• Journal of Microbiology and Biotechnology
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• v.13 no.6
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• pp.846-852
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• 2003

rpoB DNAs (279 bp) from 34 species of 5 actinomycete genera were sequenced and a phylogenetic tree was constructed based on the sequences obtained. The genera were clearly differentiated in the rpoB tree, forming clades specific to their respective genus. In addition, 2 signature amino acid residues specific to Streptomyces were found in a multiple alignment of the deduced amino acid sequences. To empirically confirm that this rpoB gene analysis system could be used to differentiate actinomycete isolates, the proposed system was used to identify 16 actinomycete isolates from Jeju Island. All isolates were successfully differentiated into the genera Streptomyces and Micromonospora. Accordingly, this is the first report that an rpoB sequence analysis has been effectively used to differentiate actinomycete strains at the genus level.

• Journal of Microbiology and Biotechnology
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• v.23 no.5
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• pp.602-613
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• 2013

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.8
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• pp.1085-1090
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• 2009

There are currently five primary breeds of Chinese gamecock, the Henan, Luxi, Tulufan, Xishuangbanna andZhangzhou. Though there is historical evidence of cockfighting in China dating as far back as 2,800 years, the origin and genetic relationships of these breeds are not well understood. We used sequence variation from the mtDNA cytb gene and control region (1,697 bp) to examine the domestication history and genetic relationship of the Chinese gamecock. From 75 samples (14-16 per breed) we found 34 haplotypes, and 45 variable nucleotides. Phylogenetic reconstruction indicated multiple origins of the gamecock breeds. The breeds in the north and center of China, Tulufan, Luxi and Henan, clustered together in a haplogroup and may have the same ancestor. However the southern breeds, Zhangzhou and Xishuangbanna clustered into two isolated haplogroups, suggesting another two origins of Chinese gamecock. Meanwhile, extensive admixture was also found because samples from different breeds, more or less, were always grouped together in the same clades. Based on these results, we discuss the possibilities of multiple origins of gamecock breeds, from both ancestral gamecocks as well as other domestic chickens and red jungle fowl.

• The Plant Pathology Journal
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• v.23 no.3
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• pp.151-154
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• 2007

Phytoplasma was identified from leaf lettuce (Lactuca sativa) cultivated in commercial green-house in Korea. Diseased leaf lettuce revealed proliferation of shoots, and yellowing and shrinking of leaves (lettuce proliferation-K). Polymerase chain reaction (PCR) with universal primer pair P1/P6, and aster yellows (AY) specific primer pair R16F1/R1 amplified 1.5kb and 1.1kb length of DNA fragments, respectively. Nucleotide sequences of 16S rRNA gene were determined (Gen Bank accession no EF489024). Phylogenetic analysis of 16S rDNA showed the closest relationship with AY phytoplasma (GenBank accession no. AY389822 and AY389826), indicating that lettuce proliferation-K is a member of AY. Phytoplasma bodies were detected in phloem sieve tubes of diseased lettuce by transmission electron microscopy. The structures had round or pleomorphic shapes with a diameter of 130-300nm. Phylogenetic analysis of 16S rRNA gene, microscopic observation of phytoplasma bodies and symptomatology indicated that lettuce proliferation-K is caused by phytoplasma in the AY group. This is the first report of phytoplasma disease in lettuce in Korea.

• Parasites, Hosts and Diseases
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• v.48 no.4
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• pp.303-307
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• 2010

Stellantchasmus falcatus is a minute intestinal fluke in the family Heterophyidae. Metacercariae, the infective stage, were reported in a marine fish, mullet Liza subviridis, and a fresh water fish, Dermopgenus pusillus, in Thailand. Adults were found in chicks, rats, cats, and humans. Morphological studies were done for comparing Stellantchasmus sp. worms found in 2 different fish hosts; their shapes and organ arrangements were very similar except for the prepharynx length. Therefore, the present study aimed to compare their DNA fingerprints using the HAT-RAPD method for both types of Stellantchasmus and several other related species. Ten arbitrarily selected primers (OPA-04, OPA-09, OPN-02, OPN-03, OPN-09, OPN-12, OPP-11, OPR-15, OPX-13, and OPAD-01) were used. It was found that OPA-09, OPN-03, and OPAD-01 were able to generate S. falcatus specific fragments in mullets which consisted of 200, 760, and 280 bp, respectively. In addition, the results of morphologic, DNA fingerprinting, and phylogenetic analyses strongly suggest that the fresh water and marine specimens of Stellantchamus may be different species.

• Food Science of Animal Resources
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• v.27 no.3
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• pp.357-362
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• 2007

Nine brand populations of Hanwoo cattle were characterized using 11 microsatellite DNA markers. The studied populations were: Ansung, Yangpyang, DaeGwanryeng, Palkongsangkangwoo, Hoengseong, Jangsu, Sumjinkang, Hadong, Nam-hae. The observed heterozygosity, expected heterozygosity, and polymorphism information content were calculated. Allele frequencies were calculated and used for the characterization of each brand population and to study their genetic relationships. Genetic distances were estimated using Nei's DA genetic distance and the resultant DA matrix was used in the construction of phylogenetic trees. The NJ tree showed that Ansung and Yangpyang, Sumjinkang and Jangsu, Namhae and Ha-Dong are closely related and are considered to have undergone genetic exchange within the same locale. This study will contribute to the local Hanwoo brand industry.

• Journal of Species Research
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• v.4 no.1
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• pp.49-56
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• 2015

Zeuzera is one of the most important wood borer pests in South East Asia. Like of most other genera of moths, the systematic of this genus is still in dispute, especially on the monophyly and the relationship within this genus due to the fact that genus is very varied. This genus was defined based on external characters only such as cross vein Sc-Rs present, humeral plate approximately triangular in shape and anal plate moderately long to moderately short. Therefore, the monophyly of this genus need to be evaluated based on more comprehensive data. To clarify the monophyly of the genus Zeuzera, to reveal the phylogenetic relationships among the Indonesian species, and to establish the genetic characters of Indonesian Zeuzera, we analyzed seven species of Indonesian Zeuzera including three other species distributed around the world based on nucleotide sequence variation across a 580-bp region in the CO I gene. The results showed that the monophyly of Zeuzera was supported by bootstrap tests at the MP and ML tree building methods (>95%). Genus Zeuzera was divided into two groups (A and B) with Z. borneana was excluded from the two groups and occupied at the basal node. Indonesian species was distributed into two different clades. CO I gene alone was able to fully resolve the relationships among species within clade B. However, further investigations were needed by including more species and other genes that the more conserved to test the validity of the phylogenetic hypothesis proposed here.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.6
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• pp.1013-1020
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• 1997

The cellular fatty acids of 47 marine bacteria representing the genus Alteromonas, Arthrobacter, Bacillus, Micrococcus, Pseudomonas, Shewanella, Staphylococcus and Stenotrophomonas were determined by a gasliquid chromatographic analysis. Sixty-eight different fatty acids with 10 to 20 carbon atoms were detected in marine bacteria. Of the eight genus examined, 14:0, 16:0 and i17:0 were detected in all, while i14:0, a15:0, i16:0, and 15:0 were found in most of all. There were significant differences in the fatty acid patterns between Gram positive and Gram negative bacteria. Bacteria of Gram positive genus showed relatively high contents of the branched type fatty acids, while the major fatty acids in Gram negative were unsaturated and straight forms. Phylogenetic relationships between marine bacteria defined by the cellular fatty acid patterns represented obvious differences between Gram positive and Gram negative genera, even in respective genus. Therefore, the bacterial classification and identification can be accomplished more easily and rapidly based on the cellular fatty acid profiles than the conventional methods.

• Korean Journal of Plant Taxonomy
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• v.40 no.4
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• pp.208-217
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• 2010

Crossosomatales is a recently recognized order in the rosid II clade with about 64 species in eight morphologically distinct families that have been previously classified in as many as 15 other orders. Phylogenetic relationships among the families and genera within Crossosomatales were investigated using chloroplast atpB, matK, and rbcL sequences employing maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic framework was used to examine the patterns of morphological evolution and synapomorphies for subclades within Crossosomatales. The combined data with representative species from all genera in the order strongly supported monophyly of Crossosomatales. Strong support was found for the families in the Southern Hemisphere, in which Aphloiaceae is sister to the clade of (Geissolomataceae, (Ixerbaceae + Strasburgeriaceae)). The sister relationship between the Southern Hemisphere clade and families distributed primarily in the Northern Hemisphere was also supported. As in the previous studies, following relationships were found within the Northern Hemisphere clade: Staphyleaceae is sister to a clade of (Guamatelaceae, (Stachyuraceae + Crossosomataceae)). The pattern analysis indicates that evolutionary pattern of morphological characters is complex, requiring multiple changes within Crossosomatales. Several reproductive traits, such as inflorescence, aril, stigma, and conspicuous protrusion from pollen aperture, corroborate the molecular phylogeny.

• Journal of Aquaculture
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• v.22 no.1
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• pp.83-91
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• 2009

The Korean doty barbel Hemibarbus mylodon (Cypriniformes; Cyprinidae) is a critically endangered freshwater fish species mainly because of its natural habitat degradation. Three full-length complementary DNA (cDNA) clones representing different muscle actin isoforms were isolated and characterized. The three muscle actin isoforms were 1,294-1,601 bp long with the identical open reading frames of 1,134 bp with the deduced amino acid residues of 377. They showed 83.9-87.2% identities in the coding nucleotide level and 96.8-98.1% identities in the amino acid level. Phylogenetic analysis with the coding nucleotide sequences revealed that three muscle actin isoforms of H. mylodon formed strongly supported monophyletic groups with one of cypriniform skeletal $\alpha$-actin (acta1), cypriniform aortic $\alpha$-actins (acta2), and uncharacterized Danio rerio muscle actin isoform/Salmo trutta slow muscle actin (a novel muscle actin type). Our phylogenetic tree further suggested that cypriniform acta2 only showed the orthologous relationship to tetrapod acta2. Other multiple actin isoforms from diverse teleostean taxa were however clustered to no tetrapod orthologs, i.e., acta1, cardiac $\alpha$-actins (aetc1), acta2, and enteric $\gamma$-actin (actg2). This result strongly suggested that teleostean muscle actins have experienced different and complicated evolutionary history in comparison to mammalian counterparts.