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Oligonucleotide Primers for Targeted Amplification of Single-Copy Nuclear Genes in Apocritan Hymenoptera
- Source :
- PLOS ONE, 7(6):e39826, PLoS ONE, Vol 7, Iss 6, p e39826 (2012), PLoS ONE
- Publication Year :
- 2012
- Publisher :
- Public Library of Science (PLoS), 2012.
-
Abstract
- 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.
- Subjects :
- Nuclear gene
Molecular Sequence Data
Gene Dosage
lcsh:Medicine
Genes, Insect
Hymenoptera
Biochemistry
Polymerase Chain Reaction
Nasonia vitripennis
DNA amplification
Genome Analysis Tools
Phylogenetics
Molecular Systematics
Sequence Homology, Nucleic Acid
Animals
Evolutionary Systematics
Gasteruptiidae
lcsh:Science
Biology
Phylogeny
DNA Primers
Cell Nucleus
Electrophoresis, Agar Gel
Whole genome sequencing
Genetics
Evolutionary Biology
Multidisciplinary
Phylogenetic tree
biology
Gene Ontologies
lcsh:R
fungi
DNA
Genomics
Comparative Genomics
Genome Scans
Invertebrate genomics
Polymerase chain reaction
Gene amplification
Ants
Animal phylogenetics
Oligonucleotides
Nucleotide sequencing
Amplicon
biology.organism_classification
Nucleic acids
lcsh:Q
Research Article
Subjects
Details
- ISSN :
- 19326203
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....80a5a6ad283880fb31d4d6f474352a30