Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications

Abstract

Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.

Keywords: Coleoptera; Monolepta; high-throughput sequencing; mitochondrial genome; phylogeny.

Figure 1

Circle maps of the four complete mitochondrial genomes of Monolepta species, with different colors to distinguish different genes.

Figure 2

Relative synonymous codon usage (RSCU) of the four new mitogenomes.

Figure 3

The secondary structure of tRNA-Ser1 (AGN) in the four newly determined mitogenomes, and the predicted secondary structure of tRNA-Val in the M. bicavipennis mitogenome. The pink circle represents a mismatched base, and the orange square represents a matched base.

Figure 4

Non-synonymous (Ka) to synonymous (Ks) substitution rates of 13 PCGs among four sequenced species.

Figure 5

The chart of substitution saturation for the three different mitogenomes’ datasets. The plots show uncorrected pairwise divergences in transitions (s) (blue) to transversions (v) (orange) compared with divergences calculated by GTR model.

Figure 6

Phylogenetic tree reconstructed by Bayesian inference method based on ND1 gene (34 species) under CAT-GTR model. Newly sequenced species in this study are highlighted in red color. The numbers above nodes are Bayesian posterior probabilities. Tips of synonymous species are highlighted in black color. Asterisk indicates that the bootstrap value of the node is lower than 0.50. Different colored backgrounds represent the different genera or outgroups.

Figure 7

Phylogenetic tree reconstructed by Bayesian inference method based on 13 PCGs-AA (18 species) under CAT-GTR model. Newly sequenced species in this study are highlighted in red color. The numbers above nodes are Bayesian posterior probabilities. Tips of synonymous species are highlighted in black color. Asterisk indicates that the bootstrap value of the node is lower than 0.50. Different colored backgrounds represent the different genera.