Assessing the Small Nuclear Ribosomal Subunit (18S rRNA) as a Potential Barcoding Gene for Amphipoda (Malacostraca: Peracarida) Along with the Design of a Unique Primer Set to Target the Amphipod 18S rRNA Gene.
- 1Department of Biological Sciences, Florida A&M University, Tallahassee, FL 32307, USA.
- 2Department of Biology, Miami University, Oxford, OH 45056, USA.
Abstract
The mitochondrial cytochrome oxidase I (COI) gene is frequently used as a barcoding gene for the identification of numerous taxa, including crustaceans such as amphipods. The gene's variability, which makes it useful for barcoding, can also create primer annealing issues that can inhibit amplification and sequencing, and nuclear copies of mitochondrial DNA (NUMTs) can sometimes preferentially amplify over the mitochondrial COI target locus. The small nuclear ribosomal gene (18S rRNA) can overcome issues of amplification and sequencing as primers can be designed to target highly conserved regions, making it useful across a wide variety of taxa. Due to its conserved nature, the 18S rRNA gene has not been considered a strong candidate for barcoding. Peracarid crustaceans have an insertion within the V4 hypervariable region, and amphipods are unique amongst the peracarids with an additional insertion in the V5 hypervariable region, which could make this part of the gene large and variable enough to target for barcoding. Herein, we present three primer sets designed for Amphipoda that amplify the majority of the 18S rRNA gene, including one pair (18S450F-18S1500R) that captures the V4/V5 hypervariable regions. Analyses utilizing tree-building algorithms and two species delimitation models demonstrate the potential utility of the gene region amplified by the 18S450F-18S1500R primers for barcoding. The utility of this gene for barcoding will depend on researchers incorporating this locus into future species descriptions and phylogenetic studies.
Related
- Molecular Identification of Insects on Imperata cylindrica (Poales: Poaceae) and Exploration of Potential Natural Enemies Using DNA Barcoding.
- Assessing Genetic Divergence and Adaptive Potential of Aroeira (Myracrodruon urundeuva Allemão LC, Anacardiaceae) Across Brazilian Biomes
- Assessing the relationship between a Neotrypaea californiensis parasite and a potential host for natural biocontrol in shellfish aquaculture
- Assessing the potential of deep learning to distinguish wild and domesticated grapevine pollen
- Assessing the Potential Distribution of Eriocheir sinensis Under Climate Change: Regional Contrasts and Spatial Mismatches in Terrestrial and Nearshore Suitability
BibTeX
@article{sawicki2026assessing,
title = {{Assessing the Small Nuclear Ribosomal Subunit (18S rRNA) as a Potential Barcoding Gene for Amphipoda (Malacostraca: Peracarida) Along with the Design of a Unique Primer Set to Target the Amphipod 18S rRNA Gene.}},
author = {Thomas R Sawicki and Andrew G Cannizzaro and Joshua M Sisco},
journal = {Biology},
year = {2026},
month = oct,
doi = {10.3390/biology15191752},
url = {https://europepmc.org/article/MED/42883424},
note = {CC BY},
}
RIS
TY - JOUR
TI - Assessing the Small Nuclear Ribosomal Subunit (18S rRNA) as a Potential Barcoding Gene for Amphipoda (Malacostraca: Peracarida) Along with the Design of a Unique Primer Set to Target the Amphipod 18S rRNA Gene.
AU - Thomas R Sawicki
AU - Andrew G Cannizzaro
AU - Joshua M Sisco
PY - 2026
DA - 2026/10/02
JO - Biology
DO - 10.3390/biology15191752
UR - https://europepmc.org/article/MED/42883424
AB - The mitochondrial cytochrome oxidase I (COI) gene is frequently used as a barcoding gene for the identification of numerous taxa, including crustaceans such as amphipods. The gene's variability, which makes it useful for barcoding, can also create primer annealing issues that can inhibit amplification and sequencing, and nuclear copies of mitochondrial DNA (NUMTs) can sometimes preferentially amplify over the mitochondrial COI target locus. The small nuclear ribosomal gene (18S rRNA) can overcome issues of amplification and sequencing as primers can be designed to target highly conserved regions, making it useful across a wide variety of taxa. Due to its conserved nature, the 18S rRNA gene has not been considered a strong candidate for barcoding. Peracarid crustaceans have an insertion within the V4 hypervariable region, and amphipods are unique amongst the peracarids with an additional insertion in the V5 hypervariable region, which could make this part of the gene large and variable enough to target for barcoding. Herein, we present three primer sets designed for Amphipoda that amplify the majority of the 18S rRNA gene, including one pair (18S450F-18S1500R) that captures the V4/V5 hypervariable regions. Analyses utilizing tree-building algorithms and two species delimitation models demonstrate the potential utility of the gene region amplified by the 18S450F-18S1500R primers for barcoding. The utility of this gene for barcoding will depend on researchers incorporating this locus into future species descriptions and phylogenetic studies.
SN - 2079-7737
ER -