The design and testing of mini-barcode markers in marine lobsters

Abstract

Full-length mitochondrial cytochrome c oxidase I (COI) sequence information from lobster phyllosoma larvae can be difficult to obtain when DNA is degraded or fragmented. Primers that amplify smaller fragments are also more useful in metabarcoding studies. In this study, we developed and tested a method to design a taxon-specific mini-barcode primer set for marine lobsters. The shortest, most informative portion of the COI gene region was identified in silico, and a DNA barcode gap analysis was performed to assess its reliability as species diagnostic marker. Primers were designed, and cross-species amplification success was tested on DNA extracted from a taxonomic range of spiny-, clawed-, slipper- and blind lobsters. The mini-barcode primers successfully amplified both adult and phyllosoma COI fragments, and were able to successfully delimit all species analyzed. Previously published universal primer sets were also tested and sometimes failed to amplify COI from phyllosoma samples. The newly designed taxon-specific mini-barcode primers will increase the success rate of species identification in bulk environmental samples and add to the growing DNA metabarcoding toolkit.

The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes

“…According to the previous studies 20,25 , the usage of short DNA fragments, such as mini-barcodes, can effectively mitigate this problem. Additionally, with the advancement in high-throughput sequencing and metabarcoding, the development of mini-barcode primers is encouraged, which will, in turn, improve the efficiency of taxon discovery and identification 60,61 , especially in mixed samples. In the present study, metabarcoding was performed via sequencing of two mini-barcode amplicons, and quantitative assessments were conducted on three artificial communities.…”

Phylogeography of Acartia tonsa Dana, 1849 (Calanoida: Copepoda) and phylogenetic reconstruction of the genus Acartia Dana, 1846

“…Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12526-020-01043-1) contains supplementary material, which is available to authorized users. mitochondrial markers such as mtCOI, have been used to identify cryptic species in numerous marine organisms, including copepods (Lee 2000;Rocha-Olivares et al 2001;Dawson and Jacobs 2001;Lee and Frost 2002;Caudill and Bucklin 2004;Holland et al 2004;Hare 2008, 2011;Johnson et al 2008;Dippenaar et al 2010;Marrone et al 2010;Blanco-Bercial et al 2014;Cornils and Held 2014;Oyama et al 2019;Govender et al 2019;Han et al 2019;Hupało et al 2019;Figueroa et al 2019;Chan et al 2019). A comprehensive review of DNA barcoding of copepods based on mtCOI is presented by Blanco-Bercial et al (2014), where they show that this marker was able to accurately identify to species level 1381 sequences for 195 species of copepods, showcasing the utility of this marker for taxonomic research.…”

Metabarcoding of marine zooplankton in South Africa

“…Of an estimated 12 000 marine faunal species in South Africa, 13% have publicly available DNA barcodes (www.barcodinglife.org). Regionspecific DNA barcode reference databases have been shown to improve taxonomic resolution and the detection rates of species during metabarcoding (Govender et al 2019;Questel et al 2021), particularly where endemism is high, such as in South Africa where ⁓36% of marine species are endemic (Griffiths et al 2010;Griffiths and Robinson 2016). Compilation of a region-specific reference database for southern African zooplankton is therefore advised; however, it has been hampered by the limited funding available for biodiversity surveys and too few trained taxonomists (Bezeng and van der Bank 2019).…”