The complete mitogenome of Orcula dolium (Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM

Abstract

BackgroundWith the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages.ResultsA sequence of the complete mitochondrial genome of the pupilloid landsnail Orcula dolium is presented. The mitogenome was amplified in a single long-range (LR) PCR and sequenced on an Ion Torrent PGM (Life Technologies). The length is 14,063 nt and the average depth of coverage is 1112 X. This is the first published mitogenome for a member of the family Orculidae. It has the typical metazoan makeup of 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S) and 22 transfer RNAs (tRNAs). Orcula is positioned between Pupilla and the Vertiginidae as the sister-group of Gastrocopta and Vertigo, together. An ancestral gene order reconstruction shows that Orthurethra in contrast to other Stylommatophora, have tRNA-H before tRNA-G and that the gene order in the ‘non-achatinoid’ clade is identical to that of closely related non-stylommatophoran taxa.ConclusionsWe show it is feasible to ultra-deep sequence a mitogenome from a single LR-PCR. This approach is particularly relevant to studies that have low concentrations of input DNA. It results in a more efficient use of NGS capacity (only the targeted fraction is sequenced) and is an effective selection against nuclear mitochondrial inserts (NUMTS). In contrast to previous studies based in particular on 28S, our results indicate that phylogeny reconstructions based on complete mitogenomes might be more suitable to resolve deep relationships within Stylommatophora. Ancestral gene order reconstructions reveal rearrangements that characterize systematic groups.Electronic supplementary materialThe online version of this article (doi:10.1186/s41065-017-0028-2) contains supplementary material, which is available to authorized users.

The complete mitogenome of Helix pomatia and the basal phylogeny of Helicinae (Gastropoda, Stylommatophora, Helicidae)

“…From annotated, previously published sequences (accession numbers NC_001816, NC_021747 and NC_017872), we extracted the individual genes following the annotation in the NCBI RefSeq database. However, previous studies, which used the sequence of Ce.nemoralis in mitogenomic phylogenetic analyses, repeatedly resulted in a spuriously long branch for this species (Knudsen et al 2006, González et al 2016, Minton et al 2016, Groenenberg et al 2017). A closer examination of the mitogenome sequence and translation of its protein coding regions revealed a very low quality of the sequence (see also White et al 2011).…”

“…Mitochondrial genome sequences may then become handy for primer design, to facilitate assembly of further mitochondrial genomes from outputs of high-throughput sequencing, or directly as the data for phylogenetic analyses. In fact, one of the best resolved backbone phylogenies of Stylommatophora to date was reconstructed from mitochondrial genome sequences (Groenenberg et al 2017).…”

The complete mitochondrial genome of the terrestrial snail Monacha cartusiana (O.F. Müller, 1774) (Gastropoda, Eupulmonata, Hygromiidae)

“…Phylogenetic analyses of the stylommatophoran mitogenomes (González et al 2016;Romero et al 2016) showed them in a well-supported clade among Panpulmonata (with PP and bootstrap values 1 and 99, respectively). Previous mitogenome phylogenies of stylommatophoran superfamilies (Groenenberg et al 2017;Harasewych et al 2017;Yang et al 2019;Doğan et al 2020) showed a clade of Helicoidea separate from other superfamilies, although mitogenomes of only 11 stylommatophoran superfamilies (Yang et al 2019) out of 26 listed by Bouchet et al (2017) are represented in GenBank. According to Bouchet et al (2017), Helicoidea includes 17 families but hitherto phylogenetic relationships could be analysed only for three or four of them, namely Helicidae, Camaenidae, Geomitridae, and Polygyridae (González et al 2016;Lin et al 2016;Minton et al 2016a;Harasewych et al 2017;Doğan et al 2020).…”

Analysis of genetic diversity in two different shell colors of the giant triton snail (Charonia tritonis) based on mitochondrial COI sequences

“…The mitochondrial DNA genome is widely used in several research fields, including genetics, evolution, and species genetic diversity, due to its unique structural features and genetic characteristics (Brown et al, 1982;Wang et al, 2019;Zhang et al, 2021), and it has become a very important molecular genetics tool. The mitochondrial genome has been widely used in the study of genetic variation and phylogeny of gastropod populations (Grande et al, 2008;Groenenberg et al, 2012;Groenenberg et al, 2017). Mitochondrial cytochrome oxidase (COI) genes in mitochondrial DNA are very conserved and highly homologous and are often used to analyze and explore population phylogenetic relationships (Miya et al, 2001).…”