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

Abstract

Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes.

The mitochondrial genome of the semi-slug Omalonyx unguis (Gastropoda: Succineidae) and the phylogenetic relationships within Stylommatophora

“…Our results located Succineoidea as a sister group of Helicoidea + Urocoptoidea with Arionoidea grouping outside. These findings are consistent with the most recent results from Doğan et al [ 7 ]. However, earlier phylogenies based on individual genes showed close relationships between Arionoidea and Limacoidea, while they failed to clarify the relationships of Elasmognatha (Succineidae + Athoracophoridae) within “achatinoids” [ 32 ].…”

“…Metazoa mitochondrial (mt) genome is a circular double stranded DNA that typically encodes two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 13 protein-coding genes (i.e., cytochrome c oxidase subunits I-III ; cytochrome b ; ATP synthase subunits 6 and 8 ; NADH dehydrogenase subunits 1–6 and 4L ), with a size ranging from 14 to 20 kb [ 1 – 4 ]. In recent years, the development of new technologies and the decrease in sequencing costs produced a significant increase in available animal mitogenomes, and currently more than 90,000 mitochondrial genomes are deposited in NCBI database [ 5 – 7 ]. Despite this and considering that mollusks are the second most specious animal phylum, they continue to be a poorly represented taxon with only 1,440 known mitogenomes (approximately 0.04% of species represented) [ 8 ].…”

The queen conch mitogenome: intra- and interspecific mitogenomic variability in Strombidae and phylogenetic considerations within the Hypsogastropoda

“…Ministrombus variabilis is unique with Ala (GCG) and stop (UAG) codons as less frequently used. As shown previously in other gastropods 45 , 46 , the codons rich in A and T are used more frequently in all mitogenomes analyzed here than codons with C or G content, and codons with A or T at the third position are even more utilized (RSCU from 0.89 to 2.62) than those with C or G (RSCU from 0.07 to 0.98).…”

“…The two mitogenomes of Aliger gigas , however, present two different codons in the top 5 frequently used codons: Thr (ACU) and Val (GUU) (order is specimen dependent) instead of Arg and Pro. Leu (UUA), Ser (UCU), and Ala (GCU) are the most frequently used codons reported for gastropods 13 , 45 , 46 . The codons least frequently used (lower RSCU values) for both A. gigas specimens were Ser2 (UCG) and Thr (ACG), whereas the other Strombidae species presented variation: L. lambis [Arg (CGC) and Ser2 (UCG)], H. chiragra [Ala (GCG) and Leu1 (CUG)], C. luhuanus [Ala (GCG) and Thr (ACG)], T. dentatus [Leu1 (CUG) and Pro (CCG)], S. pugilis [Ala (GCG) and Arg (CGC)], and L. canarium [Ser2 (UCG) and Leu1 (CUG)].…”

“…The codons least frequently used (lower RSCU values) for both A. gigas specimens were Ser2 (UCG) and Thr (ACG), whereas the other Strombidae species presented variation: L. lambis [Arg (CGC) and Ser2 (UCG)], H. chiragra [Ala (GCG) and Leu1 (CUG)], C. luhuanus [Ala (GCG) and Thr (ACG)], T. dentatus [Leu1 (CUG) and Pro (CCG)], S. pugilis [Ala (GCG) and Arg (CGC)], and L. canarium [Ser2 (UCG) and Leu1 (CUG)]. Generally, these codons are reported less frequently in other gastropods as well 13 , 45 , 46 except for Thr (ACG). Ministrombus variabilis is unique with Ala (GCG) and stop (UAG) codons as less frequently used.…”