Data from: Oligonucleotide primers for targeted amplification of single-copy nuclear genes in apocritan Hymenoptera

BACKGROUND: Published nucleotide sequence data from the mega-diverse insect order Hymenoptera (sawflies, bees, wasps, and ants) are taxonomically scattered and still inadequate for reconstructing a well-supported phylogenetic tree for the order. The analysis of comprehensive multiple gene data sets obtained via targeted PCR could provide a cost-effective solution to this problem. However, oligonucleotide primers for PCR amplification of nuclear genes across a wide range of hymenopteran species are still scarce. FINDINGS: Here we present a suite of degenerate oligonucleotide primer pairs for PCR amplification of 154 single-copy nuclear protein-coding genes from Hymenoptera. These primers were inferred from genome sequence data from nine Hymenoptera (seven species of ants, the honeybee, and the parasitoid wasp Nasonia vitripennis). We empirically tested a randomly chosen subset of these primer pairs for amplifying target genes from six Hymenoptera, representing the families Chrysididae, Crabronidae, Gasteruptiidae, Leucospidae, Pompilidae, and Stephanidae. Based on our results, we estimate that these primers are suitable for studying a large number of nuclear genes across a wide range of apocritan Hymenoptera (i.e., all hymenopterans with a wasp-waist) and of aculeate Hymenoptera in particular (i.e., apocritan wasps with stingers). CONCLUSIONS: The amplified nucleotide sequences are (a) with high probability from single-copy genes, (b) easily generated at low financial costs, especially when compared to phylogenomic approaches, (c) easily sequenced by means of an additionally provided set of sequencing primers, and (d) suitable to address a wide range of phylogenetic questions and to aid rapid species identification via barcoding, as many amplicons contain both exonic and fast-evolving intronic nucleotides.

研究背景：已发表的物种多样性极高的昆虫纲膜翅目(Hymenoptera，包含叶蜂、蜜蜂、胡蜂与蚂蚁)的核苷酸序列数据在分类学上分布零散，且仍不足以构建该类群支持度优异的系统发育树。通过靶向聚合酶链式反应(PCR)获取的多基因综合数据集的分析，可为解决该问题提供一种成本效益优异的方案。然而，可用于跨多种膜翅目物种核基因PCR扩增的寡核苷酸引物(oligonucleotide primer)仍较为匮乏。
研究结果：本文报道一套可用于扩增膜翅目154个单拷贝核蛋白编码基因的简并寡核苷酸引物对(degenerate oligonucleotide primer pair)。该套引物基于9种膜翅目昆虫的基因组序列数据设计得到，其中包含7种蚂蚁、蜜蜂以及寄生蜂丽蝇蛹集金小蜂(Nasonia vitripennis)。我们针对6个膜翅目类群（分别隶属于青蜂科(Chrysididae)、方头泥蜂科(Crabronidae)、褶腹蜂科(Gasteruptiidae)、痣翅小蜂科(Leucospidae)、蛛蜂科(Pompilidae)以及冠蜂科(Stephanidae)），随机选取部分引物对开展实验以验证其扩增靶基因的效果。基于实验结果，我们推测该套引物可用于跨多种细腰亚目膜翅目(apocritan Hymenoptera，即所有具有“蜂腰”结构的膜翅目昆虫)的大量核基因研究，尤其适用于针尾部膜翅目(aculeate Hymenoptera，即带螯针的细腰亚目蜂类)的相关研究。
研究结论：本研究扩增得到的核苷酸序列具备以下优势：(a) 极大概率来自单拷贝基因；(b) 实验操作简便且成本低廉，相较于系统基因组学方法优势尤为显著；(c) 可通过配套提供的测序引物(sequencing primer)轻松完成测序；(d) 可用于解决诸多系统发育相关问题，并可借助DNA条形码(DNA barcoding)技术辅助快速物种鉴定，因多数扩增产物同时包含外显子与快速进化的内含子核苷酸序列。