• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.217-217
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• 2022

Pullulanase (PUL), a debranching enzyme, has been utilized in hydrolyzing the a-1,6 glucosidic linkages in starch, amylopectin, pullulan, as well as related oligosaccharides. It has also been indicated that PUL is a novel indicator of inherent RS (Resistant Starch) formation in rice. In this study, we performed haplotype analysis on 320 bred rice accessions, and additional 54 wild accessions were added to study genetic diversity along with other population-based analyses of the PUL gene. Through these investigations, we summarized a total of 10 functional (non-synonymous) SNPs from 7 different exons on chromosome 4. There were 10 haplotypes, of which only six haplotypes were functional, implicating different subpopulations. Diversity reduction was noticed in temperate japonica (0.0005) compared to the highest one (aus, 0.0154), illustrating their higher genetic differentiation by F_ST-value (0.926). The highest Tajima^ D value was observed in indica (3.6613), indicating PUL gene domestication signature under balancing selection, while the lowest Tajima's D value was found in temperate japonica (-2.2191) which might have undergone under positive selection and purified due to the excess of rare alleles. PCA, population structure, and phylogenetic analyses provide information on the genetic relatedness between and or among the cultivated subpopulations and the wild based on PUL genomic region.

• Molecules and Cells
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• 제28권3호
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• pp.155-165
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• 2009

The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys($St{\aa}l$) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage of H. halys are about average when compared with values observed in 19 other published hemipteran mitochondrial genomes. Phylogenetic analyses using these 20 hemipteran mitochondrial genomes support the currently accepted hypothesis that suborders Heteroptera and Auchenorrhyncha form a monophyletic group. The mitochondrial gene arrangements of the 20 genomes are also consistent with our results.

• Asian-Australasian Journal of Animal Sciences
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• 제22권1호
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• pp.13-19
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• 2009

In the present study, genetic analyses of diversity and differentiation were performed on four breeds of Indian zebu cattle (Bos indicus). In total, 181 animals belonging to Ponwar, Kherigarh, Gangatiri and Kenkatha breeds were genotyped for 20 cattle specific microsatellite markers. Mean number of alleles observed per locus (MNA) varied between 5.75 (Kenkatha) to 6.05 (Kherigarh). The observed and expected heterozygosity for the breeds varied from 0.48 (Gangatiri) to 0.58 (Kherigarh) and 0.65 (Kenkatha) to 0.70 (Kherigarh), respectively. $F_{IS}$ estimates of all the breeds indicated significant deficit of heterozygotes being 28.8%, 25.9%, 17.7% and 17.7% for Gangatiri, Ponwar, Kherigarh and Kenkatha, respectively. The $F_{ST}$ estimates demonstrated that 10.6% was the average genetic differentiation among the breeds. Nei's genetic distance DA and Cavalli- Sforza and Edwards Chord distance ($D_C$) and the phylogenetic tree constructed from these reflected the close genetic relationship of Gangatiri and Kenkatha, whereas Ponwar appears to be more distant.

• Mycobiology
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• 제45권1호
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• pp.39-43
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• 2017

Leaf spot disease on black chokeberry (Aronia melanocarpa) was observed at several locations in Korea during 2014-2015. Leaf spots were distinct, scattered over the leaf surface and along the leaf border, subcircular to irregular and brown surrounded by a distinct dark color, and were expanded and coalesced into irregularly shaped lesions. Severely infected leaves became dry and fell off eventually. The causative agent was identified as Pseudocercospora pyricola. Morphological observations and phylogenetic analyses of multiple genes, including internal transcribed spacer, translation elongation factor 1-alpha, actin, and the large subunit ribosomal DNA were conducted. The pathogenicity test was conducted twice yielding similar results, fulfilling Koch's postulates. To our knowledge, this is the first report on P. pyricola infection of A. melanocarpa globally.

• Animal cells and systems
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• 제13권3호
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• pp.305-314
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• 2009

The control region of mitochondrial DNA (13516-14619) is located between srRNA and $tRNA^{lle}$ gene in swimming crab, Portunus trituberculatus. The present study was investigated the genetic polymorph isms of the control region in samples of P. trituberculatus collected at coastal waters of the Yellow Sea in Korea. A total of 300 substitution and indel polymorphic sites were identified. In addition to SNPs and indel variation, a hypervariable microsatellite motif was also identified at position from 14358 to 14391, which exhibited 10 alleles including 53 different suballeles. When the hypervariable microsatellite motif was removed from the alignment, 95 haplotypes were identified (93 unique haplotypes). The nucleotide and haplotype diversities were ranged from 0.024 to 0.028 and from 0.952 to 1.000, respectively. The statistically significant evidence for geographical structure was not detected from the analyses of neighbor-joining tree and minimum-spanning network, neither. This result suggest that population of P. trituberculatus are capable of extensive gene flow among populations. We believed that the polymorph isms of the control region will be used for informative markers to study phylogenetic relationships of P. trituberculatus.

• Animal Systematics, Evolution and Diversity
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• 제24권3호
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• pp.327-332
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• 2008

Soft coral Dendronephthya gigantea (Verrill, 1864) is a conspicuous species dominating shallow sea waters of Jejudo Island, Korea. Recently its whole mitochondrial genome sequencing was completed by us and the sequence information provided an opportunity to test the age of Octocorallia and time of evolutionary separation between some representative orders of the subclass Octocorallia. Molecular phylogenetic analyses based on 13 mitochondrial protein encoding genes revealed a polyphyletic relationship among octocorallians representing two orders (Alcyonacea and Gorgonacea) and four families (Alcyoniidae, Nephtheidae, Briareidae, and Gorgoniidae). Estimates of divergence times among octocorallians indicate that the first splitting might occur around end of or after Cretaceous period (50-79 million years ago (Ma)). The age is relatively young compared to the long history of stony sea corals (>240 Ma). Taken together our result suggests a possible relatively recent radiating evolution at least in the order Alcyonacea and Gorgonacea. Molecular dating and phylogenetic analysis based on much broader taxon sampling and many genes might give an insight into this interesting hypothesis.

• ALGAE
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• 제20권4호
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• pp.261-270
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• 2005

We analyzed chloroplast ATP synthetase beta subunit(atpB) sequences from 32 strains of the zygnemophycean green algae, Staurastrum, Staurodesmus, and a single species of Xanthidium. A total of 42 atpB sequences including previously published ones was aligned for phylogenetic analyses. The phylogenies were validated with bootstrap analysis and Kishino-Hasegawa test. Taxa of Staurastrum excluding S. muticum indicate that they can be characterized by taxa having the ornamented cell wall or the process of cells. However, the genus Staurodesmus was grouped with taxa having the smooth cell wall and the absence of process or arms. The results suggest that the genus Staurodesmus could be extended to include Staurastrum muticum, Desmidium, Onychonema and Xanthidium. Further taxon sampling of Staurodesmus and putative relatives is necessary for a solid classification of the genus.

• Journal of Microbiology and Biotechnology
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• 제18권6호
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• pp.1016-1023
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• 2008

Lichens are predominant and important components of flora in the terrestrial ecosystem of Antarctica. However, relatively few researches on the phylogenetic position of Antarctic lichen-forming fungi have been accomplished. In this study, partial sequences of nuclear large subunit rDNAs from 50 Antarctic specimens were obtained and the phylogeny was reconstructed. Antarctic lichen species were distributed in 4 orders, including the monophyletic order Agyrales, paraphyletic orders Pertusariales and Teloschistales, and polyphyletic order Lecanorales. Species diversity was highest in the order Lecanorales, followed by Teloschistales and Pertusariales. Based on the phylogeny and sequence similarity analyses, it is proposed that the taxonomy of Stereocaulon alpinum, Physcia caesia, Usnea aurantiacoatra, and Cladonia species should be revised by careful examination of their phenotypic and molecular characteristics. Six species known to be endemic to Antarctica, Catillaria corymbosa, Himantormia lugubris, Leptogium puberulum, Pertusaria pertusa, Rhizoplaca aspidophora, and Umbilicaria antarctica, formed unique lineages, implying independent origins in the Antarctic area.

• Journal of Microbiology and Biotechnology
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• 제23권5호
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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.

• Journal of Microbiology and Biotechnology
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• 제20권2호
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• pp.397-402
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• 2010

A Gram-negative, rod-shaped, gliding, aerobic bacterium, designated $12157^T$, was isolated from the desert of Xinjiang, China and subjected to a polyphasic taxonomic study. The strain $12157^T$ grew optimally at pH 7.0 and $30^{\circ}C$. MK-7 was the predominant respiratory menaquinone. The DNA G+C content was 42.0 mol%. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolate was mostly related to members of the genus Pedobacter, with similarities ranging from 90.0% to 93.7%. Phylogenetic evidence and the results of phenotypic and genotypic analyses support the establishment of a novel species, Pedobacter xinjiangensis sp. nov., with strain $12157^T$ (=CCTCC AB $208092^T$=NRRL B-$51338^T$) as the type strain.