Use of PCR-RFLP for the discrimination of Japanese Porphyra and Pyropia species (Bangiales, Rhodophyta)

Kobayashi, Masahiro; Fujiyoshi, Eiji; Tamaki, Motoya; Kikuchi, Norio; Murase, Noboru

doi:10.1007/s10811-012-9856-7

Cited by 11 publications

(8 citation statements)

References 24 publications

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“…Touhata et al [ 16 ] demonstrated that the dried Pyropia products produed in China, Japan, and South Korea could be identified using PCR-RFLP analysis of the ITS-1 region. Abe et al [ 9 ] distinguished 18 Pyropia species from Japan using restriction enzymes on mtDNA related to the atp6 gene and partial mtDNA including the trnC , rps11 , sdh3 , trnG , trnN , trnP , and rns genes. However, these methods are hampered by the need for interpretation of complex RFLP patterns as well as the inter-laboratory differences and are relatively difficult to apply in the field.…”

Section: Resultsmentioning

confidence: 99%

“…This method is beginning to be used for identifying different Pyropia species or breeding cultivars that could presumably be applied for mariculture in warming ocean waters. Japanese researchers have revealed clear differences between native Pyropia species based on PCR-RFLP analysis of plastid, internal transcribed spacer (ITS), and mitochondrial DNA (mtDNA) [ 9 , 10 , 11 ]. Chinese and Korean researchers have mainly used this method to identify and discriminate among seaweed diseases and pest species [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

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An Efficient PCR-RFLP Method for the Rapid Identification of Korean Pyropia Species

Kim¹,

Choi²,

Choi³

2017

Molecules

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The present study utilizes polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis using partial plastid rbcL and mitochondrial trnC–trnP gene sequences to distinguish the six representative Pyropia species produced via mariculture in Korea. The rbcL, trnC, and trnP sequences of 15 Pyropia species from the NCBI database were aligned to determine specific restriction enzyme sites of the six Pyropia species. To confirm the presence of restriction sites of eight enzymes, PCR amplicons were digested as follows: a 556 bp fragment within the rbcL region of chloroplast DNA was confirmed in P. yezoensis using BglI, whereas Tth111I, AvaII, BsrI, and BsaAI enzymes produced fragments of 664, 271, 600, and 510 bp, respectively, from the rps11–trnG region of mitochondrial DNA in P. seriata, P. dentata, P. suborbiculata, and P. haitanensis. In the case of P. pseudolinearis, HindIII, SacII, and SphI enzymes each had two cleavage sites, at positions 174 and 825, 788 and 211, and 397 and 602 bp, respectively. All six species were successfully distinguished using these eight restriction enzymes. Therefore, we propose that PCR-RFLP analysis is an efficient tool for the potential use of distinguishing between the six Pyropia species cultivated via mariculture in Korea.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

An Efficient PCR-RFLP Method for the Rapid Identification of Korean Pyropia Species

Kim¹,

Choi²,

Choi³

2017

Molecules

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“…In 2011, the red algal order Bangiales has been revised based on combined analyses of the nuclear SSU rRNA gene and the RuBisCo L gene [11]. Mitochondrial DNA was also used for the discrimination of 18 Japanese Porphyra and Pyropia species [12]. From these previous studies, Kunimoto et al [2] and Niwa et al [8] reported diverse nucleotide sequences in the ITS region among P. yezoensis wild-collected and culture strains.…”

Section: Introductionmentioning

confidence: 99%

“…Recent studies characterized the phylogenetic relationship in Pyropia spp. by analyses of mitochondrial and plastid DNA [11,12]. Therefore, mitochondrial and plastid DNA analysis may also be useful for species and origin identification of the Korean dried nori products.…”

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confidence: 99%

Origin identification of dried seaweed product “nori” by PCR–RFLP analysis of Pyropia yezoensis in the internal transcribed spacer ITS-1 region

Touhata

Namikoshi²,

Suzuki

et al. 2013

Fish Sci

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Nucleotide sequences in internal transcribed spacer (ITS)-1 region derived from dried nori products produced in Japan, China, and the Republic of Korea were compared. Thalli contained in the Japanese products were genetically homogenous, and their nucleotide sequences in ITS-1 were identical to those of the reference strains of Pyropia yezoensis f. narawaensis. In Chinese products, the thalli were related to P. yezoensis strain Minomiasakusa. In contrast, the thalli in the Korean products were genetically heterogeneous, and several different P. yezoensis strains and other Pyropia spp. were used for dried nori products. In some thalli produced in both China and Korea, the DNA sequences of the ITS-1 region were identical with that of Japan, suggesting that the cultivar strains might have been transplanted from Japan to China in recent years. The 432-bp-long nucleotide sequences in the ITS-1 region of thalli derived from Japanese origin were cleaved to two restriction fragments at 154 and 278 bp by cleavage of PCR-amplified products using MspI. Conversely, almost all of the corresponding sequences derived from China and Korea were lacking MspI or other restriction patterns, except for nori products from some areas that cultivate a closely related strain to the Japanese cultivar.

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“…In panel (c), the relative ‰uorescence intensities of the PtMIE orf169 trnV mtDNA fragments to the PyU51 orf169 trnV mtDNA fragments were derived from the exponential phase of ampliˆcation (18 22 cycles) in panel (a), and the data were plotted as a function of the relative ‰uorescence intensity versus total DNA content of PtMIE. 6,7,12)…”

mentioning

confidence: 99%

Development of quality control and evaluation techniques for dried sheets of Asakusa-nori: Simple estimation of <i>Pyropia tenera</i> thallus content in dried sheets using PCR analysis

柿沼¹,

平²,

岩出³

2015

NSUGAF

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In order to develop quality control and evaluation techniques for dried sheets of Asakusa-nori, a simple, rapid method was created for using PCR analysis to estimate Pyropia tenera thallus content. Based on the mitochondrial DNA (mtDNA) nucleotide sequences of P. tenera and P. yezoensis, PCR primer sets were designed to amplify two mtDNA regions (orf169 trnV and cox1 regions) with nucleotide polymorphisms between both species. After PCR ampliˆcation of P. tenera and P. yezoensis total DNAs with the mtDNA-speciˆc primers, structural diŠerences between both species such as gene loss and rearrangement in the orf169 trnV and cox1 regions were easily detected, indicating that PCR analysis of these mtDNA regions is useful for discriminating P. tenera from P. yezoensis. Pyropia tenera content consisting of thallus pieces randomly collected from commercially-available sheets of dried Asakusa-nori was successfully estimated by PCR analysis of these mtDNA regions. In addition, the mtDNA fragments originating from P. tenera and P. yezoensis were ampliˆed by competitive-PCR using total DNAs extracted from the punches of the dried-Asakusa nori sheets as the template. These results indicate that these techniques enable rapid, simple estimation of P. tenera thallus content in dried-Asakusa nori sheets.

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Use of PCR-RFLP for the discrimination of Japanese Porphyra and Pyropia species (Bangiales, Rhodophyta)

Cited by 11 publications

References 24 publications

An Efficient PCR-RFLP Method for the Rapid Identification of Korean Pyropia Species

An Efficient PCR-RFLP Method for the Rapid Identification of Korean Pyropia Species

Origin identification of dried seaweed product “nori” by PCR–RFLP analysis of Pyropia yezoensis in the internal transcribed spacer ITS-1 region

Development of quality control and evaluation techniques for dried sheets of Asakusa-nori: Simple estimation of <i>Pyropia tenera</i> thallus content in dried sheets using PCR analysis

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