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Mitogenome Report

The complete mitochondrial genome of water flea Ceriodaphnia dubia (Crustacea: Cladocera) NIES strain

ORCID Icon, , ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 831-835 | Received 09 Jun 2022, Accepted 21 Jul 2023, Published online: 07 Aug 2023

References

  • 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.
  • 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.
  • Crease TJ. 1999. The complete sequence of the mitochondrial genome of Daphnia pulex (Cladocera: Crustacea). Gene. 233(1–2):89–99. doi: 10.1016/s0378-1119(99)00151-1.
  • De Coster W, D’Hert S, Schultz DT, Cruts M, Van Broeckhoven C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics. 34(15):2666–2669. doi: 10.1093/bioinformatics/bty149.
  • Fields PD, Obbard DJ, McTaggart SJ, Galimov Y, Little TJ, Ebert D. 2018. Mitogenome phylogeographic analysis of a planktonic crustacean. Mol Phylogenet Evol. 129:138–148. doi: 10.1016/j.ympev.2018.06.028.
  • Grant JR, Enns E, Marinier E, Mandal A, Herman EK, Chen C, Graham M, Van Domselaar G, Stothard P. 2023. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Res. 51(W1):W484–W492. doi: 10.1093/nar/gkad326.
  • Gu YL, Liu P, Han BP. 2021. Complete mitochondrial genome of freshwater flea Simocephalus sibiricus Sars, 1899 (Crustacea: Cladocera: Anomopoda). Mitochondrial DNA B Resour. 6(11):3100–3102. doi: 10.1080/23802359.2021.1981787.
  • Hayasaka D, Korenaga T, Suzuki K, Sánchez-Bayo F, Goka K. 2012. Differences in susceptibility of five cladoceran species to two systemic insecticides, imidacloprid and fipronil. Ecotoxicology. 21(2):421–427. doi: 10.1007/s10646-011-0802-2.
  • Hiki K, Oka K, Nakajima N, Yamamoto H, Yamagishi T, Sugaya Y. 2021. The complete mitochondrial genome of the non-biting midge Chironomus yoshimatsui (Diptera: Chironomidae). Mitochondrial DNA B Resour. 6(10):2995–2996. doi: 10.1080/23802359.2021.1975511.
  • 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.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30(4):772–780. doi: 10.1093/molbev/mst010.
  • Lee JS, Kim DH, Choi BS, Kato Y, Watanabe H, Lee JS. 2020. Complete mitochondrial genome of the freshwater water flea Daphnia magna NIES strain (Cladocera, Daphniidae): rearrangement of two ribosomal RNA genes. Mitochondrial DNA Part B. 5(2):1822–1823. doi: 10.1080/23802359.2020.1750995.
  • Liu P, Xu S, Huang Q, Dumont HJ, Lin Q, Han BP. 2017. The mitochondrial genome of Diaphanosoma dubium with comparison with Daphnia magna. Mitochondrial DNA B Resour. 2(2):926–927. doi: 10.1080/23802359.2017.1413295.
  • Mano H, Sakamoto M, Tanaka Y. 2010. A comparative study of insecticide toxicity among seven cladoceran species. Ecotoxicology. 19(8):1620–1625. doi: 10.1007/s10646-010-0547-3.
  • Martins Ribeiro M, Facchin S, Pereira AH, Kalapothakis E, Xu S, Han BP, Dumont HJ, Cecília Rietzler A. 2019. Mitogenome of Daphnia laevis (Cladocera, Daphniidae) from Brazil. Mitochondrial DNA Part B Resour. 4(1):194–196. doi: 10.1080/23802359.2018.1545547.
  • Nam SE, Kim J, Rhee JS. 2022. First complete mitochondrial genome from family Moinidae, Moina macrocopa (Straus, 1820) (Cladocera; Moinidae). Mitochondrial DNA B Resour. 7(6):980–982. doi: 10.1080/23802359.2022.2080024.
  • 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. doi: 10.1093/molbev/msu300.
  • Ohtsuki H, Norimatsu H, Makino T, Urabe J. 2022. Invasions of an obligate asexual daphnid species support the nearly neutral theory. Sci Rep. 12(1):7305. doi: 10.1038/s41598-022-11218-4.
  • Pan J, Liu P, Pajk F, Dumont HJ, Han BP. 2021. The mitochondrial genome of Diaphanosoma excisum Sars, 1885 (Crustacea: Branchiopoda: Cladocera) from Hainan Island, China. Mitochondrial DNA B Resour. 6(3):1279–1280. doi: 10.1080/23802359.2021.1907252.
  • Ryu JS, Hwang UW. 2010. Complete mitochondrial genome of the longtail tadpole shrimp Triops longicaudatus (Crustacea, Branchiopoda, Notostraca). Mitochondrial DNA. 21(5):170–172. doi: 10.3109/19401736.2010.503809.
  • Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 14(2):178–192. doi: 10.1093/bib/bbs017.
  • Tladi M, Dalu T, Rogers DC, Nyamukondiwa C, Parbhu SP, Teske PR, Emami-Khoyi A, Wasserman RJ. 2020. The complete mitogenome of the fairy shrimp Streptocephalus cafer (Lovén, 1847) (Crustacea: Branchiopoda: Anostraca) from an ephemeral pond in Botswana, southern Africa. Mitochondrial DNA B Resour. 5(1):623–625. doi: 10.1080/23802359.2019.1711222.
  • Tokishita S, Ichi Shibuya H, Kobayashi T, Sakamoto M, Ha JY, Yokobori S i, Yamagata H, Hanazato T. 2017. Diversification of mitochondrial genome of Daphnia galeata (Cladocera, Crustacea): comparison with phylogenetic consideration of the complete sequences of clones isolated from five lakes in Japan. Gene. 611:38–46. doi: 10.1016/j.gene.2017.02.019.
  • Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 9(11):e112963. doi: 10.1371/journal.pone.0112963.
  • Watanabe H, Tamura I, Abe R, Takanobu H, Nakamura A, Suzuki T, Hirose A, Nishimura T, Tatarazako N. 2016. Chronic toxicity of an environmentally relevant mixture of pharmaceuticals to three aquatic organisms (alga, daphnid, and fish). Environ Toxicol Chem. 35(4):996–1006. doi: 10.1002/etc.3285.
  • Wei W, Zhang K, Shi Q. 2021. Complete mitochondrial genome of Bosmina fatalis (Cladocera: Bosminidae) and its phylogenetic analysis. Mitochondrial DNA B Resour. 6(9):2567–2568. doi: 10.1080/23802359.2021.1959442.
  • Yu G, Smith DK, Zhu H, Guan Y, Lam TTY. 2017. Ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 8(1):28–36. doi: 10.1111/2041-210X.12628.