• The Plant Pathology Journal
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• 제27권2호
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• pp.148-155
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• 2011

Our previous sequence and phylogenetic analyses of the Korean Rice stripe virus (RSV) suggested possible genetic reassortment of RNA segments, but whether this RNA variation contributed to the recent RSV outbreaks in Korea is yet unclear. To further clarify these RSV-RNA segment variations, we developed a reverse transcription-polymerase reaction/restriction enzyme (RT-PCR/RE) analysis-based method. We identified five REs, including DraI, EcoR1, NdeI/AseI, and SpeI, that could differentiate RSV RNA 1-4 subtypes, respectively. Our RT-PCR/RE results provided a clear pattern of RNA reassortment, i.e., different groups of isolates having their RNA segments derived from two to three different RSV ancestors, such as from Eastern and Southwestern Chinese or Japanese M and T isolates. We also found that the migratory small brown planthopper from Eastern China caught by aerial net traps that possesses RSV-RNA3 genotypes corresponds mainly to Eastern China, with a few for Southwestern China based on RT-PCR/RE, sequence and phylogenetic analyses, indicating that RSV populations in Eastern China may also have strong RNA variation. The development of an RE analysisbased method proved a useful epidemiological tool for rapid genotyping and identification of mixed infections by RSV strain and by different subtype.

• Journal of Life Science
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• 제21권9호
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• pp.1281-1287
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• 2011

Phyllostachys consists of high and fast growing trees and is a genus in the family Gramineae. The genus has many species in Asia, with main distribution being in India and China. One of the most popular sequences for phylogenetic inference at the generic and infrageneric levels in plants is the internal transcribed spacer (ITS) region of the 18S-5.8S-26S nuclear ribosomal cistron. We evaluated four taxa with the ITS region to estimate phenotypic relationships within the genus Phyllostachys in Korea. Alignment of the DNA sequences required the addition of numerous gaps. Sequence variation within the Phyllostachys was mostly due to natural selection, although several indels and inserts were found. Within the genus Phyllostachys, P. nigra and P. nigra var. henonis were the relatives in the three phylogenetic analyses (MP, ML, and NJ). However, some external nodes were poorly supported. Morphological traits and simple repeats (ISSR) represented the result of a relationship similar to the that of ITS sequences in the genus Phyllostachys. This suggests that ITS sequences are very informative for identification of these taxa.

• Korean Journal of Plant Taxonomy
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• 제53권2호
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• pp.157-165
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• 2023

Paraphlomis koreana (Lamiaceae) was newly named and added to Korean flora in 2014. Paraphlomis belongs to the tribe Paraphlomideae, along with Ajugoides and Matsumurella. However, a recent study has suggested that P. koreana is morphologically similar to Matsumurella chinensis, making them difficult to distinguish from each other. Therefore, we aimed to examine the phylogenetic placement of P. koreana within the tribe and compare its genetic relationship with M. chinensis. We sequenced an additional complete plastid genome for an individual of P. koreana and generated sequences of nuclear ribosomal (nr) DNA regions of internal and external transcribed spacers (ITS and ETS) for two individuals of P. koreana. Maximum likelihood analyses based on two nrDNA regions (ITS and ETS) and four plastid DNA markers (rpl16 intron, rpl32-trnL, rps16 intron, and trnL-F) covering 13 Paraphlomis species and M. chinensis were conducted. Phylogenetic analyses concordantly supported that P. koreana forms a monophyletic group with M. chinensis. Moreover, our study revealed that P. koreana includes nrDNA sequences of M. chinensis as minor intra-individual variants, suggesting that the genetic divergence between the two taxa is incomplete and may represent intraspecific variation rather than distinct species. In conclusion, our findings suggest that the independent species status of P. koreana within Paraphlomis should be reconsidered.

• Asian-Australasian Journal of Animal Sciences
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• 제26권2호
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• pp.163-170
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• 2013

In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1-C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3-C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.

• Korean Journal of Fisheries and Aquatic Sciences
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• 제37권5호
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• pp.414-422
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• 2004

To infer phylogenetic relationships among Epinephelus species inhabiting coastal regions of Korean peninsula, mitochondrial cytochrome b genes from 9 species belonging to the subfamily Epinephelinae were PCR-amplified, cloned and sequenced. Aligned cytochrome b sequences of 10 species containing one additional sequence from GenBank were 1,140 base pairs in length, including 439 variable and 330 parsimony informative sites. The cytochrome b genes of 10 species, as other vertebrates studied to date, exhibit unequal base compositions: an entirely low G content ($15.2{\pm}0.3{\%}$on average) and almost equal T, C and A contents ($29.3{\pm}0.8{\%},\;30.7{\pm}1.0{\%},\;and\;24.8{\pm}0.5{\%}$ on average, respectively).In third codon positions, transitional substitutions especially between Epinephelus species and outgroup species are almost certainly saturated or near saturation. Phylogenetic analyses were performed with sequence data from 8 Epinephelus species and 2 outgroup species (Cephalopholis urodela and Vaviola louti) by using distance-based (neighbor-joining and minimum evolution) and parsimony-based (maximum parsimony) methods. The results showed that the monophyly of the genus Epinephelus was supported by relatively high bootstrap values. However, phylogenetic relationships among E. areolatus, E. moara, E. septemfasciatus, and Epinephelus sp were poorly resolved. Within the genus Epinephelus, three resolved monophyletic groups were found: clade 1 included E. akaara and E. awoara;, clade 2 included E. fasciatus and E. merra; and clade 3 included E. akaara, E. awoara, E. fasciatus, E. merra, E. areolatus, E. moara, E. septemfasciatus and Epinephelus Sp.

• The Korean Journal of Zoology
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• 제38권3호
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• pp.324-329
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• 1995

The phylogenetic relationships between Cheju native horses and Tsushima native horses were studied by protein polymorphism analyses in 16 gene loci (Trypsin inhibitor: Ti, Chymotrypsin inhibitor: CTi, Albumin: Al, Esterase: Es, Transferrin: Tf, Hemoglobin: Hb, Catalase: Cat, Esterase D: EsD, Glutamate oxaloacetate transaminase: GOT, Glyoxalase I: GLO I, Acid phosphatase: AcP, Superoxide dismutase: SOD, Lactate dehydrogenase: LDH, Hexokinase: HK, Malate dehydrogenase: MDH, Malic enzyme: ME). All allelic patterns of the protein loci, except 5 loci (SOD, LDH, HK, MDH, ME), were polymorphic in both two populations. Gene frequencies of the polymorphic loci of the population of Cheju native horses were higher than those of Tsushima native horses. Average heterozygosity in Cheju native horses was 0.375, showing higher than that of Tsushima native horses (0.304). The Da distance and gene identity of two populations were 0.108 and 0.868, respectively. The phylogenetic tree constructed by these results and those previously reported in other horse populations, consisted of three clusters. From this phylogenetic tree, it could be suggested that Cheju native horses and Tsushima native horses had diverged from the Mongolian wild horse (Equus prsewolskii).

• ALGAE
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• 제20권1호
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• pp.1-13
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• 2005

The taxonomic status of three closely related species of the genus Sphacelaria, S. rigidula Kützing, S. fusca (Hudson) C.F Gray and S. didichotoma Saunders was reassessed on the basis of morphological observations from herbarium specimens and phylogenetic analysis of RUBISCO spacer sequences. Sphacelaria rigidula was characterized by having only 2-armed propagules and somewhat slender filaments. Culture experiments revealed that its propagules commonly formed secondary arms, even though they were rarely produced in the field. It is concluded that S. divaricata Montagne characterized by dichotomously branched arms in propagules shoud be synonymized with S. rigidula, based on propagule morphology and measurements. Sphacelaria fusca clearly be separated from S. rigidula by having 2-4 armed propagules. These morphological differences were highly supported by the differences in the RUBISCO spacer sequences. S. didichotoma resembles S. rigidula in having propagules with two dichotomously branched arms. However, it commonly produces the secondary arms in the field. Additionally, this species has shorter primary arms than S. rigidula. Phylogenetic analyses supported the distinction of S. didichotoma from S. rigidula. The northwestern Pacific plants, previously recorded as S. divaricata, were recognized as S. didichotoma.

• ALGAE
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• 제31권4호
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• pp.303-315
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• 2016

Compsopogon specimens collected in China were examined based on morphology and DNA sequences. Five molecular markers from different genome compartments including rbcL, COI, 18S rDNA, psbA, and UPA were identified and used to construct a phylogenetic relationship. Phylogenetic analyses indicated that two different morphological types from China clustered into an independent clade with Compsopogon specimens when compared to other global samples. The Compsopogon clade exhibited robust support values, revealing the affiliation of the samples to Compsopogon caeruleus. Although the samples were distributed in a close geographical area, unexpected sequence divergences between the Chinese samples implied that they were introduced by different dispersal events and from varied origins. It was speculated that Compsopogon originated in North America, a portion of the Laurentia landmass situated in the Rodinia supercontinent at approximately 573.89-1,701.50 million years ago during the Proterozoic era.Although Compsopogonhad evolved for a rather long time, genetic conservation had limited its variability and rate of evolution, resulting in the current monospecific global distribution. Additional global specimens and sequence information were required to increase our understanding of the evolutionary history of this ancient red algal lineage.

• The Plant Pathology Journal
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• 제18권3호
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• pp.109-114
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• 2002

To evaluate the phylogenetic and taxonomic status of the phytoplasmas associated with water dropwort (Oenanthe javanica DC) disease in Korea and Japan, their 16S rDNA was analyzed. DNAs extracted from water dropworts collected in Korea (Kyongnam province) and Japan (Chiba prefecture) affected by witches' broom and yellows were subjected to PCR using phytoplasma-specific primers, which amplified a 1.4-kbp fragment that included the 16S rDNA. Phytoplasmas were characterized by RFLP analysis using AluI, HaeIII, HhaI, KpnI, MseI, and RsaI restriction enzymes and by sequence analysis of the PCR products. The mater dropwort witches'broom (WDWB) and water dropwort yellows (WDY) 16S rDNA sequences were identical and closely related to onion yellows (OY, 99.9% identity), which belong to the aster yellows (AY) 16S-subgroup. However, the KpnI RFLP analyses clearly distinguished the WDY and WDWB phytoplasmas from the OY phytoplasma. The phylogenetic analysis based on 16S rDNA showed that WDWE and WDY phytoplasmas are members of a relatively homogeneous group that evolved from a common ancestor.

• The Plant Pathology Journal
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• 제28권4호
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• pp.381-389
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• 2012

Molecular characterization of Cucumber mosaic virus (CMV) was done by using samples from tomato and cucurbitaceous plants collected from different locations in the northwest region of Iran. After screening by enzyme-linked immunosorbent assay, 91 CMV-infected samples were identified. Biological properties of eight representative isolates were compared with each other revealing two distinct phenotypes on squash and tomato plants. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP), movement protein (MP) and 2b of the new isolates, together with that of previously reported isolates, led to the placement of the Iranian isolates in subgroups IA and IB according to CP and MP genes, but in subgroup IA according to the 2b gene. These data suggest that reassortment may have been a major event in the evolution of CMV in Iran, and that the Iranian isolates are derived from a common recent ancestor that had passed through a bottleneck event.