The mitochondrial genome of Lamellomphalus manusensis Zhang & Zhang, 2017 (Gastropoda: Neomphalida) from deep-sea hydrothermal vent

Figures & data

Figure 1. Relationships of Lamellomphalus manusensis to representive members of the Gastropoda. Nucleotide sequences of all protein-coding genes and ribosomal genes were individually aligned using MAFFT v. 7 (Katoh et al. 2019), ambiguous positions removed using GBlocks (Talavera and Castresana 2007), then concatenated, leading to alignments with 10,979 nucleotide positions for protein-coding genes and 1982 positions for the rRNA genes. ModelFinder (Kalyaanamoorthy et al. 2017) was used to select the best-fit partition model (Edge-unlinked) using BIC criterion. Maximum likelihood phylogenies were inferred using IQ-TREE (Nguyen et al. 2015) under the GTR + R4 + F model for 10,000 ultrafast (Minh et al. 2013) bootstraps, as well as the Shimodaira–Hasegawa–like approximate likelihood-ratio test (Guindon et al. 2010). Bayesian Inference phylogenies were inferred using MrBayes 3.2.6 (Ronquist et al. 2012) under partition model (2 parallel runs, 2,000,000 generations), in which the initial 25% of sampled data were discarded as burn-in. Branch support shown as maximum-likelihood bootstrap values (when ≥50)/Bayesian posterior probability (when ≥0.8).

Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20(4):1160–1166.

 PubMed Web of Science ®Google Scholar

Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577.

 PubMed Web of Science ®Google Scholar

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589.

 PubMed Web of Science ®Google Scholar

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274.

 PubMed Web of Science ®Google Scholar

Minh BQ, Nguyen MA, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195.

 PubMed Web of Science ®Google Scholar

Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59(3):307–321.

 PubMed Web of Science ®Google Scholar

Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 61(3):539–542.

 PubMed Web of Science ®Google Scholar

Data availability statement

The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] under the accession no. OK552681. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA798177, SRR17651057, and SAMN25049529, respectively.