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Open AccessArticle

Chloroplast Genome-Based Hypervariable Markers for Rapid Authentication of Six Korean Pyropia Species

by Sung-Je Choi 1,†, Yonguk Kim 2,† and Chulyung Choi 2,*
1
Ocean and Fisheries Science Institute Haenam Branch, Haenam-gun, Jeollanamdo 59046, Korea
2
Jeonnam Institute of Natural Resources Research, Jangheung-gun, Jeollanamdo 59338, Korea
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Diversity 2019, 11(12), 220; https://doi.org/10.3390/d11120220
Received: 28 October 2019 / Revised: 14 November 2019 / Accepted: 19 November 2019 / Published: 20 November 2019
(This article belongs to the Section Marine Diversity)
We previously established that polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis using partial plastid rbcL and mitochondrial trnC–trnP gene sequences can be used to distinguish the six representative Pyropia species produced via mariculture in Korea. In this study, we develop progressive InDel markers by comparing seven complete Pyropia chloroplast genomes obtained from The National Center of Biotechnology Informnation (NCBI) GenBank. Comparative analyses of nucleotide diversity among the genomes revealed seven hypervariable sites (cemA, rps13, trnM-argB, petD-petB, trnR-trnQ, ccs1-orf24, and ycf12-ftrB) among 637 sliding windows with nucleotide diversity > 0.025 (Pi). These sites included two genes and five gene-intergenic regions, three of which (cemA, trnM-argB, trnR-trnQ) showed complete amplification for all six test species. Finally, trnM-argB, an InDel-variable locus with high discriminatory power, was selected as a DNA barcode candidate. These results suggest that the obtained trnM-argB region can be used for the effective exploration of the variation present in six Korean Pyropia and for further evolutionary, phylogenetic, barcoding and genetic engineering studies of Pyropia species. View Full-Text
Keywords: Pyropia; chloroplast genome; InDel; nucleotide diversity; DNA barcode Pyropia; chloroplast genome; InDel; nucleotide diversity; DNA barcode
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Choi, S.-J.; Kim, Y.; Choi, C. Chloroplast Genome-Based Hypervariable Markers for Rapid Authentication of Six Korean Pyropia Species. Diversity 2019, 11, 220.

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