• Journal of Microbiology and Biotechnology
• /
• v.19 no.9
• /
• pp.851-857
• /
• 2009

We developed and characterized 36 polymorphic microsatellite markers for the oyster mushroom (Pleurotus ostreatus). In total, 169 alleles were identified with an average of 4.7 alleles per locus. Values for observed ($H_o$) and expected ($H_E$) heterozygosities ranged from 0.027 to 0.946 and from 0.027 to 0.810, respectively. Nineteen loci deviated from Hardy-Weinberg equilibrium. Significant (P<0.05) excess heterozygosity was observed at nine loci. Linkage disequilibrium (LD) was significant (P<0.05) between pairs of locus alleles. Cluster analysis revealed that five species of genus Pleurotus made a distinct group, and the individual cultivars were grouped into major five groups from G-1 to G-5. The diverse cultivars of P. ostreatus were discriminated and the other four species revealed a different section in the UPGMA tree. These microsatellite markers proved to be very useful tools for genetic studies, including assessment of the diversity and population structure of P. ostreatus.

• KSBB Journal
• /
• v.19 no.1
• /
• pp.42-49
• /
• 2004

A gene coding for epoxide hydrolase (EH) of Aspergillus niger LK, a fungus possessing the enantioselective hydrolysis activity for racemic epoxides, was characterized by phylogenetic analysis. The deduced protein of A. niger LK epoxide hydrolase shares significant sequence similarity with several bacterial EHs and mammalian microsomal EHs (mEH) and belongs to the a/${\beta}$ hydrolase fold family. EH from A. niger LK had 90.6% identity with 3D crystal structure of lqo7 in Protein Data Bank. Sequence comparison with other source EHs suggested that Asp$\^$l92/, Asp$\^$374/ and His$\^$374/ constituted the catalytic triad. Based on the multiple sequence comparison of the functional and structural domain sequence, the phylogenetic tree between relevant epoxide hydrolases from various species were reconstructed by using Neighbor-Joining method. Genetic distances were so far as 1.841-2.682 but characteristic oxyanion hole and catalytic triad were highly conserved, which means they have diverged from a common ancestor.

• Journal of Life Science
• /
• v.9 no.1
• /
• pp.84-89
• /
• 1999

To determine phylogenetic relatedness of four silk-producing silkmoths (B. mori, B. mandarina, A. yamamai and A. pernyi), internal coding region of arylphorin which is a storage protein in hemolymph protein of insects were amplified by polymerase chain reaction and then sequenced and compared each other. The nucleotide composition was biased toward adenine and thymine(59% A+T) and a strong bias for use of C in the third position of codons was found for Phe and Tyr. Together TTC(Phe) and TAC(Tyr) account for about 16.8% (10 for TTC and 8 for TAC) of all codon usage. The nucleotide similarity of arylphorin gene from B. mori showed 99%, 98% and 97% homology with those of B. mandarina, A. yamamai and A. pernyi, respectively. Also, the nucleotide sequence of arylphorin gene from B. mandarina showed 98% and 97% homology with those of A. yamamai and A.pernyi, respectively. Between A. yamamai and A. pernyi, the sequence homology was 97%. The deduced amino acid sequences in B. mori, B. mandarina and A. yamamai showed almost 99% homology. Although the aryphorin gene provided insufficient variability among the four insect species, A UPGMA tree is generated that supported the monophyly of silk-producing insects, with M. sexta placed basal to it. It is suggest that silk-producing insects have a close relationship and a homogeneous genetic background from comparison with those of other insects.

• Applied Microscopy
• /
• v.38 no.4
• /
• pp.329-338
• /
• 2008

Pollen morphological studies using light and scanning electron microscopy were conducted to determined the sub-sectional boundary and species relationship of 12 species of subsect. Meleuphorbia and related taxa. Based on the sculpturing patterns of pollen grains and UPGMA tree from numerical analyses using 8 quantitative pollen characters 12 species were divided into two types: type I, having microperforate pollen grains in E. epicyparissias, E. inermis, E. pillansii, E. obesa, E. bubalina, E. meloformis, E. nesemanii, and E. jansenvillensis, and type II, having fossulate sculpturing pattern in E. longituberculosa, E. monteiri, E. caput-medusae and E. grantii. The resulting pollen data suggest that the subsect. Meleuphorbia should not be a natural group, but closely related to the species from subsect. Anthacantha and sect. Treisia and sect. Medusea. Thus, the pollen morphological data recommended to combine above taxa as a single taxonomic group.

• Animal cells and systems
• /
• v.13 no.4
• /
• pp.419-427
• /
• 2009

The Minke whale, Balaenoptera acutorostrata, is the smallest baleen whale in the suborder Mysticeti. Because this species inhabits coastal areas, it became a main target species of coastal small-type whaling in the North Atlantic and the Northwest Pacific Oceans, and the species' population size dramatically decreased because of over-exploitation. As a result, the International Whaling Commission declared a global moratorium on whaling and launched the development of a management procedure for protecting the whales. Morphological studies, whaling history analysis, and genetic studies conducted mainly by Japanese scientists showed the existence of one unique "E" stock that inhabits the waters around the Korean peninsula and mixes with the "O" stock in the southern part of the Sea of Okhotsk. We used the mitochondrial DNA control region polymorphism of 348 Minke whales bycaught or stranded in Korean waters from 30 October 1998 to 25 June 2005 to assess the whale population structure by year. The frequency of the 10 major haplotypes from the 40 identified haplotypes was not significantly different among groups, suggesting that a subpopulation was not present. A comparison of the genetic distances calculated with Tamura-Nei's method showed that the distances between groups were lower than those within groups, which suggests that there was no genetic difference in the Minke whale populations. The Fst comparison between groups and the phylogenetic tree constructed using the unweighted pair group method with arithmetic mean (UPGMA) and Neighbor Joining (NJ) method also detected no obvious sub-stock structure.

• Animal cells and systems
• /
• v.3 no.1
• /
• pp.89-96
• /
• 1999

Nucleotide sequences of a 501 base-pair (bp) fragment in the mitochondrial cytochrome b (cyt b) gene were analyzed for 12 populations of Rana rugosa from Korea and Japan using a polymerase chain reaction (PCR) and direct silver sequencing. Two genetically distinct groups (type-A and type-B) were found in Korea. Type-A was found throughout most of South Korea and type-B was restricted to the mid-southeastern regions (Samchok, Yongdok, Chongsong and Pohang). But in the Tonghae population, both types were found. The level of mitochondrial DNA (mtDNA) sequence differences ranged from 0% to .0.8% among six populations of type-A, and 0 to 1.0% among 4 populations of type-B. However, sequence differences between type-A and type-B ranged from 5.4% to 6.6%, Using Kimura's two-parameter distance, the level of genetic sequence divergence between type-A and type-B was 6.7%. The Japanese R. rugosa was clustered very far from the Korean R. rugosa with 14.7%. In the neighbor-joining and UPGMA tree, all Korean samples were grouped, but subdivided into two types in 99% of the bootstrap iteration.

• Korean Journal of Plant Resources
• /
• v.28 no.4
• /
• pp.411-418
• /
• 2015

Lonicera caerulea var. edulis is a rare species found in some alpine region of Korea. Genetic variation in L. caerulea var. edulis has been investigated by examining 161 individuals from six natural populations: Mt. Seorak 1, Mt. Seorak 2, Mt. Jeombong, Mt. Bangtae, Mt. Gyebang, Mt. Halla. The mean genetic diversity for all the six populations was 0.25 (S.I.). The highest genetic diversity was found in Mt. Seorak (S.I.=0.3158) and the lowest was in Mt. Gyebang (S.I.=0.1047). Comparatively low level of genetic diversity was observed (Ae=1.25, P= 64.6%, S.I.=0.25), which is a typical pattern for rare tree species. AMOVA showed exceptionally large proportion of genetic variations both for among populations (34.69%) and within populations (65.31%). Excluding Mt. Gyebang, the genetic variation among and within population was 18.71% and 81.29% respectively. The UPGMA dendrogram based on genetic distance is not suitable for geographic relationship. Genetic distance of Mt. Gyebang was most distant from the other populations. Excluding Mt. Gyebang, the genetic identities among the five populations were 0.95 to 0.97, which is very high similarity level of genetic identity. This low level of genetic variations and the lack of site in nature indicates that Lonicera caerulea var. edulis demanded a serious conservation.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.54 no.1
• /
• pp.88-103
• /
• 2009

The volatile and semi-volatile compounds of 5 accessions of domestic scented and 25 accessions of introduced scented were extracted by solid phase microextraction (SPME) and analyzed by gas chromatographymass spectrum (GC-MS). A total of 156 volatile and semivolatile compounds were identified from 30 accessions of aromatic rice, including 32 alcohols, 25 acids, 25 ketones, 21 hydrocarbon, 18 esters, 16 aldehydes, 4 ethers, 5 amines, 2 phenols, 2 bases, and 8 miscellaneous compounds. By UPGMA/Neighbor-join tree analysis, the thirty accessions of aromatic rice could be classified into seven groups according to the major odor or aroma compounds. Group I included indica type of Basmati varieties. Group II and Group IV included japonica type introduced scented. Group III consisted only Hyangmibyeo1ho in domestic scented. Group V and Group VII included indica type of Basmati and non-Basmati varities. Group VI included four of domestic scented of seven accessions excepted Basmati6129, Basmati 6311, and Seratus Malam.

• The Korean Journal of Ecology
• /
• v.27 no.6 s.122
• /
• pp.325-333
• /
• 2004

Birds were censused to investigate the composition of landscape structure for bird diversity around Ulsan between May and November 2002. Associations with three main categories of habitat variables were evaluated: 1) amount and type of forest; 2) residual habitats not classified as forest or crops; 3) land-use variables. Cluster analysis of bird community shows the highest forest variables of $79.06\%$, and the others are residual habitat variables ($17.98\%$), land-use variables ($2.94\%$) in spring, and forest variables of $57.77\%$, land-use variables ($23.16\%$), residual habitat variables ($18.47\%$) in autumn, respectively. In Principal Component Analysis of a total of 196 sites, the populations are strongly correlated to Component I ($54.8\%$) based forest habitats and to Component II based on land-use. Species preferring sites were clearly separated with heterogenous forest along the first axis. In autumn, the populations are moderately correlated to Component I based land-use and to component II based forest habitats. Species preferring local habitats were also clearly separated. Fifty three species of 1,700 birds were recorded: Brown-eared Bulbul, Vinous-throated Parrotbill, Great Tit, Tree Sparrow and Black-billed Magpie accounted for over $60\%$ of the observed birds in spring and autumn. The important species were Brown-eared Bulbul, Vinous-throated Parrotbill, Great Tit and Tree Sparrow in spring and autumn. Four habitats in terms of their species richness were computed as follows: Wonhyosan has the highest an expected species number, $E[S_{59}]=19$. Moonsusan has the lowest expected species number, $E[S_{59}]=17$ in spring. In autumn, Kuenamsan has the highest expected species number, $E[S_{63}]=16$. Moonsusan has the lowest expected species number, $E[S_{63}]=12$. Pairwise similarity declined with increasing distance between recording site and recording site from Moonsusan-Wonhyosan (0.62), the same geographical regions clustered separately in a UPGMA cluster tree in spring, and in autumn from Moonsusan-ChungJoksan (0.53).

• Korean Journal of Plant Taxonomy
• /
• v.43 no.1
• /
• pp.63-68
• /
• 2013

ITS DNA sequences of two variants of Pinus spp. having single fasciculate leaf or two to three fasciculate leaves within an individual were analysed in order to determine their origin. Also, the same DNA locus of P. densiflora, P. rigida and P. koraiensis, distributed at the same region together with the OTUs having leaf variations, were analysed to compare with each other. Aligned sequences including ITS1, 5.8S and ITS2 were 580~584 bp in length. The 5.8S region was well conserved among all the OTUs we tested except for P. koraiensis, which has two nucleotide substitutions. The partial ITS1 region upstream of the 5.8S region showed relatively high sequence diversity compare to the ITS2 and has 181~185 bp in length. In this region, the sequences of the two variants were identical to that of P. densiflora. The ITS2 has identical for all OTUs in length and the two variants also have same sequences compare to that of P. densiflora. These two variants and samples of P. densiflora were grouped together in the UPGMA tree with 100% similarity level. The result strongly suggest that these two variants were originated from P. densiflora.