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.

The complete mitogenome ofArion vulgarisMoquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

“…The usage of all mitochondrial genes and codon positions (P123RNA dataset) under both approaches resulted with identical tree topology ( Figs. S3 and S4), which were similar to the results of Yang et al (2019) obtained using only amino acid sequences of mitochondrial PCGs. The results of these analyses supported the monophyly of all included superfamilies with high nodal supports except for the superfamily Helicoidea which recovered with low nodal support [Bayesian Posterior Probability (BPP) = 0.75, Bootstrap support (BS) = 58%] and recovered Arionoidea superfamily as sister group to Urocoptoidea + (Polygyroidea + Helicoidea) clade (BPP = 1.00, BS = 100%), and Succineoidea + Orthalicoidea clade was recovered as sister group to Arionoidea + (Urocoptoidea + (Polygyroidea + Helicoidea)) (BPP = 1.00, BS = 50%).…”

“…The tree (Fig. 4) reticulatum (Limacoidea: Agriolimacidae) at the most basal placement and did not support the monophyly of the suborder Helicina similar to the tree in Yang et al (2019). A chronogram for Stylommatophora divergence times based on the obtained tree topology is shown in Fig.…”

“…In the A. vulgaris mitogenome, most of the PCGs initiated with typical ATN start codon, except for COX1, ND5 and ATP8 genes which use TTG, ACA and GTG triplets as start codons, respectively ( Table 2). The TTG and GTG start codons are also accepted as canonical start codons for invertebrate mitogenomes (Yang et al, 2019), however, ACA as start codon for ND5 gene was reported for the first time for stylommatophoran mitogenomes. Most of the PCGs were inferred to use TAR as termination codon, except for ND4L and COX3 which have an abbreviated T-termination codon and their products are probably completed via post-transcriptional polyadenylation (Anderson et al, 1981;Ojala, Montoya & Attardi, 1981).…”

“…Mitogenomes have become widely used tools in recent phylogeny, phylogeography and molecular dating analyses in various taxa, because of their (1) relatively small size, (2) the high copy number, (3) maternal inheritance type and (4) relatively rapid rate of evolutionary change (Moritz, Dowling & Brown, 1987;Gray, 1989). The sequence information of mitogenomes has also been used in reconstructing phylogenies of several taxonomic groups within/including Gastropoda (White et al, 2011;Stöger & Schrödl, 2013;Sevigny et al, 2015;Uribe et al, 2016a;Uribe et al, 2016b;Romero, Weigand & Pfenninger, 2016;Yang et al, 2019). Although there have been some criticisms about the usage of mitogenomes in construction of gastropod phylogeny because of long branch attraction, substitution saturation and strand-specific skew bias (Stöger & Schrödl, 2013), within the recently diversified lineages of gastropods, the use of mitogenomes resulted in highly resolved phylogenies (Williams, Foster & Littlewood, 2014;Osca, Templado & Zardoya, 2014).…”

“…Besides the use of the mitogenome in sequencebased phylogenies, mitogenome rearrangements can also provide phylogenetic signals (Grande, Templado & Zardoya, 2008;Stöger & Schrödl, 2013;Xie et al, 2019b). Although the mitogenome is widely used in phylogeny of many gastropod groups (Arquez, Colgan & Castro, 2014;Osca, Templado & Zardoya, 2014;Sevigny et al, 2015;Uribe, Zardoya & Puillandre, 2018), there are limited numbers of reported stylommatophoran mitogenomes and phylogenetic studies in Stylommatophora in terms of usage of mitogenome sequence and rearrangement (Romero, Weigand & Pfenninger, 2016;Xie et al, 2019a;Yang et al, 2019). To date, complete or nearly complete mitogenomes have been reported for only 34 stylommatophoran species (NCBI, September, 2019).…”