• Ocean and Polar Research
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• 제44권2호
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• pp.161-177
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• 2022

Microalgae can attach to the surface of ships and then spread to various areas by means of ship transport. The introduction of invasive species through ships is recognized as a marine problem worldwide. Identification of attached microalgae is necessary to investigate such movement between countries through ships. In the present study, through analytical methods we reviewed research data to identify the taxa of domestic attached microalgae and assess the ecological impacts of such microalgae. A total of 87 genera and 153 species (143 species of diatoms, 10 species of cyanobacteria, and 4 genera of dinoflagellates) were identified as native attached microalgae in Korea, and diatoms accounted for 93% of the total. Most of these attached microalgae were identified through research on natural substrates such as seaweeds and bedrock, and some were also identified through experiments using artificial adherent plates. To date, there is no information on microalgae attached to international ships and introduced into Korea. Molecular genetic analysis and systematic management through on-site sampling of international ships, microscopic analysis, and meta-barcoding are necessary to assess the inflow and spread path of hull-attached marine alien species and evaluate the risk they pose to the domestic ecosystem.

• 한국수산과학회지
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• 제55권4호
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• pp.478-483
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• 2022

A single specimen (522.0 mm in total length) of the family Muraenidae, collected from the waters off south-western Jeju-do Island in November 2021, was identified as Echidna nebulosa on the basis of morphological and molecular methods (DNA barcoding). This species is characterized by several morphological traits as follows: 10 rounded molar, median intermaxillary, and vomerine teeth; 4 predorsal vertebrae, 50 preanal vertebrae and 123 total vertebrae; and a pale background color with two rows of 17-20 blackish brown starry blotches along the head and body. As this is the first record of E. nebulosa in Korea, we propose the new Korean names, "Dung-Geun-Ni-Gom-Chi-Sog" for the genus Echidna, and "Beol-Kkok-Gom-Chi" for E. nebulosa.

• ALGAE
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• 제30권3호
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• pp.217-222
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• 2015

Pythium species (Pythiales, Oomycetes) are well known as the algal pathogen that causes red rot disease in Pyropia / Porphyra species (Bangiales, Rhodophyta). Accurate species identification of the pathogen is important to finding a scientific solution for the disease and to clarify the host-parasite relationship. In Korea, only Pythium porphyrae has been reported from Pyropia species, with identifications based on culture and genetic analysis of the nuclear internal transcribed spacer (ITS) region. Recent fungal DNA barcoding studies have shown the low taxonomic resolution of the ITS region and suggested the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene as an alternative molecular marker to identify Pythium species. In this study, we applied an analysis of both the ITS and cox1 regions to clarify the taxonomic relationships of Korean Pythium species. From the results, the two closely related Pythium species (P. chondricola and P. porphyrae) showed the same ITS sequence, while the cox1 marker successfully discriminated P. chondricola from P. porphyrae. This is the first report of the presence of P. chondricola from the infected blade of Pyropia yezoensis in Asia. This finding of the algal pathogen provides important information for identifying and determining the distribution of Pythium species. Further studies are also needed to confirm whether P. chondricola and P. porphyrae are coexisting as algal pathogens of Pyropia species in Korea.

• ALGAE
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• 제33권2호
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• pp.157-166
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• 2018

Cryptic species complexes are increasingly recognized in phycological research, obscuring taxonomy and raising questions about factors influencing speciation. A recent exploration of kelp genetic diversity on Haida Gwaii, British Columbia revealed the existence of a new species, Saccharina druehlii, which is cryptic with Saccharina sessilis. This suggests that molecular investigations further north may be required to elucidate the taxonomy and evolutionary history of this lineage. Although, for several decades, S. sessilis was considered a single highly variable species, its taxonomy has been far from straightforward. In particular, Hedophyllum subsessile (Areschoug) Setchell is now recognized as a synonym of S. sessilis in North America, but as a growth form of Saccharina bongardiana in Far East Russia. To resolve this taxonomic confusion, we sequenced mitochondrial (CO1-5P) and nuclear (internal transcribed spacer) markers of S. sessilis populations from the Aleutian Islands, Alaska, USA. Interestingly, none of our sequences matched S. sessilis sensu stricto. Instead, CO1-5P sequences from populations in the central and eastern Aleutians matched exactly S. druehlii with increasing sequence divergence occurring westward. Samples from Attu, the western-most island, composed a genetic group that clearly represents Kjellman's concept of Hafgygia bongardiana f. subsessilis and is distinct enough from S. druehlii and S. sessilis to potentially constitute a distinct species. Therefore, Saccharina subsessilis comb. nov. is proposed for this entity. Our results suggest the existence of a species complex at the crown node of S. sessilis and thus further investigation of Saccharina in Alaskan waters should be conducted to reconstruct the evolutionary history of this fascinating lineage.

• Journal of Plant Biotechnology
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• 제47권1호
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• pp.15-25
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• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• 한국수산과학회지
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• 제54권5호
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• pp.685-690
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• 2021

Harmful shell-boring species of the genus Polydora (Polychaeta: Spionidae) were frequently reported from commercially important mollusk species in Korea, Japan and China. The traditional approach based on the morphological characteristics showed limitations for species discrimination among shell-boring species. Therefore, DNA barcoding was adopted to identify Polydora species using molecular markers. Two Polydora species (P. haswelli and P. hoplura) in abalone shells were reported from our previous molecular phylogenetic study. In this study, we additionally reported the presence of shell-boring Polydora haswelli in commercially sold shellfish. The taxon-specific cox1 marker used in this study successfully allowed the isolation of P. haswelli from cockle Scapharca subcrenata, mussel Mytilus galloprovincialis, oyster Crassostrea gigas and scallop Argopecten irradians. Polydora hoplura was not found in these shellfish species. The genetic variations were found on the intraspecific level of P. haswelli and the same genotype was also detected in different shellfish species. This result can provide information on a new host and accurate parasitic Polydora species. Moreover, this report can be used as the biodiversity data of Polydora species on the invasion and transition of harmful Polydora species in mollusk aquaculture farms.

• Horticulture, Environment, and Biotechnology : HEB
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• 제59권6호
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• pp.865-873
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• 2018

Allium ochotense and Allium microdictyon are commonly known as 'Mountain garlic' and are popular, economically important species in many countries such as Korea, China, and Mongolia. Their leaves are used as culinary side dishes and in traditional medicines. In Korea, these two species are at risk of extinction due to damage to their natural habitat and thus, conservation and breeding programs are needed. However, their identification relies mostly on morphological data, which is limited and until recently, led to classifying these two species under A. victorialis. In the present study, a simple and reliable method of molecular identification was developed to distinguish A. ochotense from A. microdictyon that targets four barcoding regions: the internal transcribed spacer (ITS), the maturase K gene (matK), the chloroplast psbA-trnH intergenic region, and the ribulose-bisphosphate carboxylase large subunit gene (rbcL). Single nucleotide polymorphisms (SNPs) were found in ITS and matK regions, and species-specific primers were designed based solely on the SNP at position 680 of the ITS region that could differentiate A. ochotense from A. microdictyon. Using these primers in amplification refractory mutation system (ARMS)-PCR, A. ochotense, and A. microdictyon could be simultaneously and efficiently distinguished. This study is the first to report a simple, rapid, and efficient method for discriminating A. ochotense and A. microdictyon, indicating the utility of species-specific markers in the development of conservation and breeding programs.

• 한국균학회지
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• 제49권4호
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• pp.455-467
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• 2021

Macrofungi are valuable resources as novel drug candidates, new biomaterials, and edible materials. Recently, genetic approaches pertaining to macrofungi have been continuously growing for their identification, molecular breeding, and genetic engineering. However, purification and amplification of fungal DNA is challenging because of the rigid cell wall and presence of PCR inhibitory metabolites. Here, we established a direct PCR method to provide a rapid and efficient method for PCR-grade macrofungal DNA preparation applicable to both conventional PCR and real-time PCR. We first optimized the procedure of lysis and PCR using the mycelia of Lentinula edodes, one of the most widely consumed macrofungal species. Lysates prepared by neutralizing with (NH₄)₂SO₄ after heating the mycelia in a mixture of TE buffer and KOH at 65℃ for 10 min showed successful amplification in both conventional and real-time PCR. Moreover, the addition of bovine serum albumin to the PCR mixture enhanced the amplification in conventional PCR. Using this method, we successfully amplified not only internal transcribed spacer fragments but also low-copy genes ranging in length from 500 to 3,000 bp. Next, we applied this method to 62 different species (54 genera) of macrofungi, including edible mushrooms, such as Pleurotus ostreatus, and medicinal mushrooms such as Cordyceps militaris. It was found that our method is widely applicable to both ascomycetes and basidiomycetes. We expect that our method will contribute to accelerating PCR-based approaches, such as molecular identification, DNA marker typing, gene cloning, and transformant screening, in macrofungal studies.

• 환경생물
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• 제40권4호
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• pp.464-476
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• 2022

가속화되는 기후변화로 인해 전 세계 각지의 연안에서 해조류 대발생(macroalgal bloom)이 빈번하게 일어나고 있다. 특히, 녹조류의 대량 증식으로 인한 녹조(파래) 대발생(green tide) 현상은 지역 경제뿐만 아니라 연안 생태계 환경에도 막대한 피해를 주고 있다. 우리나라의 경우 2000년대부터 제주도 동북부 해안을 중심으로 파래대발생이 연중 지속적으로 관찰되며, 최근에는 남해와 동해 일대에서도 국지적으로 관찰되고 있다. 파래대발생의 원인 종은 갈파래속(Chlorophyta; genus Ulva)으로 알려져 있으며, 기후변화의 영향으로 해수 온도의 상승과 담지하수 및 인근지역 오염수 배출로 인한 질소와 인의 대량 유입으로 인한 영양염류 증가가 주요 원인으로 추정되고 있다. 갈파래속은 환경변화에 의해 형태적 발현의 가소성이 높은 표현형 적응성(phenotypic plasticity) 때문에 형태적 종 동정은 거의 불가능하다. 갈파래류 종 판별을 위해서는 분자유전학적 분석이 수행되어야 하나 현재 분자데이터를 이용한 갈파래 종 분포, 군집구조와 같은 생태조사연구는 매우 미흡한 실정이다. 파래대발생 피해 저감을 위해서는 파래대발생 주요 종들을 분자계통학적 분석을 통하여 정확하게 파악하는 것이 우선이다. 선행 연구에서는 2015년 파래대발생을 일으키는 주요 종 파악을 위해 핵 DNA ITS와 엽록체 DNA tufA (chloroplast elongation factor Tu) 유전자를 이용하여 분자계통학적 분석을 수행하였으며, 종 동정에는 tufa 유전자가 더 정확한 결과를 나타냈다. 따라서 본 연구에서는 tufA 유전자를 이용해 2015~2020년 제주도 연안에서 파래대발생을 일으키는 주요 구성 갈파래 종의 군집구조 및 종 다양성을 파악하고 종 구성의 시간적 변이를 확인하고자 하였다. 본 연구에서는 온대와 아열대 해역에서 주로 생장하는 것으로 알려진 큰갈파래와 구멍갈파래 종이 파래대발생의 주요 구성 종임을 확인하였다. 구멍갈파래는 2015년(35.75%)에서 2020년(36.18%) 기간 상대빈도의 변화가 거의 없고 안정적으로 유지되었으나, 큰갈파래의 경우 2015년(20.77%)에 비해 2020년(36.84%) 빈도가 대략 16% 증가하였다. 이러한 결과는 기후변화와 연관된 평균 해수면 온도의 상승에 큰갈파래의 높은 성장률 및 적응력과 관련이 있을 수 있으며, 제주도의 갈파래 군집을 구성하는 종 수는 2015년에는 9종이었으나 2020년에는 7종으로 감소하는 것으로 나타났다. 또한, 유럽 원산지 외래종인 긴통갈파래와 굽은갈파래가 2015년과 2020년 모두 제주 연안에서 관찰되어 이 두 종에 대한 향후 지속적인 모니터링이 필요하다. 본 연구의 결과는 우리나라 연안에서 발생하는 파래대발생의 저감을 위해 주요 종인 갈파래속(genus Ulva)에 대한 분자유전학적 데이터에 대한 정보를 제공하고자 한다.

• Weed & Turfgrass Science
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• 제4권1호
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• pp.18-25
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• 2015

DNA 바코드는 게놈 DNA의 단편을 이용해 형태적 지식없이 종을 동정하는 방법으로 전 세계적으로 최근에 많이 이용하고 있으며 고등식물에서는 엽록체 rbcL과 matK 유전자를 이용하고 있다. 본 연구에서는 표준 식물 바코드마커와 핵 ITS 부위를 이용하여 국내 포아풀아과 잡초 16속 29종 163생태형의 바코드 데이터를 생산하는 것을 목적으로 하였다. 더불어 포아풀아과의 바코드에서 각 마커의 효율성도 조사하였다. 바코드 결과 PCR 증폭과 염기서열 분석성공률은 rbcL에서 가장 높았으며 matK에서 가장 낮았다. 반대로 바코드 갭은 matK에서 가장 높은 반면 rbcL에서 가장 낮았으며, 종 식별 해상력은 matK에서 가장 높고, ITS에서 가장 낮았다. 그러나 바코드 갭과 종 식별 해상력이 가장 높은 matK를 포아풀아과에서 바코드 마커로 이용하는 것은 너무 낮은 PCR 증폭과 염기서열 분석성공률(58.3%) 때문에 고려해야할 것으로 생각된다. 단일마커로 rbcL과 ITS는 포아풀아과의 바코드에 적절하게 이용될 수 있으며, 두 마커를 조합으로 이용하면 공통으로 분석된 샘플에 따라 바코드 갭과 종 식별 해상력을 높일 수 있었다. 포아풀아과의 바코드데이터는 미국의 국립생물공학정보센터에 기탁하여 genbank 번호를 부여받아 공개하였다.