The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis

Abstract

The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.

Keywords: Philomycus bilineatus; mitochondrial genome; phylogenetic analysis.

Figure 1

Circular map of the mitogenome of Philomycus bilineatus. The outside and inside of the ring indicate that the gene is encoded by a heavy chain and light chain of mitochondrial genes. Different colors represent different gene families: The yellow shows the NADH dehydrogenase family gene, the pink part is the cytochrome c oxidase family gene, the red shows two different ribosomal RNAs, the green acts as two ATPase family genes, the purple represents the cytochrome c biogenesis gene, and the deep blue region is the translation region of the transport RNA.

Figure 2

Mitochondrial DNA control region secondary structure of P. bilineatus, built using the Predict a Secondary Structure Web Server [35]. The structure is colored by base-pairing probabilities. For unpaired regions, the color denotes the probability of being unpaired.

Figure 3

The relative synonymous codon usage (RSCU) in the mitogenomes of (A) P. bilineatus and (B) Meghimatium bilineatus.

Figure 4

Codon distribution in the P. bilineatus and M. bilineatum mitogenome. Numbers to the left refer to the total number of the codon. Codon families are provided on the X-axis.

Figure 5

Graphical illustration showing the AT and GC skew in the protein-coding genes (PCGs) of (A) P. bilineatus and (B) M. bilineatus.

Figure 6

Predicted secondary structures for the transfer RNA (tRNA) genes in the P. bilineatus (Pb) and M. bilineatus (Mb).

Figure 7

Phylogeny of P. bilineatus. The phylogenetic tree was inferred from the amino acid sequences of the 13 PCGs in the mitogenome. The numbers on the branches indicate the posterior probabilities (BI/ML). Chitonida species (C. cavema and N. californica) were used as the outgroups. Different colors represent different superfamilies.

Figure 8

The biological evolution trend of respiration: (A) Aplysia californica; (B) Pleurobranchaea nobaezealandiae; (C) Pleurobranchaea sp.; (D) Homoiodoris japonica; (E) Peronia verruculata; (F) Onchidium reevesii; (G) P. bilineatus.