Abstract
BackgroundAssessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy.Methodology/Principal FindingsA total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans.Conclusions/SignificanceNewly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.
Highlights
Human activities pose severe threats to planetary biodiversity, yet most marine species remain undescribed [1,2,3]
We present data for a newly developed pair of primers that target the mitochondrial 12S ribosomal DNA sequence of many metazoans
We identified two conserved regions suitable for designing a pair of PCR primers by performing careful alignments of the 64 complete mitochondrial genomes chosen to represent all metazoan classes (Fig. 1)
Summary
Human activities pose severe threats to planetary biodiversity, yet most marine species remain undescribed [1,2,3]. Unlike the situation with microbes, where analysis of the 16S ribosomal DNA sequence is standard, the appropriate gene for metazoan metagenetic studies is less clear. Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and tested their efficacy
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