title: The complete mitogenome ofOrcula dolium(Draparnaud, 1801); ultra-deep sequencing from a single long-range PCR using the Ion-Torrent PGM.
abstract: BACKGROUND
  With 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 thecompletemitogenome, 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.
  
  
  RESULTS
  A sequence of the complete mitochondrial genome of the pupilloid landsnailOrcula doliumis 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).Orculais positioned betweenPupillaand the Vertiginidae as the sister-group ofGastrocoptaandVertigo, 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
authors.forename: D S J
authors.initials: DSJ
authors.lastname: Groenenberg
authors.affiliation: Central Research Laboratories, Museum of Natural History Vienna, Vienna, Austria.|Department of Biology, Shinshu University, Matsumoto, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Harl
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Duijm
authors.affiliation: Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
authors.forename: E
authors.initials: E
authors.lastname: Gittenberger
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D023061:Gene Order; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA; D012908:Snails / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D012335:RNA, Ribosomal; D012343:RNA, Transfer
keywords: Gene arrangement; Mitochondrial genome; Orthurethra; Stylommatophora