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

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 stu...

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Bibliographic Details
Published inDiversity (Basel) Vol. 11; no. 12; p. 220
Main Authors Choi, Sung-Je, Kim, Yonguk, Choi, Chulyung
Format Journal Article
LanguageEnglish
Published Basel MDPI AG 20.11.2019
Subjects
Biomarkers
Biotechnology
Chloroplasts
Comparative analysis
Deoxyribonucleic acid
DNA
Gene polymorphism
Gene sequencing
Genetic engineering
Genomes
Marine aquaculture
Mitochondria
Morphology
Nucleotides
Phylogenetics
Phylogeny
Polymerase chain reaction
Polymorphism
Pyropia
Restriction fragment length polymorphism
Species
TrnP gene
South Korea
China
Japan
Spain
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Summary: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.
ISSN:1424-2818
1424-2818
DOI:10.3390/d11120220