A new set of primers for COI amplification from freshwater microcrustaceans

Abstract

Despite the contribution of DNA barcoding towards understanding the biodiversity and distribution of species, the success of COI amplification has been quite variable when it comes to freshwater zooplankton (Elías-Gutiérrez & Valdez-Moreno 2008; Jeffery et al. 2011). Some genera of microcrustaceans seem to be more difficult to amplify than others. For example, Macrothrix, Scapholeberis, Diaphanosoma and cyclopoids have yielded limited results. Among several possible reasons for the inability to barcode freshwater microcrustaceans is that there does not exist a specific set of primers for COI amplification. To this end, we developed a zooplankton - specific set of primers, which significantly increased average amplification success (20% increase). With these primers, we observed an overall success of over 70% for Sididae and Chydoridae, and more than 80% for Daphniidae, Moinidae, Bosminidae, Macrothricidae, Ilyocryptidae and Diaptomidae. We also demonstrate a simple alteration to a common specimen fixation method that increases the overall recovery of barcodes from freshwater zooplankton. Collectively, we believe our results will greatly aid the recovery of barcodes from these difficult groups.

Barcode-based species delimitation in the marine realm: a test using Hexanauplia (Multicrustacea: Thecostraca and Copepoda)

“…In addition to further research on species boundaries in taxonomically problematic groups, additional protocol development is needed for groups with low amplification and sequencing success. This may include primer design and investigation of the importance of specimen fixation in cold conditions immediately following field collection (Prosser et al 2013). Finally, the adoption of internal methods for clustering verification, such as the analyses presented here, is encouraged in DNA barcode studies to enable rapid biodiversity study and exploration of unknown faunas.…”

DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera)

“…A checklist of all "species-group nominal taxa" sensu ICZN [106] composed by AAK (it is partly represented in [70]) contains 78 formal names which could be attributed to the genus Moina . Among them, there are four taxa from the brachiata -group, 15 taxa from the macrocopa -group, 11 taxa from the micrura -group, and four taxa from the salina -group (Table 2).…”

“…Tatsuta et al [69] isolated a set of microsatellite markers for Moina macrocopa suitable "for assessing cryptic genetic structure", but these markers were never used in any subsequent studies. The DNA barcoding studies of the genus were started by Elías-Gutiérrez et al [35], followed by Jeffrey et al [36], Prosser et al [70] and Dumont et al [65]. Finally, a comprehensive study of the Moina brachiata group in Hungary was made by Nédli et al [42].…”

Faunistic survey of the zooplankton community in an oligotrophic sinkhole, Cenote Azul (Quintana Roo, Mexico), using different sampling methods, and documented with DNA barcodes

“…All samples were sieved and washed with 96% ethanol to extract all water, and finally fixed with 96% ethanol. They were transported on ice from the field, and stored at -18°C for seven days (Prosser et al, 2013;Elías-Gutiérrez et al, 2018).…”