763
Views
0
CrossRef citations to date
0
Altmetric
Rapid Communication

The mitochondrial genomes of five spring and groundwater amphipods of the family Crangonyctidae (Crustacea: Amphipoda) from eastern North America

, &
Pages 1662-1667 | Received 04 Aug 2020, Accepted 01 May 2021, Published online: 18 May 2021

References

  • Aunins AW, Nelms DL, Hobson CS, King TL. 2016. Comparative mitogenomic analyses of three North American stygobiont amphipods of the genus Stygobromus (Crustacea: Amphipoda). Mitochondrial DNA Part B. 1(1):560–563.
  • Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
  • Bernt M, Donath A, Jühling F, Externbrink F, Florentz C, Fritzsch G, Pütz M, Middendorf M, Stadler PF. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 69:313–319.
  • Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
  • Boore JL, Lavrov DV, Brown WM. 1998. Gene translocation links insects and crustaceans. Nature. 392:667–668.
  • Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17(4):540–552.
  • De Melo Rodovalho C, Lyra ML, Ferro M, Bacci M Jr. 2014. The mitochondrial genome of the leaf-cutter ant Atta laevigata: a mitogenome with a large number of intergenic spacers. PLOS One. 9(5):e97117.
  • Dierckxsens N, Mardulyn P, Smits G. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45(4):e18.
  • Holsinger JR. 1967. Systematics, speciation, and distribution of the subterranean amphipod genus Stygonectes (Gammaridae). Smithsonian Contrib Zool. 259:1–176.
  • Holsinger JR. 1977. A review of the systematics of the Holarctic amphipod family Crangonyctidae. Crustaceana Suppl. 4:244–281.
  • Holsinger JR. 1978. Systematics of the subterranean amphipod genus Stygobromus (Crangonyctidae): part II. Species of the eastern United States. Smithsonian Contrib Zool. 266:1–144.
  • Hubricht L, Mackin J. 1940. Descriptions of nine new species of fresh-water Amphipod Crustaceans with notes and new localties for other species. Am Midland Nat. 23(1):187–218.
  • Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. 2012. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 40(7):2833–2845.
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
  • Kilpert F, Podsiadlowski L. 2006. The complete mitochondrial genome of the common sea slater, Ligia oceanica (Crustacea, Isopoda) bears a novel gene order and unusual control region features. BMC Genomics. 7(1):241.
  • Konemann S, Holsinger JR. 2002. Systematics of the North American subterranean amphipod genus Bactrurus (Crangonyctidae). Beaufortia. 51:1–56.
  • Krebes L, Bastrop R. 2012. The mitogenome of Gammarus duebeni (Crustacea Amphipoda): a new gene order and non-neutral sequence evolution of tandem repeats in the control region. Comp Biochem Physiol D Genomics Proteomics. 7(2):201–211.
  • Lanfear R, Calcott B, Ho SY, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29(6):1695–1701.
  • Niemiller ML, Porter ML, Keany J, Gilbert H, Fong DW, Culver DC, Hobson CS, Kendall KD, Davis MA, Taylor SJ. 2018. Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae). Conserv Genet Resour. 10(2):247–257.
  • Ojala D, Montoya J, Attardi G. 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature. 290:470–474.
  • Pons J, Bauzà-Ribot MM, Jaume D, Juan C. 2014. Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea). BMC Genomics. 15(1):566.
  • Romanova EV, Aleoshin VV, Kamaltynov RM, Mikhailov KV, Logacheva MD, Sirotinina EA, Gornov AY, Anikin AS, Sherbakov DY. 2016. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics. 17(14):1016.
  • Romanova EV, Bukin YS, Mikhailov KV, Logacheva MD, Aleoshin VV, Sherbakov DY. 2020. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Mol Phylogenet Evol. 144:106710.
  • 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. 61:539–542.
  • Shoemaker CR. 1938. A new species of fresh-water amphipod of the genus Synpleonia, with remarks on related genera. Proc Biol Soc Washington. 51:137–142.
  • Stokkan M, Jurado-Rivera J, Carlos J, Damià J, Pons J. 2015. Mitochondrial genome rearrangements at low taxonomic levels: three distinct mitogenome orders in the genus Pseudoniphargus. Mitochondrial DNA. 27:3579–3589.
  • Wheeler DL, Church DM, Federhen S, Lash AE, Madden TL, Pontius JU, Schuler GD, Schriml LM, Sequeira E, Tatusova TA, et al. 2003. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 31(1):28–33.
  • Yang HM, Song JH, Kim MS, Min GS. 2017. The complete mitochondrial genomes of two talitrid amphipods, Platorchestia japonica and P. parapacifica (Crustacea, Amphipoda). Mitochondrial DNA Part B. 2(2):757–758.
  • Yang JS, Yang WJ. 2008. The complete mitochondrial genome sequence of the hydrothermal vent galatheid crab Shinkaia crosnieri (Crustacea: Decapoda: Anomura): a novel arrangement and incomplete tRNA suite. BMC Genomics. 9(1):257.
  • Zhang D, Gao F, Li WX, Jakovlić I, Zou H, Zhang J, Wang GT. 2020. PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20(1):348–355.
  • Zhang J. 1997. Systematics of the freshwater Amphipod genus Crangonyx (Crangonyctidae) in North America [Doctor of Philosophy (PhD), dissertation]. Biological Sciences, Old Dominion University.