The complete mitochondrial genome of Tenomerga trabecula (Coleoptera: Archostemata: Cupedidae) and phylogenetic analysis among Coleoptera

Abstract

Tenomerga trabecula belongs to the Cupedidae family of Coleoptera. The first complete mitogenome of Cupedidae is reported in this paper. The genome is 16,741 bp in length and contains the typical 37 genes with 22 transfer RNA genes, 13 protein-coding genes, and 2 ribosomal RNA genes, which are arranged in the same order as the putative ancestor of beetles. The average base composition of the mitogenome is 42.9% for A, 14.5% for C, 8.7% for G, and 33.9% for T. The percentage of A + T is 76.8%. The genome organization, nucleotide composition, and codon usage are similar to other beetles. Phylogenetic analysis shows that Archostemata is monophyletic. Myxophaga, Adephaga, and Polyphaga are also monophyletic.

Keywords:

• Cupedidae
• mitogenome
• phylogeny
• Tenomerga trabecula

Tenomerga trabecula Neboiss, 1984 (Coleoptera: Archostemata: Cupedidae), is distributed in Taiwan, Fujian, and Hong Kong, China (Neboiss 1984; Rodriguez-Miron and Lopez-Perez 2019). Within 45 extant species of Archostemata in the world, Cupedidae is the richest family with 36 species (Rodriguez-Miron and Lopez-Perez 2019). Only one complete mitogenome from Archostemata (Ommatidae: Tetraphalerus bruchi, EU877953) has been sequenced to date (Sheffield et al. 2008).

The specimen used in this study was collected using a flight interception trap (FIT) in Hong Kong (22.389327°N, 114.081250°E) and deposited in the National Zoological Museum of China, Institute of Zoology, Chinese Academy of Sciences (IOZ, CAS) ([email protected]), with voucher number IOZ(E)2081544. It was identified by Yandong Chen of IOZ, CAS. Genomic DNA was extracted by a DNeasy Blood and Tissue kit (Qiagen, Germany) and deposited in a refrigerator at −20 °C at IOZ, CAS.

The complete mitogenome of T. trabecula was sequenced by the Illumina HiSeq 6000 platform with 400 bp insert size and a pair-end 150 bp sequencing strategy. The sequence reads were first filtered by the programs following Bolger et al. (2014); then, the remaining high-quality reads were assembled using mitoZ (Meng et al. 2019) and Getorganelle (Dierckxsens et al. 2017). The annotation of genes was performed by Geneious 8.0.5 software (Kearse et al., 2012) and MITOS (Bernt et al. 2013).

The mitogenome of T. trabecula was found to be a double-stranded circular molecule with 16,741 bp in length (GenBank accession number MW820160), containing the entire set of 37 genes usually present in most insect mtDNA (13 PCGs, 22 tRNA genes, and 2 rRNA genes) and a large non-coding region (control region). Twenty-three genes were transcribed on the majority strand (J-strand), whereas the others were oriented on the minority strand (N-strand). The overall organization of the mitogenome of T. trabecula is very compact, and numerous overlaps between genes are found. Five PCGs (ND2, ATP6, ND4, ND6, ND1) begin with an ATA start codon, and 4 PCGs (ATP8, ND3, ND5, ND4L) begin with an ATT start codon, while COX2, COX3, and CYTB begin with an ATG start codon. Nine PCGs terminate with an TAA stop codon, and only ND1 terminates with an TAG stop codon, whereas three genes (ATP6, ND6, COX2) terminate with incomplete T stop codons, which is frequently found in the mitogenome of beetles (Sheffield et al. 2008).

The aligned data from each locus were concatenated with PhyloSuite v1.2.2 (Zhang et al. 2020). A phylogenetic IQ-tree was constructed using PhyloSuite under the TVM + F + I + G4 model with 1000 bootstrap replicates (Nguyen et al. 2015). Nodal support values were estimated using the SH-aLRT branch test, which is computationally efficient and relatively unbiased.

The IQ-tree based on the concatenated 13 PCGs (Figure 1) shows that Coleoptera were recovered as monophyletic. The available suborder rank of Coleoptera ((Myxophaga + Adephaga) + (Archostemata + Polyphaga)) was resolved with strong support. This topology supports the monophyly of four suborders and the sister group relationships between Adephaga and Myxophaga and between Polyphaga and Archostemata, which is consistent with the analysis using the mitogenomes of 50 representative species from Coleoptera (Zhang et al. 2016).

Figure 1. The IQ-tree based on 13PCGs combined data sets. Numbers on nodes indicate bootstraps. Red branch is the new data in this study.

Acknowledgments

The authors thank Kinfung Chan, Yin Yip, Kahong Cheung, Yingming Lee, Manhin Leung, and the fellows of the Beetle Working Group of AFCD for the field work in Hong Kong; Yandong Chen and Xu He from Institute of Zoology, Chinese Academy of Sciences, for specimens sorting and identification; and Rei’E Nie from Institute of Zoology, Chinese Academy of Sciences, for data analysis.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The genome sequence data supporting the findings of this study are openly available in the NCBI GenBank at https://www.ncbi.nlm.nih.gov/ under accession number MW820160. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA750629, SRR15293804, and SAMN20448115, respectively.

Additional information

Funding

This work was supported by the National Science & Technology Fundamental Resources Investigation Program of China (Grant Nos. 2019FY100400, 2019FY101800), the National Natural Science Foundation of China (No. 31961143002), the Bureau of International Cooperation, Chinese Academy of Sciences, GDAS Special Project of Science and Technology Development (Nos. 2020GDASYL-20200102021, 2020GDASYL-20200301003), the Second Tibetan Plateau Scientific Expedition and Research Program (STEP), Grant No. 2019QZKK05010101.