Moškrič Ajda, Verovnik Rudi
Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia.
University of Ljubljana, Biotechnical Faculty, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
Data Brief. 2019 Jun 12;25:104134. doi: 10.1016/j.dib.2019.104134. eCollection 2019 Aug.
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.
本文展示的数据包括为推断端足目甲壳动物尼氏钩虾科的系统发育关系而选择的5个成功扩增的蛋白质编码标记。这些标记首次从尼氏钩虾样本中高效扩增出来，为尼氏钩虾科可靠的系统发育评估提供了框架。它们在其他端足目属的系统发育研究中也很有用。具体而言，数据由两部分组成：1. 关于标记、特定寡核苷酸引物对以及使特定核苷酸片段成功扩增的PCR反应条件的信息。构建了两对新型寡核苷酸引物，分别能够对两个管家基因：精氨酸激酶（ArgKin）和甘油醛-3-磷酸脱氢酶（GAPDH）进行部分序列扩增。此外，已证明用于谷氨酰-脯氨酰tRNA合成酶（EPRS）、视蛋白（OP）和磷酸烯醇式丙酮酸羧激酶（PEPCK）的蛋白质编码位点的3种现有寡核苷酸引物对组合适合从选定的端足目标本中扩增特定核苷酸片段；2. 来自尼氏钩虾科端足目分类群和相关外类群分类群的新核苷酸序列信息。使用贝叶斯分析构建了单基因座系统发育树，显示了选定分类群之间的关系。来自92个尼氏钩虾科标本和相关外类群端足目分类群的总共299个新核苷酸序列已存入GenBank（NCBI）数据库，可供进一步用于系统发育分析。
