Another paper I have made a contribution to have just recently been published in Molecular Ecology Resources. The paper (1), which is lead-authored by Xin-Cun Wang and Chang Liu at the Institute of Medicinal Plant Development in Beijing, investigates the usability of the ITS1 and ITS2 as separate barcodes across the Eukaryotes. The study is a large scale meta-analysis comparing available high-quality sequence data in as many taxonomic groups at possible from three different aspects: PCR amplification, DNA sequencing efficiency and species discrimination ability. Specifically, we have looked for the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality, using bioinformatic approaches. We found that the ITS1 had significantly higher efficiencies than the ITS2 in 17 of 47 families and 20 of 49 investigated genera, which was markedly better than the performance of ITS2. We conclude that, in general, ITS1 represents a better DNA barcode than ITS2 for a majority of eukaryotic taxonomic groups. This of course doesn’t mean that using the ITS2 or the ITS region in its entirety should be dismissed, but our results can serve as a ground for making informed decisions about which region to choose for your amplicon sequencing project. The results complement what have previously been observed for e.g. fungi, where the difference between ITS1 and ITS2 were much less pronounced (2).
- Wang X-C, Liu C, Huang L, Bengtsson-Palme J, Chen H, Zhang J-H, Cai D, Li J-Q: ITS1: A DNA barcode better than ITS2 in eukaryotes? Molecular Ecology Resources. Early view. doi: 10.1111/1755-0998.12325 [Paper link]
- Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H: ITS1 versus ITS2 as DNA metabarcodes for fungi. Molecular Ecology Resources. Volume 13, Issue2, Page 218-224. doi: 10.1111/1755-0998.12065 [Paper link]