Comparative analysis of different DNA barcodes for applications in the identification and production of Pyropia

Abstract

To evaluate the potential application of the DNA barcoding method for Pyropia identification and to select the most appropriate barcode or barcode combination, five barcodes (UPA, V9, Cox1, 5.8S rDNA-ITS, and rbcL) were used to analyze twenty-two different Pyropia samples (including naturally distributed, aquaculture, and processed samples). A total of 99 sequences were obtained from amplification and sequencing of the five barcodes for Bayesian analysis. Except for Cox1, the other four barcodes could accurately identify five different species, i.e., Py. dentata, Py. sp., Py. yamadae, Py. haitanensis and Py. yezoensis. The 5.8S rDNA-ITS region could distinguish closely related species, with interspecific genetic distance values ranging from 40% to 70% and high resolution for intraspecific samples (0.7%). UPA had the shortest sequence length among all five barcodes, with mean length of 410 bp and could also correctly distinguish interspecific samples. Despite some limitations of the candidate markers, the data strongly suggest that DNA barcodes can be used to identify Pyropia. Further, the ability to successfully extract, PCR amplify, and sequence DNA from processed Pyropia samples indicates that processed samples can be analyzed using DNA barcodes. We also found that barcode combination cannot increase genetic distances compared with a single barcode. Our results indicate that 5.8S rDNA-ITS can be used for Pyropia traceability, while UPA is the most viable for quality inspection of Pyropia.