in the present study by using high-throughput sequencing. This mitogenome is 15,422 bp in size and comprises 37 typical coding genes and a control region. All protein-coding genes are initiated with ATN, except for COX1 and ND4L use TTG as the start codon, and terminate with TAA or TAG with the exception of COX2, COX3 and ND1 which use a single T residue as the stop codon. Twenty-one of the 22 transfer RNA genes have the typical clover-leaf structure except for tRNASer(AGN). The monophyly of the family Lygaeidae and the sister relationship between T. sinensis and T. cruciger is supported by maximum likelihood analysis based on the protein-coding and ribosomal RNA gene sequences.
Lygaeoidea is the second largest superfamily in the Pentatomomorpha, which includes more than 4,290 described species classified into seventeen families (Henry Citation2017). Most Lygaeoidea species are phytophagous, whereas a few species are predators. Tropidothorax sinensis (Reuter, 1888) is an important agricultural and forest pest, mainly distributed in China mainland and Japan. In the present study, we describe the complete mitogenome of T. sinensis, which will be useful for the molecular identification of this important pest and phylogenetic study of the family Lygaeidae.
The sample was collected from Zunyi, Guizhou, China (28°23′27″N, 107°36′65″E). Voucher specimen is stored at the Entomological Museum of China Agricultural University (No. HEM-098, Weidong Huang, [email protected]). Genomic DNA extraction was performed using the DNeasy Blood and tissue kit (Qiagen, Germany) following the manufacturer’s protocol. An Illumina TruSeq library was prepared with an average insert size of 350 bp and sequenced using the Illumina Hiseq 2500 platform with 150 bp paired-end reads. Raw reads were trimmed of adapters using Trimmomatic (Bolger et al. Citation2014) and low quality and short reads were removed using Prinseq (Schmieder and Edwards Citation2011). High quality reads were then used to produce a de novo assembly using IDBA-UD (Peng et al. Citation2012) with minimum and maximum k values of 41 and 141 bp, respectively. The mitogenome sequence of T. sinensis was identified by Geneious 10.1.3 (http://www.geneious.com). Genomic annotations were performed using MITOS2 (Bernt et al. Citation2013) and tRNAscan-SE 2.0 (Lowe and Chan Citation2016), and the result was further confirmed using NCBI-BLAST (http://blast.ncbi.nlm.nih.gov).
The complete mitogenome of T. sinensis is 15,422 bp in size, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a control region. The gene order and orientation is identical to the putative ancestral arrangement of insects (Cameron Citation2014). The A + T content of the mitogenome is 75.8% (A = 41.7%, T = 33.3%, C = 14.5%, G = 10.5%) which is significantly biased toward AT. Eleven PCGs initiate with ATN codons (2 with ATA, 5 with ATG, and 4 with ATT), whereas two genes, namely COX1 and ND4L, start with TTG. The stop codon TAA or TAG was assigned to 10 PCGs (2 with TAG, 8 with TAA). The remaining three PCGs (COX2, COX3 and ND1) use a single T residue as an incomplete stop codon, a phenomenon commonly observed in true bugs (Zhang et al. Citation2019). There are 22 tRNA genes, ranging from 60 to 75 bp in length. The secondary structure of 21 tRNAs were typical clover-leaf structure except for the tRNASer(AGN), in which the dihydrouridine (DHU) arm formed a loop. The length of lrRNA and srRNA is 1,255 bp and 769 bp, respectively. The control region is located between srRNA and tRNAIle, which is 941 bp in length with an A + T content of 76.3%.
Sequences of 13 PCGs and two rRNAs from 12 Lygaeoidea species and two outgroup taxa from Pyrrhocoroidea (Li et al. Citation2017; Liu et al. Citation2019), were aligned by MAFFT 7.0 (Katoh and Standley Citation2013) and concatenated for phylogenetic analysis. Phylogenetic tree was inferred from the maximum likelihood (ML) analysis using IQ-TREE 1.6.5 (Trifinopoulos et al. Citation2016) under the best fitting GTR + I + G model. The result supports the monophyly of the family Lygaeidae (), as well as the sister relationship between T. sinensis and T. cruciger with high bootstrap value (100).
Figure 1. Maximum likelihood phylogeny of 12 Lygaeoidea species based on the concatenated nucleotide sequences of 13 PCGs and two rRNAs. Number at nodes represent ML bootstrap percentages (1000 replicates). GenBank accession numbers for published sequences are incorporated. The newly sequenced T. sinensis mitogenome is highlighted using bold and black.
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability statement
The data that support the findings of this study will be available in GenBank at https://www.ncbi.nlm.nih.gov/, accession number MW547017, SRR13712603.
Additional information
Funding
References
- Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G, Putz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319.
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30:2114–2120.
- Cameron SL. 2014. Insect mitochondrial genomics: implications for evolution and phylogeny. Annu Rev Entomol. 59:95–117.
- Henry TJ. 2017. Biodiversity of Heteroptera. In Foottit RG, Adler PH, editors. Insect biodiversity: science and society. Vol. I. 2nd ed. New Jersey: Wiley-Blackwell; p. 279–335.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
- Li H, Leavengood JM Jr, Chapman EG, Burkhardt D, Song F, Jiang P, Liu J, Zhou X, Cai W. 2017. Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs. Proc R Soc B. 284(1862):20171223.
- Liu Y, Li H, Song F, Zhao Y, Wilson J, Cai W. 2019. Higher-level phylogeny and evolutionary history of Pentatomomorpha (Hemiptera: Heteroptera) inferred from mitochondrial genome sequences. Syst Entomol. 44(4):810–819.
- Lowe TM, Chan PP. 2016. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44:W54–W57.
- Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics. 28(11):1420–1428.
- Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 27:863–864.
- Trifinopoulos J, Nguyen LT, Haeseler AV, Minh BQ. 2016. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44:W232–W235.
- Zhang DL, Gao J, Li M, Yuan J, Liang J, Yang H, Bu W. 2019. The complete mitochondrial genome of Tetraphleps aterrimus (Hemiptera: Anthocoridae): genomic comparisons and phylogenetic analysis of Cimicomorpha. Int J Biol Macromol. 130:369–377.