Complete mitochondrial genome of Laeocathaica amdoana Möllendorff, 1899 and phylogenetic analysis of Camaenidae (Gastropoda: Stylommatophora: Helicoidea)

References

• Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389–3402. doi: 10.1093/nar/25.17.3389.
   Google Scholar
• Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477. doi: 10.1089/cmb.2012.0021.
   PubMed Web of Science ®Google Scholar
• Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz J, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69(2):313–319. doi: 10.1016/j.ympev.2012.08.023.
   PubMed Web of Science ®Google Scholar
• Birney E, Clamp M, Durbin R. 2004. GeneWise and genomewise. Genome Res. 14(5):988–995. doi: 10.1101/gr.1865504.
   PubMed Web of Science ®Google Scholar
• Boetzer M, Pirovano W. 2012. Toward almost closed genomes with GapFiller. Genome Biol. 13(6):R56. doi: 10.1186/gb-2012-13-6-r56.
   PubMed Web of Science ®Google Scholar
• Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 25(15):1972–1973. doi: 10.1093/bioinformatics/btp348.
   PubMed Web of Science ®Google Scholar
• Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 34(17):i884–i890. doi: 10.1093/bioinformatics/bty560.
   PubMed Web of Science ®Google Scholar
• Chen Z-Y, Lyu Z-T, Wu M. 2021. Systematic revision of Stegodera Martens, 1876 (Gastropoda, Stylommatophora, Camaenidae), with description of a new genus. Zookeys. 1059:1–21. doi: 10.3897/zookeys.1059.68385.
   PubMedGoogle Scholar
• Deng P-J, Wang W-M, Huang X-C, Wu X-P, Xie G-L, Ouyang S. 2016. The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(2):1441–1442. doi: 10.3109/19401736.2014.953083.
   PubMedGoogle Scholar
• Fourdrilis S, de Frias Martins AM, Backeljau T. 2018. Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda. Sci Rep. 8(1):17964. doi: 10.1038/s41598-018-36428-7.
   PubMed Web of Science ®Google Scholar
• Ghiselli F, Gomes-dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. 2021. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci. 376(1825):20200159. doi: 10.1098/rstb.2020.0159.
   PubMed Web of Science ®Google Scholar
• Groenenberg DSJ, Duijm E. 2019. The complete mitogenome of the Roman snail Helix pomatia Linnaeus 1758 (Stylommatophora: Helicidae). Mitochondrial DNA Part B. 4(1):1494–1495. doi: 10.1080/23802359.2019.1601512.
   Web of Science ®Google Scholar
• Groenenberg DSJ, Pirovano W, Gittenberger E, Schilthuizen M. 2012. The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics. 13(1):114. doi: 10.1186/1471-2164-13-114.
   PubMedGoogle Scholar
• Huang C-W, Lin S-M, Wu W-L. 2016. Mitochondrial genome sequences of landsnails Aegista diversifamilia and Dolicheulota formosensis (Gastropoda: Pulmonata: Stylommatophora). Mitochondrial DNA A DNA Mapp Seq Anal. 27(4):2793–2795. doi: 10.3109/19401736.2015.1053070.
   PubMedGoogle Scholar
• Jirapatrasilp P, Huang C-W, Hwang C-C, Sutcharit C, Lee C-T. 2022. Convergent evolution of Amphidromus-like colourful arboreal snails and phylogenetic relationship of East Asian camaenids, with description of a new Aegistohadra species (Helicoidei: Camaenidae: Bradybaeninae). Invertebr Syst. 36(3):244–290. doi: 10.1071/IS21015.
   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. doi: 10.1038/nmeth.4285.
   PubMed Web of Science ®Google Scholar
• Li X-J, Yang J, Wang J-H, Ren Q-L, Li X, Huang Y. 2013. Methods and software tools for mitochondrial genome assembly and annotation. Chin J Appl Entomol. 50:298–304.
   Google Scholar
• Lin J-H, Zhou W, Ding H-L, Wang P, Ai H-M. 2016. The mitochondrial genome of the land snail Cernuella virgata (Da Costa, 1778): the first complete sequence in the family Hygromiidae (Pulmonata, Stylommatophora). ZooKeys. 589:55–69. doi: 10.3897/zookeys.589.7637.
   Google Scholar
• Massouras A, Hens K, Gubelmann C, Uplekar S, Decouttere F, Rougemont J, Cole ST, Deplancke B. 2010. Primer-initiated sequence synthesis to detect and assemble structural variants. Nat Methods. 7(7):485–486. doi: 10.1038/nmeth.f.308.
   PubMed Web of Science ®Google Scholar
• Minh BQ, Nguyen MAT, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Mol Biol Evol. 30(5):1188–1195. doi: 10.1093/molbev/mst024.
   PubMed Web of Science ®Google Scholar
• Möllendorff OF. 1899. Binnen-Mollusken aus Westchina und Centralasien. I. Annuaire du Musée Zoologique de L’Académie Impériale Des St.-Pétersburg. 4:46–144.
   Google Scholar
• Nawrocki EP, Eddy SR. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 29(22):2933–2935. doi: 10.1093/bioinformatics/btt509.
   PubMed Web of Science ®Google Scholar
• Nguyen L-T, 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. doi: 10.1093/molbev/msu300.
   PubMed Web of Science ®Google Scholar
• Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna 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. doi: 10.1093/sysbio/sys029.
   PubMed Web of Science ®Google Scholar
• Saccone C, De Giorgi C, Gissi C, Pesole G, Reyes A. 1999. Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene. 238(1):195–209. doi: 10.1016/s0378-1119(99)00270-x.
   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. doi: 10.1080/10635150701472164.
   PubMed Web of Science ®Google Scholar
• Wade CM, Hudelot C, Davison A, Naggs F, Mordan PB. 2007. Molecular phylogeny of the helicoid land snails (Pulmonata: Stylommatophora: Helicoidea), with special emphasis on the Camaenidae. J. Molluscan Stud. 73(4):411–415. doi: 10.1093/mollus/eym030.
   Web of Science ®Google Scholar
• Wade CM, Mordan PB, Clarke B. 2001. A phylogeny of the land snails (Gastropoda: Pulmonata). Proc Biol Sci. 268(1465):413–422. doi: 10.1098/rspb.2000.1372.
   PubMed Web of Science ®Google Scholar
• Wang P, Yang H, Zhou W, Hwang C, Zhang W, Qian Z. 2014. The mitochondrial genome of the land snail Camaena cicatricosa (Müller, 1774) (Stylommatophora, Camaenidae): the first complete sequence in the family Camaenidae. ZooKeys. 451:33–48. doi: 10.3897/zookeys.451.8537.
   PubMed Web of Science ®Google Scholar
• Wu M, Shen W, Chen Z-G. 2023. Land snail diversity in central China: revision of Laeocathaica Möllendorff, 1899 (Gastropoda, Camaenidae), with descriptions of seven new species. Zookeys. 1154:49–147. doi: 10.3897/zookeys.1154.86237.
   PubMedGoogle Scholar
• Xia X. 2018. DAMBE7: new and improved tools for data analysis in molecular biology and evolution. Mol Biol Evol. 35(6):1550–1552. doi: 10.1093/molbev/msy073.
   PubMed Web of Science ®Google Scholar
• Xiang C-Y, Gao F, Jakovlić I, Lei H-P, Hu Y, Zhang H, Zou H, Wang G-T, Zhang D. 2023. Using PhyloSuite for molecular phylogeny and tree-based analyses. iMeta. 2(1):e87. doi: 10.1002/imt2.87.
   Google Scholar
• Yamazaki N, Ueshima R, Terrett JA, Yokobori S, Kaifu M, Segawa R, Kobayashi T, Numachi K, Ueda T, Nishikawa K, et al. 1997. Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures. Genetics. 145(3):749–758. doi: 10.1093/genetics/145.3.749.
   PubMed Web of Science ®Google Scholar
• Yang X, Xie G-L, Wu X-P, Ouyang S. 2016. The complete mitochondrial genome of Chinese land snail Aegista aubryana (Gastropoda: Pulmonata: Bradybaenidae). Mitochondrial DNA A DNA Mapp Seq Anal. 27(5):3538–3539. doi: 10.3109/19401736.2015.1074207.
   PubMedGoogle Scholar