The First Two Complete Mitochondrial Genomes for the Subfamily Meligethinae (Coleoptera: Nitidulidae) and Implications for the Higher Phylogeny of Nitidulidae

Abstract

The phylogenetic status of the family Nitidulidae and its sister group relationship remain controversial. Also, the status of the subfamily Meligethinae is not fully understood, and previous studies have been mainly based on morphology, molecular fragments, and biological habits, rather than the analysis of the complete mitochondrial genome. Up to now, there has been no complete mitochondrial genome report of Meligethinae. In this study, the complete mitochondrial genomes of Meligethinus tschungseni and Brassicogethes affinis (both from China) were provided, and they were compared with the existing complete mitochondrial genomes of Nitidulidae. The phylogenetic analysis among 20 species of Coleoptera was reconstructed via PhyloBayes analysis and Maximum likelihood (ML) analysis, respectively. The results showed that the full lengths of Meligethinus tschungseni and Brassicogethes affinis were 15,783 bp and 16,622 bp, and the AT contents were 77% and 76.7%, respectively. Each complete mitochondrial genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (A + T-rich region). All the PCGs begin with the standard start codon ATN (ATA, ATT, ATG, ATC). All the PCGs terminate with a complete terminal codon, TAA or TAG, except cox1, cox2, nad4, and nad5, which terminate with a single T. Furthermore, all the tRNAs have a typical clover-leaf secondary structure except trnS1, whose DHU arm is missing in both species. The two newly sequenced species have different numbers and lengths of tandem repeat regions in their control regions. Based on the genetic distance and Ka/Ks analysis, nad6 showed a higher variability and faster evolutionary rate. Based on the available complete mitochondrial genomes, the results showed that the four subfamilies (Nitidulinae, Meligethinae, Carpophilinae, Epuraeinae) of Nitidulidae formed a monophyletic group and further supported the sister group relationship of Nitidulidae + Kateretidae. In addition, the taxonomic status of Meligethinae and the sister group relationship between Meligethinae and Nitidulinae (the latter as currently circumscribed) were also preliminarily explored.

Keywords: barcode gene; evolution rate; identification; pollen beetle; species-specific markers.

Figure 1

Circle map of the complete mitochondrial genome of Meligethinus tschungseni.

Figure 2

Circle map of the complete mitochondrial genome of Brassicogethes affinis.

Figure 3

Relative synonymous codon usage (RSCU) of the PCGs of 10 species of Nitidulidae. The numbers above the bar graph indicate the frequency of amino acids.

Figure 4

Predicted secondary structure for the tRNAs of Meligethinus tschungseni (A-U, G-C regular paired keys marked with red and black lines, respectively; G-U, C-U, A-C, A-G mismatched keys marked with blue, green, gray, and yellow lines, respectively; U-U mismatched keys marked with solid black dots).

Figure 5

Predicted secondary structure for the tRNAs of Brassicogethes affinis (A-U, G-C regular paired keys marked with red and black lines, respectively; G-U, C-U, A-C, A-G mismatched keys marked with blue, green, gray, and yellow lines, respectively; U-U, A-A mismatched keys marked with solid black dots).

Figure 6

Structure of the control regions in the Nitidulidae mitochondrial genomes. Orange circles and box represent tandem repeat regions, and green boxes represent non-repeat regions. The brown, black, and purple regions represent poly (T), poly (C), and poly (A), respectively.

Figure 7

Sliding window analysis of 13 PCGs, 22 tRNAs, and 2 rRNAs in the mitochondrial genomes of 10 species of Nitidulidae. The red line represents the nucleotide diversity (Pi) value (window size = 200 bp, step size = 20 bp); the arrows represent the direction of gene coding—above the arrow is the Pi value of each gene, and below the arrow is the name of each gene; the blue arrows represent 13 PCGs, the pink arrows represent 22 tRNAs, and the orange arrows represent two rRNAs.

Figure 8

Genetic distances and ratios of non-synonymous (Ka) to synonymous (Ks) substitution rates of 13 PCGs among 10 species of Nitidulidae. The average value for each PCG is shown below the gene name.

Figure 9

Phylogenetic tree generated based on the ML analysis of the PCG123 dataset under the best model. The bootstrap support values of the corresponding nodes are represented by Arabic numerals.

Figure 10

Phylogenetic tree generated based on the PhyloBayes analysis of the PCG123 dataset under the site-heterogeneous mixture CAT + GTR substitution model. The Bayesian posterior probabilities of the corresponding nodes are represented by Arabic numerals.