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. 2022 Dec 12;7(12):2040–2043. doi: 10.1080/23802359.2022.2151829

Complete mitochondrial genome and phylogenetic analysis of Mastax latefasciata Liebke 1931 (Insecta: Coleoptera: Carabidae)

Yu Bai a, Lin Ye b, Kang Yang b, Xuyuan Gao c,d,✉
PMCID: PMC9754013  PMID: 36530456

Abstract

The genus Mastax Fischer von Waldheim 1827 belongs to the family Carabidae. Specimens of adult Mastax latefasciata Liebke, 1931 were collected from Yājì Hill, Huáihuà City, Húnán Province, China. The complete mitochondrial genome (GenBank accession number ON674050.1) of M. latefasciata was sequenced, annotated, and characterized. The results showed that it was a circular DNA molecule of 16,735 bp with 81.07% AT content and comprised 13 protein-coding genes (PCG), 22 tRNA genes, 2 rRNA genes, and 1 control region. The PCGs were initiated using typical ATN (Met) and TTG (Met) start codons and terminated using typical TAN stop codons. The phylogenetic position of Mastax within the Carabidae was first evaluated using complete mitogenomes, and the results showed that it was close to Cicindela anchoralis and Manticora tibialis.

Keywords: Mastax latefasciata, Carabidae, mitochondrial genome, phylogenetic analysis

The genus Mastax Fischer von Waldheim 1827 belongs to the tribe Brachinini of the family Carabidae (Liang and Yu 2004), and eight species have been recognized in China (Liang and Yu 2004). Jedlička in Eastern Asia provided a key for Mastax latefasciata Liebke, 1931 (Liebke 1931; Liang and Yu 2004), which is the basal half of the elytra with one yellow square band and a band width of approximately two-fifths the length of the elytra (Liang and Yu 2004; Figure 1). At present, the nucleotide database of the National Center for Biotechnology Information (NCBI) has not publicly published the mitochondrial information of the genus Mastax, with the exception of the 16S ribosomal RNA (rRNA) gene of M. formosana. M. latefasciata is relatively common and readily available in China. In this study, the complete mitochondrial genome (mitogenome) of M. latefasciata was first sequenced, annotated and characterized, which would have significance for contributing to the research on phylogenetic position of the genus Mastax.

Figure 1.

Figure 1.

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Species reference image of Mastax latefaciata. (A) the ventral view of M. latefaciata; (B) the dorsal view of M. latefaciata. M. latefaciata was imaged using VHX-2000 digital microscope system.

Specimens of adult M. latefasciata were collected from Yājì Hill (110.55° N, 27.85° E), Zhòngxià Village, Xùpǔ County, Huáihuà City, Húnán Province, China, on April 24, 2022, and deposited in the Insect Collection of Institute of Plant Protection, Guangxi Academy of Agricultural Sciences (http://www.gxaas.net/s.php/zwbhyjs/, Xuyuan Gao, gxy@gxaas.net) under the voucher number GIPP-20220424-001.

Genomic DNA was isolated using the Qiagen DNeasy Blood and Tissue Extraction kit (Qiagen, Germantown, MD, USA) and subjected to paired-end sequencing (2 × 150 bp) of 300 bp inserts using an Illumina NovaSeq 6000 platform (Illumina, Inc., San Diego, CA, USA). The obtained raw reads were filtered to obtain clean reads using fastp v0.23.2 (https://github.com/OpenGene/fastp) (Chen et al. 2018). The quality control (QC) standards of reads from DNA were: (1) Trimming adapter sequences with >6 bases, (2) Removing reads with >0 unidentified nucleotides (N), (3) Removing reads with >20% bases with Phred quality < Q30, (4) Removing reads with <150 bases. We obtained approximately 30.13 Gb of clean high-quality data from the raw data of 35.80 Gb. The complete circular mitogenome (GenBank accession number: ON674050.1) of M. latefasciata was assembled de novo using NOVOPlasty v4.3.1 (https://github.com/ndierckx/NOVOPlasty) (Dierckxsens et al. 2017) with default parameters and the mitogenome of Harpalus sinicus (GenBank accession number: MN310888.1/NC_045094.1) (Yu et al. 2019) used as a seed sequence, which was found to be 16,735 bp (nucleotide composition: 40.34% A, 40.73% T, 7.52% C, and 11.41% G) in length with 81.07% AT content. The AT-skew [(A − T)/(A + T)] and GC-skew [(G − C)/(G + C)] of the sequence were estimated to investigate the nucleotide composition bias using Perna and Kocher’s formula (Perna and Kocher 1995). The AT and GC skews of the major strand of the mitogenome were estimated to be −0.00479 and 0.20581, respectively. The mitogenome of M. latefasciata was initially annotated using GeSeq v2.03 (https://chlorobox.mpimp-golm.mpg.de/geseq.html) (Tillich et al. 2017), using the third-party software tRNAscan-SE v2.0.7 (Chan and Lowe 2019), ARWEN v1.2.3 (Laslett and Canbäck 2008), BLAT v36 × 7 (Kent 2002) with the mitogenome of Harpalus sinicus (MN310888.1/NC_045094.1) as a reference. In addition, the start and stop codons of protein-coding genes (PCGs) were corrected manually using the genomes of Harpalus sinicus (MN310888.1/NC_045094.1) (Yu et al. 2019), Promethis valgipes valgipes (Bai et al. 2021), Tenebrio obscurus (Bai et al. 2018), and Zophobas atratus (Bai et al. 2019) as references. The mitogenome of M. latefasciata comprises 13 PCGs, 1 control region (CR), 22 tRNA genes, and 2 rRNA genes. The order and orientation of the genes were determined and drawn (Figure 2) using the OGDRAW web server (https://chlorobox.mpimp-golm.mpg.de/OGDraw.html) (Greiner et al. 2019).

Figure 2.

Figure 2.

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Mitogenome pattern map of Mastax latefaciata. Gray arrows indicate 5′→3′; genes inside the circle are transcribed clockwise, genes outside the circle counter clockwise; the grey circle inside was the GC content graph, which marks the 50% threshold.

All 13 PCGs had a typical ATN (Met) start codon, with the exception of nad1 (a typical TTG start codon): seven PCGs (nad2, cox1, atp8, nad3, nad5, nad4l, and nad6) initiated with an ATT start codon; five PCGs (cox2, atp6, cox3, nad4, and cob) initiated with an ATG start codon. All 13 PCGs contained a typical TAN stop codon: cob terminated with a TAG stop codon; seven PCGs (nad2, atp8, atp6, nad3, nad4l, nad6, and nad1) ended with a TAA stop codon; five PCGs (cox1, cox2, cox3, nad5, and nad4) terminated with an incomplete stop codon (T), consisting of a codon that was completed by the addition of A nucleotides at the 3′ end of the encoded mRNA. The 22 tRNA ranged from 61 (trnA-UGC) to 71 bp (trnQ-UUG and trnK-CUU). The rrnL and rrnS were 1319 and 781 bp in length, respectively. The CR, also an AT-rich region, was 1,890 bp in length with an 88.78% AT content and located between the rrnS and trnI-GAU genes.

For phylogenetic analyses, mitogenomes of 16 Carabidae species and two outgroup species [Morphostenophanes sinicus (MW853764.1) (Bai et al. 2021) and Lepisma saccharina (MT108230.1) (Bai et al. 2020)] were used to evaluate the phylogenetic relationships within the Carabidae using MEGA v11.0.13 (Tamura et al. 2021). The amino acid sequences of 13 PCGs in their mitogenomes were aligned using MEGA (Tamura et al. 2021) with the MUSCLE program (Edgar 2004) using default specifications. The maximum-likelihood (ML) model with the lowest Akaike Information Criterion corrected (AICc) score was considered to be the best. Based on the AICc value (88830.21), general reversible mitochondrial model (mtREV24) with amino acid frequencies (+F), gamma distribution (+ G, parameter = 0.4951, five rate categories) and invariant sites (+I, 22.29% sites) was chosen as the optimal phylogenetic model with 500 bootstrap replications for phylogenetic analysis (Figure 3). The structure of the phylogenetic tree is similar to reported in previous studies (Yu et al. 2019). The phylogenetic position of Mastax within the Carabidae was first evaluated using complete mitogenomes, and the results showed that it was close to Cicindela anchoralis and Manticora tibialis. In this study, the complete mitogenome characteristics of M. latefasciata would improve the understanding of the evolution of this species and phylogenetic position of the genus Mastax with the related taxa.

Figure 3.

Figure 3.

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Maximum-Likelihood phylogenetic tree of 18 species based on amino acid sequences of 13 PCGs of their mitogenomes. The highest log-likelihood of the phylogenetic tree was -44748.30. The percentage of trees is shown in red. The complete mitogenome of M. latefasciata (ON674050) determined in this study is shown in green. The following sequences were used: Carabus changeonleei MG253028 (Wang et al. 2019), Damaster mirabilissimus mirabilissimus GQ344500 (Wan et al. 2012), Carabus lafossei KY992943 (Liu et al. 2018), Carabinae sp. BYU-CO241 GU176340 (Song et al. 2010), Notiophilus quadripunctatus MW800883 (Raupach et al. 2022), Pterostichus niger KT876909 (Linard et al. 2016), Stomis pumicatus KT876914 (Linard et al. 2016), Abax parallelepipedus KT876877 (Linard et al. 2016), Harpalus pensylvanicus MN245975 (Kieran 2020), Harpalus sinicus MN310888 (Yu et al. 2019), Omophron limbatum MW800882 (Raupach et al. 2022), Tachyta nana KX035142 (Linard et al. 2016), Cicindela anchoralis MG253029 (Wang et al. 2018), Manticora tibialis MF497821 (López-López and Vogler 2017), Lepisma saccharina MT108230 (Bai et al. 2020), and Morphostenophanes sinicus (MW853764.1) (Bai et al. 2021).

Funding Statement

This work was financially supported by the fund of Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests [2020-KF-03]; Foundational Research Fund of Guangxi Academy of Agricultural Sciences under [Grant No. 2021YT067]; Guangxi Natural Science Foundation under [Grant No. 2020GXNSFBA297162]; and Guizhou Fundamental Research Program (Natural Science Project) under [grant number QianKeHeJiChu-ZK[2022]YiBan006].

Ethical approval

This research does not involve ethical research. Insects are invertebrates, and there are no ethics involved in using them in experiments.

Author contributions

Yu Bai, analyzed the data, uploaded the analysis data, involved in certain tools for analysis, drafted of the paper, and approved the final draft. Lin Ye, collected and analyzed data. Kang Yang, performed the experiments and analyzed data. Xuyuan Gao, identified insects, contributed reagents/materials, involved in conception and design of the work, performed the experiments, prepared figure, and approved and published the final draft. All authors agree to be accountable for all aspects of the work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

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. ON674050.1. The associated BioProject, Bio-Sample, and SRA numbers are PRJNA857156, SAMN29618062, and SRR20082406 respectively.

References

  1. Bai Y, Chen J, Li G, Luo J, Wang H, Yang Y, Liang S, Ouyang B.. 2021. Complete mitochondrial genome of Promethis valgipes (Marseul) (Insecta: coleoptera: tenebrionidae). Mitochondrial DNA B Resour. 6(2):538–539. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bai Y, Chen J, Li G, Wang H, Luo J, Li C.. 2020. Complete mitochondrial genome of the common silverfish Lepisma saccharina (Insecta: Zygentoma: Lepismatidae). Mitochondr DNA Part B. 5(2):1552–1553. [Google Scholar]
  3. Bai Y, Gao X, Yu Y, Long X, Zeng X, Wei D, Ye L.. 2021. Complete mitochondrial genome of Morphostenophanes sinicus (Zhou, 2020) (Insecta: Coleoptera: Tenebrionidae). Mitochondr DNA B Resour. 6(10):2946–2948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bai Y, Li C, Yang M, Liang S.. 2018. Complete mitochondrial genome of the dark mealworm Tenebrio obscurus Fabricius (Insecta: coleoptera: tenebrionidae). Mitochondr DNA B Resour. 3(1):171–172. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bai Y, Wang H, Li G, Luo J, Liang S, Li C.. 2019. Complete mitochondrial genome of the super mealworm Zophobas atratus (Fab.)(Insecta: coleoptera: tenebrionidae). Mitochondr DNA Part B. 4(1):1300–1301. [Google Scholar]
  6. Chan PP, Lowe TM.. 2019. tRNAscan-SE: searching for tRNA Genes in Genomic Sequences. In: Kollmar M, editor. Gene prediction: methods and protocols. New York, NY: springer New York; p. 1–14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chen S, Zhou Y, Chen Y, Gu J.. 2018. FASTP: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dierckxsens N, Mardulyn P, Smits G.. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18-e18. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5):1792–1797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Greiner S, Lehwark P, Bock R.. 2019. OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res. 47(W1):W59–W64. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kent WJ. 2002. BLAT—The BLAST-like alignment tool. Genome Res. 12(4):656–664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kieran TJ. 2020. Mitochondrial, metagenomic, and phylogenetic analysis of the ground beetle Harpalus pensylvanicus (Coleoptera: Carabidae). Gene. 740:144540. [DOI] [PubMed] [Google Scholar]
  13. Laslett D, Canbäck B.. 2008. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics. 24(2):172–175. [DOI] [PubMed] [Google Scholar]
  14. Liang H-b, Yu P-Y.. 2004. On Chinese species of the genus Mastax Fischer von Waldheim (Coleoptera, Carabidae). Acta Zootaxonomica Sinica. 29(1):139–141. [Google Scholar]
  15. Liebke M. 1931. Laufkäfer Studien X. Entomologische Anzeiger. 12:146–149. [Google Scholar]
  16. Linard B, Arribas P, Andújar C, Crampton-Platt A, Vogler AP.. 2016. Lessons from genome skimming of arthropod-preserving ethanol. Mol Ecol Resour. 16(6):1365–1377. [DOI] [PubMed] [Google Scholar]
  17. Liu N, Wang S, Yang X, Song J, Wu J, Fang J.. 2018. The complete mitochondrial genome of Carabus (Damaster) lafossei (Coleoptera: carabidae). Conservation Genet Resour. 10(2):157–160. [Google Scholar]
  18. López-López A, Vogler AP.. 2017. The mitogenome phylogeny of Adephaga (Coleoptera). Mol Phylogenet Evol. 114:166–174. [DOI] [PubMed] [Google Scholar]
  19. Perna NT, Kocher TD.. 1995. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol. 41(3):353–358. [DOI] [PubMed] [Google Scholar]
  20. Raupach MJ, Deister F, Villastrigo A, Balke M.. 2022. The complete mitochondrial genomes of Notiophilus quadripunctatus Dejean, 1826 and Omophron limbatum (Fabricius, 1777): New insights into the mitogenome phylogeny of the Carabidae (Insecta, Coleoptera). Insect Syst Evol. 53(3):242–263. [Google Scholar]
  21. Song H, Sheffield NC, Cameron SL, Miller KB, Whiting MF.. 2010. When phylogenetic assumptions are violated: base compositional heterogeneity and among-site rate variation in beetle mitochondrial phylogenomics. Systematic Entomology. 35(3):429–448. [Google Scholar]
  22. Tamura K, Stecher G, Kumar S.. 2021. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 38(7):3022–3027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S.. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Wan X, Hong MY, Liao A, Kim MI, Kim K-G, Han YS, Kim I.. 2012. Complete mitochondrial genome of a carabid beetle, Damaster mirabilissimus mirabilissim (Coleoptera: carabidae). Entomol Res. 42(1):44–54. [Google Scholar]
  25. Wang AR, Kim MJ, Hong EJ, Jeong J-C, Kim SS, Kim I.. 2019. Complete mitochondrial genome sequence of Acoptolabrus changeonleei Ishikawa et Kim, 1983 (Coleoptera: carabidae). Mitochondr DNA Part B. 4(1):1883–1885. [Google Scholar]
  26. Wang AR, Kim MJ, Jeong SY, Kim I.. 2018. Complete mitochondrial genome sequence of Cicindela anchoralis Chevrolat, 1845 (Coleoptera: carabidae). Mitochondrial DNA B Resour. 3(1):282–283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Yu X, Tan W, Zhang H, Jiang W, Gao H, Wang W, Liu Y, Wang Y, Tian X.. 2019. Characterization of the complete mitochondrial genome of Harpalus sinicus and its implications for phylogenetic analyses. Genes. 10(9):724. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

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

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. ON674050.1. The associated BioProject, Bio-Sample, and SRA numbers are PRJNA857156, SAMN29618062, and SRR20082406 respectively.

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