• Journal of Crop Science and Biotechnology
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• 제10권1호
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• pp.27-32
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• 2007

RAPD, Inter-SSR, and AFLP markers were used to assess the genetic diversity of lettuce cultivars and the phylogenetic relationships in Lactuca spp. A total of 216 polymorphic bands from seven RAPD primers, four Inter-SSR primers, and five AFLP primer combinations were used to elucidate the genetic similarity among lettuce cultivars. Forty-four lettuce accessions were subdivided into discrete branches according to plant type: crisphead, butterhead, and stem type, with some exceptions. The leafy- and cos-type accessions were intermingled in other groups with no discrete branch indicating that these are more diverse than others. Three accessions, including the Korean cultivar 'Cheongchima', the Korean local landrace 'Jinjam', and the German cultivar 'Lolla Rossa' were classified as the most diverse accessions. Twenty bands were unique in specific cultivars. Among these, three were specific in a plant type; one in Korean leafy type, one in crisphead type, and one in cos type lettuce. In the phylogenetic analysis among Lactuca species, L. saligna, L. serriola, and L. georgica clustered in a sister branch of the L. sativa complex. Two L. virosa accessions show the highest intra-specific relationships. L. perennis outlied from all the other Lactuca species at a genetic similarity of 0.53 and clustered with two Cichorium species, C. intybus and C. endivia, with genetic similarity of 0.67. The phylogenetic tree was supported by data from polymorphism of chloroplast genome which was revealed by PCR-RFLP.

• Journal of Plant Biotechnology
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• 제45권3호
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• pp.236-241
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• 2018

Lilium is a perennial bulbous plant belonging to the liriotypes genus. Our aim was to study the phylogenetic relationships of the Lilium family. Two varieties of Lilium ledebourii, 44 varieties of the gene bank, and one variety from the Tulipa family served as the out group. In order to study the diversity between lilium masses, ITS regions were used to design the marker. The results showed that the guanine base is the most abundant nucleotide. Relatively high conservation was observed in the ITS regions of the populations (0.653). Phylogenetic analysis showed that sargentiae and hybrid varieties are older than other varieties of the Lilium family. Also, the location of L. ledebourii varieties (Damash and Namin) was identified in a phylogenetic tree by using the ITS marker. Overall, our research showed that ITS molecular markers are very suitable for phylogenetic studies in the Lilium family.

• 원예과학기술지
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• 제34권2호
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• pp.294-304
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• 2016

Members of the genus Brassica, which are known as oil crops or cruciferous vegetables, are widely cultivated in Canada, Australia, Asian and Europe. Because Brassica species have high yields, are well adapted to their environments, and are self-incompatible, the germplasm is abundant. Previous studies have reported abundant genetic diversity even within Brassica subspecies. In Korea, fresh cabbage leaves are eaten with roast meat, and to meet the current popular demand, new varieties are being increasingly bred. To determine the genetic diversity and relationships among the cabbage vegetables in Korea, we evaluated the genetic variation of 18 accessions based on 5S and 18S ribosomal RNA (rRNA) gene sequences. We detected many variable nucleotide sites, especially in the 5S rRNA gene sequences. Because the length of the 18S rRNA gene might influence the dissimilarity rate statistics, we used both the 5S and 18S sequences to analyze the phylogenetic relationships. S7 (B. oleracea) showed the most distant phylogenetic relationship with the other Brassica species. Interestingly, B2 (B. oleracea), B15, and B18 (B. campestris) have three different types of leaf profiles, and were divided into one group, and the other Brassica species formed another group. Statistical analysis of interspecies and intraspecies genetic distances revealed that B. campestris L. showed higher genetic diversity than B. oleracea L. This work provides additional data that facilitates the evaluation of the genetic variation and relationships among Brassica species. The results could be used in functional plant breeding programs to improve Brassica crops.

• 한국버섯학회지
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• 제12권3호
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• pp.145-153
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• 2014

Pleurotus has increased rapidly production and consumption because of highly nutritional value, natural healthy food and so on. The basic studies for Pleurotus need for development of mushroom industry. This study was to investigate the cultural characteristics among 15 strains of 6 species and to analyze their phylogenetic relationships. The cultural characteristics were investigated by mycelial growth activity at different media, temperature and pH. The optimum media for mycelial growth were YM and MCM in most species. The optimum temperature for mycelial growth were $25^{\circ}C$ and $30^{\circ}C$. The optimum pH for mycelial growth were widly range from pH 5.1 to 7.4. Through the RFLP (restriction fragment length polymorphism) of IGS (intergenic spacer) I region in ribosomal DNA, it was analyzed phylogeny of interspecies and intraspecies. Each species was discriminated well as isolates within each species formed clade to be distinguished other species. P. florida was highly similar to P. floridanus, and P. flabellatus was P. cornucopiae. P. fuscus var. ferulae was highly similar to P. eryngii but discriminated different species in analysis of RFLP of IGS I region and showed different characteristics in mycelial culture. RFLP of IGS I region was useful of studying phylogenetic relationships of species and population.

• 한국패류학회지
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• 제25권1호
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• pp.41-49
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• 2009

Random amplified polymorphic DNA (RAPD) marker and sequence analyses of the internal transcribed spacer (ITS) region of ribosomal DNA were used to assess phylogenetic relationships of four Korean oyster species. The average number of species-specific markers identified from five universal rice primers (URPs) by RAPD-PCR was 1.8 for Crassostrea gigas, 3.2 for C. nippona, 3.6 for C. ariakensis, and 4.6 for Ostrea denselamellosa. The length of the ITS (ITS1-5.8S-ITS2) region ranged from 1,001 to 1,206 bp (ITS1, 426-518 bp; 5.8S, 157 bp; and ITS2, 418-536 bp), while the GC content ranged from 55.5-61.1% (ITS1, 56.8-61.8%; 5.8S, 56-57.3%; and ITS2, 54.1-62.2%). A phylogenetic analysis of the oysters based on our RAPD, ITS1, and ITS2 sequence data revealed a close relationship between C. gigas and C. nippona and a distant relationship between the genera Crassostrea and Ostrea. Our results indicated that RAPD and ITS sequence analysis was a useful tool for the elucidation of phylogenetic relationships and for the selection of species-specific markers in Korean oysters.

• Animal cells and systems
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• 제6권1호
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• pp.13-18
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• 2002

Phylogenetic relationships of Korean Acidiella species were tested using mitochondrial 16S ribosomal RNA gene sequences. We used 16 published sequences as outgroup, and 10 new sequences for nine Korean Acidiella species as ingroup. The number of aligned sites was 1,281 bp, but 1,135 bp were used for the analysis after excluding sites with missing data or gaps. Among these 1,135 sites, 464 sites were variable and 340 were informative for parsimony analysis. Phylogenetic information was extracted from this data set using neighbor-joining, maximum likelihood and maximum parsimony methods and compared to a morphology-based phylogenetic hypothesis. Our molecular data suggest that: (1) the tribe Trypetini appears to be monophyletic even when the nine additional Acidiella species are added to our previous phylogenetic analysis; (2) all the Korean Acidiella species belong to the Trypeta group, but the genus Acidiella is not supported as monophyletic; (3) the close relationship of A. circumvaga, A. issikii, and A. sapporensis is supported; (4) the close relationship of A. pachypogon and two additional new Acidiella species is strongly supported; and (5) the possible presence of two or more cryptic species among the specimens previously identified as A. obscuripennis is suggested. Sequence data from the mitochondrial 16S rDNA allowed us to better understand the systematic status of Korean Acidiella species. They indicated that the current concept about the genus Acidiella is insufficient and needs to be refined further. This study also showed a few interesting relationships, that had not been recognized by morphological study alone. Based on this study, we were able to plan further experiments to analyze relationships within the Trypeta Group.

• Molecules and Cells
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• 제25권4호
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• pp.510-522
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• 2008

To construct the molecular systematics of the genus Megoura (Hemiptera: Aphididae), DNA based-identification was performed using four mitochondrial and three nuclear DNA regions: partial cytochrome c oxidase I (COI), partial tRNA-leucine + cytochrome c oxidase II (tRNA/COII), cytochrome b (CytB), partial 12S rRNA + tRNA-valine + 16S rRNA (12S/16S), elongation factor-1 alpha ($EF1{\alpha}$), and the internal transcribed spacers 1 and 2 (ITS1, ITS2). Pairwise sequence divergences between taxa were compared, and phylogenetic analyses were performed based on each DNA region separately, and the combined datasets. COI, CytB, $EF1{\alpha}$, ITS1, and ITS2 were relatively effective in determining species and resolving their relationships. By contrast, the sequences of tRNA/COII and 12S/16S were not able to separate the closely related species. CytB and $EF1{\alpha}$ gave better resolution with higher average sequence divergences (4.7% for CytB, 5.2% for $EF1{\alpha}$). The sequence divergence of COI (3.0%) was moderate, and those of the two ITS regions (1.8% for ITS1, 2.0% for ITS2) were very low. Phylogenetic trees were constructed by minimum evolution, maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses. The results indicated that the phylogenetic relationships between Megoura species were associated with their host preferences. Megoura brevipilosa and M. lespedezae living on Lespedeza were closely related, and M. nigra, monophagous on Vicia venosa, was rather different from M. crassicauda, M. litoralis, and M. viciae, which are oligophagous on Lathyrus and Vicia. The three populations of M. crassicauda formed a clade separated from M. litoralis and M. viciae. Nevertheless M. litoralis and M. viciae, which are morphologically similar, were not separated due to negligible sequence divergence. We discuss the phylogenetic relationships of the Megoura, and the usefulness of the seven DNA regions for determining the species level phylogeny of aphids.

• 한국환경생태학회지
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• 제32권6호
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• pp.566-574
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• 2018

한국산 나문재속 식물에 대한 계통학적 유연관계를 밝히고, 분자계통학적 연구를 통해 나문재속 종간 유연관계를 확인할 수 있는 분자마커를 찾아내기 위해 연구를 수행하였다. 핵 리보솜 DNA ITS와 엽록체 DNA matK, psbA-trnH 그리고 trnL-trnF를 분자마커로 사용하였다. ITS 영역은 칠면초와 해홍나물 그리고 해홍나물과 방석나물을 구분하지 못하였다. psbA-trnH와 trnL-trnF 영역의 염기서열은 칠면초와 방석나물을 구분하지 못하였다. 그러나 4종의 분자마커 영역을 조합하여 분석한 결과 나문재속 식물 5종이 각각 독립적인 계통을 형성하는 것을 확인하였다. 따라서 나문재속 계통관계 분석을 위해서 여러 개의 분자마커 조합이 유용할 것으로 판단된다. 나문재속 내 분류군 간의 계통관계를 명확히 밝히기 위해 차후에 좀 더 많은 생태학적, 형태학적 자료를 조사해야 할 것으로 보인다.

• Molecules and Cells
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• 제27권1호
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• pp.55-66
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• 2009

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.

• Fisheries and Aquatic Sciences
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• 제2권2호
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• pp.122-128
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• 1999

Several differences are revealed in the segmentation and setation of the antennule, maxillule, maxilliped and fifth legs between three genera of the family Metridinidae, Metridia, Pleuromamma, and Gaussia. The phylogenetic relationships are cladistically analyzed on the basis of 10 morphological characters. The cladogram shows that Gaussia and Pleuromamma form a sister group, with Metridia which is the first branch to diverge within the family. The presence Of quadritheks on the male antennules of Metridia and Pleuromamma seems to be an important synapomorphy. The loss of quadritheks in Gaussia represents likely evidence of a character reversal into the ancestral condition.