Display options
Share it on

Data Brief. 2019 Jun 12;25:104134. doi: 10.1016/j.dib.2019.104134. eCollection 2019 Aug.

Five nuclear protein-coding markers for establishing a robust phylogenetic framework of niphargid crustaceans (Niphargidae: Amphipoda) and new molecular sequence data.

Data in brief

Ajda Moškrič, Rudi Verovnik

Affiliations

  1. Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia.
  2. University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.

PMID: 31297423 PMCID: PMC6598839 DOI: 10.1016/j.dib.2019.104134

Abstract

The data presented here includes selection of 5 successfully amplified protein-coding markers for inferring phylogenetic relationships of the family of amphipod crustaceans Niphargidae. These markers have been efficiently amplified from niphargid samples for the first time and present the framework for robust phylogenetic assessment of the family Niphargidae. They are useful for phylogenetic purposes among other amphipod genera as well. In detail, the data consists of two parts: 1. Information regarding markers, specific oligonucleotide primer pairs and conditions for PCR reaction that enables successful amplification of specific nucleotide fragments. Two pairs of novel oligonucleotide primers were constructed which enable partial sequence amplification of two housekeeping genes: arginine kinase (ArgKin) and glyceraldehyde phosphate dehydrogenase (GAPDH), respectively. Additionally, 3 existing combinations of oligonucleotide primer pairs for protein-coding loci for glutamyl-prolyl tRNA synthetase (EPRS), opsin (OP) and phosphoenolpyruvate carboxykinase (PEPCK) were proven to be suitable to amplify specific nucleotide fragments from selected amphipod specimens; 2. Information on novel nucleotide sequences from amphipod taxa of the family Niphagidae and related outgroup taxa. Unilocus phylogenetic trees were constructed using Bayesian analysis and show relationships among selected taxa. Altogether 299 new nucleotide sequences from 92 specimens of the family Niphargidae and related outgroup amphipod taxa are deposited in GenBank (NCBI) repository and available for further use in phylogenetic analyses.

Keywords: Arginine kinase; EPRS; Glyceraldehyde phosphate dehydrogenase; Niphargidae; Nuclear protein-coding loci; Nucleotide sequences; Opsin; PCR; Phosphoenolpyruvate carboxykinase; Phylogenetic analyses

References

  1. Bioinformatics. 2007 Nov 1;23(21):2947-8 - PubMed
  2. Mol Phylogenet Evol. 2008 Feb;46(2):738-59 - PubMed
  3. Syst Biol. 2008 Apr;57(2):231-42 - PubMed
  4. Mol Phylogenet Evol. 2008 Sep;48(3):877-91 - PubMed
  5. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W222-8 - PubMed
  6. BMC Evol Biol. 2010 Jun 09;10:171 - PubMed
  7. Methods Mol Biol. 2012;840:81-5 - PubMed
  8. Syst Biol. 2012 May;61(3):539-42 - PubMed
  9. Bioinformatics. 2012 Jun 15;28(12):1647-9 - PubMed
  10. Evolution. 2012 Dec;66(12):3852-65 - PubMed
  11. Mol Ecol. 2014 Mar;23(6):1405-17 - PubMed
  12. PLoS One. 2013 Oct 21;8(10):e76760 - PubMed
  13. Mol Ecol. 2014 Mar;23(5):1153-66 - PubMed
  14. Mol Biol Evol. 2017 Sep 1;34(9):2422-2424 - PubMed

Publication Types