A DNA metabarcoding protocol for hyporheic freshwater meiofauna: Evaluating highly degenerate COI primers and replication strategy

Short COI markers for freshwater macroinvertebrate metabarcoding

Species diversity of metazoan bulk samples can be rapidly assessed using Cytochrome c oxidase I (COI) metabarcoding. However, in cases where only degraded DNA is available, e.g. from poorly conserved museum specimens, eDNA filtered from water or gut content analyses, universal primer sets that amplify only a short COI fragment are advantageous. Using PrimerMiner, we optimised two universal prim...

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Corrigendum: Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

In the original article, the reference for Bista et al. (2017) was incorrectly written as “Carvalho, G. R., Walsh, K., Seymour, M., Hajibabaei, M., Lallias, D., Christmas, M., et al. (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nat. Commun. 8, 1–11. doi: 10.1038/ncomms14087.” It should be “Bista, I., Carvalho, G. R., ...

Plasmid DNA sequencing using highly degenerate oligonucleotides as primers.

Sequencing double-stranded DNA templates has become an efficient procedure (1) being much less time-consuming than the preparation and subsequent sequencing of inserts in phage singlestranded DNA. The ability to use highly degenerate oligonucleotides instead of sequence-specific primers would make this method even more powerful for the rapid sequencing ofDNA that codes for a protein for which a...

MAD-DPD: designing highly degenerate primers with maximum amplification specificity.

This work introduces minimum accumulative degeneracy, a variant of the degenerate primer design problem, which is particularly useful when a large number of sequences are to be covered by a set of restricted number of primers. A primer set, which is designed on a minimum accumulative degeneracy basis, especially helps to reduce nonspecific PCR amplification of undesired DNA fragments, as fewer ...