• Journal of Microbiology
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• 제44권1호
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• pp.83-91
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• 2006

The sudden appearance and potential lethality of severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV) in humans has resulted in a focusing of new attention on the determination of both its origins and evolution. The relationship existing between SARS-CoV and other groups of coronaviruses was determined via analyses of phylogenetic trees and comparative genomic analyses of the coronavirus genes: polymerase (Orflab), spike (S), envelope (E), membrane (M) and nucleocapsid (N). Although the coronaviruses are traditionally classed into 3 groups, with SARS-CoV forming a $4^{th}$ group, the phylogenetic position and origins of SARS-CoV remain a matter of some controversy. Thus, we conducted extensive phylogeneitc analyses of the genes common to all coronavirus groups, using the Neighbor-joining, Maximum-likelihood, and Bayesian methods. Our data evidenced largely identical topology for all of the obtained phylogenetic trees, thus supporting the hypothesis that the relationship existing between SARS-CoV and group 2 coronavirus is a monophyletic one. Additional comparative genomic studies, including sequence similarity and protein secondary structure analyses, suggested that SARS-Co V may bear a closer relationship with group 2 than with the other coronavirus groups. Although our data strongly suggest that group 2 coronaviruses are most closely related with SARS-CoV, further and more detailed analyses may provide us with an increased amount of information regarding the origins and evolution of the coronaviruses, most notably SARS-CoV.

• Animal cells and systems
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• 제3권1호
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• pp.9-15
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• 1999

Monophyly and intergeneric relationships of the tribe Helleboreae, sensu Tamura, and related genera were studied using a 1,100-bp segment at the 5'end of the 26S ribosomal RNA gene. Forty-one OTUs, including eight species of the Helleboreae, were either directly sequenced or obtained from previous publications. Data were analyzed using distance and discrete character methods to infer phylogenetic relationships among the included taxa. The inferred phylogeny did not support monophyly of either Helleboreae or Cimicifugeae whose members were intermixed in our inferred phylogeny. This result is congruent with our previous study, which recommended against finely subdividing, suprageneric higher taxa within the R-chromosome group (subfamily Ranuncluloideae, sensu lato) until more molecular data were accumulated. Our data convincingly suggest the presence of the following three monophyletic groups: the Cimicifuga group (the clade of Actaea, Cimicifuga, Souliea, Eranthis, Anemonopsis, and Beesia), the Trollius group (the clade of Trollius, Megaleranthis, Adonis), and a clade including Anemonopsis and Beesia. Our data also suggest that Trollius and Megaleranthis might be congeners and Eranthis a paraphyletic group.

• 식물분류학회지
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• 제44권1호
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• pp.22-32
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• 2014

꿀풀과에 속하는 긴병꽃풀속(Glechoma)내 5종에 대한 화판과 악편의 미세 구조를 관찰하여 기재하고 그 분류학적 유용성을 판단하였으며, 분자계통학적 유연관계를 확인하기 위하여 핵 리보솜 DNA의 ITS 염기서열에 기초한 연구를 수행하였다. 기공복합체는 조사된 모든 분류군의 악편에서 분포하였으며, 공변세포의 길이는 분류군마다 다소 차이를 보였다. 긴병꽃풀속 분류군들의 화판과 악에 분포하는 모용은 5 종류(단세포 비선모, 다세포 비선모, 짧은 자루 두상 선모, 긴 자루 두상 선모, 방패형 선모)로 나타났으며, 모용의 종류, 분포, 밀도가 분류군마다 다르게 나타났다. 핵 리보솜 DNA의 ITS 염기서열에 의한 분자계통학적 연구 결과 긴병꽃풀속은 분포지역에 따라 3개의 분계조(유럽-미국, 중국-한국, 일본)로 분리되었다. 한국과 중국에 분포하는 G. longituba는 단계통군을 이루었고, 이탈리아의 특산종인 G. sardoa와 미국 및 유럽에 분포하는 G. hederacea는 단계통군을 형성하였다. G. hirsuta는 유럽의 분계조와 자매군 관계를 이루었으나, 일본에 분포하는 G. grandis는 나머지 분류군들의 상호 유연관계에서 통계적 지지를 얻지 못하였다. 본 연구 결과에서 긴병꽃풀속내의 종간 한계 설정에 있어 화판 및 악의 미세형태형질의 연구보다 핵 리보솜 DNA의 ITS 염기서열에 기초한 분자 계통학적인 연구가 유용한 방법임이 판명되었다. 그러나 구체적인 본 속내 계통 분류학적인 논의를 위해서는 외부 형태학적 형질에 대한 분석을 동시에 수행할 필요가 있으며, 계통학적 유용성이 보다 높은 DNA 구간을 추가로 분석할 필요가 있다.

• 식물분류학회지
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• 제39권3호
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• pp.135-142
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• 2009

엽록체 rbcL gene의 염기서열과 포자의 형태를 바탕으로 고사리삼과 식물의 계통과 제주고사리삼속의 계통학적 위치를 추정하였다. 엽록체 DNA rbcL 염기서열의 분석 결과 고사리삼과는 뚜렷하게 고사리삼계보 (Botrychioid lineage)와 나도고사리삼계보 (Ophioglossoid lineage)의 두 군으로 구분되었다. 고사리삼계보에 있어 제주고사리삼속(Mankyua)은 Helmintostachys속과 함께 분계의 기저에서 고사리삼속(Botrychium)의 자매분류군으로 분지하였으나, 이들 고사리삼속(Botrychium), 제주고사리삼속(Mankyua), 및 Helmintostachys속 사이의 계통적 유연관계는 결정되지 못했다. 고사리삼속의 경우 Sceptridium아속과 Botrychium아속이 뚜렷한 단계통을 형성하였으나, Botrypus아속에 속한 분류군들은 고사리삼속의 기저에서 다른 고사리삼속 분류군의 자매분류군으로 분지하면서 단계통이 아닌 것으로 밝혀졌다. 나도고사리삼계보를 형성하는 나도고사리삼속(Ophioglossum)의 경우, Ophioglossum아속은 단계통을 형성하였으며, Ophioglossum아속에 대해 Cheiroglossa아속 및 Ophioderma 아속이 차례로 자매분류군으로 분지하였다. 염기서열 계통수, 포자의 형태 및 외부형태의 고찰에 있어 제주고사리삼속은 Helminthostachys와 유사하지만, 계통수에서 patristic distance 뿐 아니라 포자소엽의 형태가 뚜렷이 구분되어 이들 2속은 독립된 속으로 판단된다.

• Journal of Microbiology and Biotechnology
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• 제28권10호
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• pp.1760-1768
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• 2018

The type strain Bacillus subtilis subsp. subtilis KCTC $3135^T$ was deeply sequenced and annotated, replacing a previous draft genome in this study. The tar and tag genes were involved in synthesizing wall teichoic acids (WTAs), and these genes and their products were previously regarded as the distinguishing difference between B. s. subtilis and B. s. spizizenii. However, a comparative genomic analysis of B. subtilis spp. revealed that both B. s. subtilis and B. s. spizizenii had various types of cell walls. These tar and tag operons were mutually exclusive and the tar genes from B. s. spizizenii were very similar to the genes from non-Bacillus bacteria, unlike the tag genes from B. s. subtilis. The results and previous studies suggest that the tar genes and the tag genes are not inherited after subspecies speciation. The phylogenetic tree based on whole genome sequences showed that each subspecies clearly formed a monophyletic group, while the tree based on tar genes showed that monophyletic groups were formed according to the cell wall type rather than the subspecies. These findings indicate that the tar genes and the presence of ribitol as a cell-wall constituent were not the distinguishing difference between the subspecies of B. subtilis and that the description of subspecies B. s. spizizenii should be updated.

• Molecules and Cells
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• 제22권3호
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• pp.314-322
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• 2006

The whole mitochondrial genome (14,915 nt) of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia, Thoracica) was sequenced and characterized. It is the shortest of the 31 completely sequenced crustacean mitochondrial genomes, with the exception of a copepod Tigriopus japonicus (14,628 nt). It consists of the usual 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 relatively short non-coding region (294 nt). The thoracican cirripeds apart from Megabalanus volcano have the same arrangement of protein-coding genes as Limulus polypemus, but there are frequent tRNA gene translocations (at least 8). Some interesting translocation features that may be specific to the thoracican cirriped lineage are as follows: 1) trnK-trnQ lies between the control region and trnI, 2) trnA-trnE lies between trnN and trnS1, 3) trnP lies between ND4L and trnT, and 4) trnY-trnC lies between trnS2 and ND1. In P. mitella there are two trnL genes (L1 and L2) in the typical crustacean positions (ND1-L1-LrRNA and CO1-L2-CO2). The present result is compared and discussed with the other three cirriped mitochondrial genomes from one pedunculate (Pollicipes polymerus) and two sessiles (Tetraclita japonica and M. volcano) published so far. Mitochondrial protein phylogenies reconstructed by the BI and ML algorithms show that the thoracican Cirripedia is monophyletic (BPP 100/BP 100) and associated with Remipedia (BPP 98/BP 35). In addition, Oligostraca, including Ostracoda, Branchiura, and Pentastomida, is a monophyletic group (BPP 99/BP 68), and is basal to all the other examined arthropods. Remipedia + Cirripedia appears as an independent lineage within Arthropoda, apart from Thoracopoda (Malacostraca, Branchiopda, and Cephalocarida). The Thoracopoda is paraphyletic to Hexapoda. The present result suggests that the monophylies of Crustacea and Maxillopoda should be reconsidered.

• Molecules and Cells
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• 제27권4호
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• pp.429-441
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• 2009

We have determined the complete mitochondrial genome of the yellow-spotted long horned beetle, Psacothea hilaris (Coleoptera: Cerambycidae), an endangered insect species in Korea. The 15,856-bp long P. hilaris mitogenome harbors gene content typical of the animal mitogenome and a gene arrangement identical to the most common type found in insect mitogenomes. As with all other sequenced coleopteran species, the 5-bp long TAGTA motif was also detected in the intergenic space sequence located between $tRNA^{Ser}$(UCN) and ND1 of P. hilaris. The 1,190-bp long non-coding A+T-rich region harbors an unusual series of seven identical repeat sequences of 57-bp in length and several stretches of sequences with the potential to form stem-and-loop structures. Furthermore, it contains one $tRNA^{Arg}$-like sequence and one $tRNA^{Lys}$-like sequence. Phylogenetic analysis among available coleopteran mitogenomes using the concatenated amino acid sequences of PCGs appear to support the sister group relationship of the suborder Polyphaga to all remaining suborders, including Adephaga, Myxophaga, and Archostemata. Among the two available infraorders in Polyphaga, a monophyletic Cucujiformia was confirmed, with the placement of Cleroidea as the basal lineage for Cucujiformia. On the other hand, the infraorder Elateriformia was not identified as monophyletic, thereby indicating that Scirtoidea and Buprestoidea are the basal lineages for Cucujiformia and the remaining Elateriformia.

• International Journal of Industrial Entomology and Biomaterials
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• 제44권2호
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• pp.65-71
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• 2022

The wild silkmoth Antheraea yamamai Guérin-Méneville, 1861 (Lepidoptera: Saturniidae) is an important producer of silk that is superior to the silk produced by traditional domesticated silkworm. In this study, we sequenced the complete mitochondrial genome (mitogenome) of An. yamamai collected from Jeju Island, which is the southernmost island approximately 100 km offshore southward from the Korean Peninsula. Determining this sequence will be necessary for tracing the biogeographic history of the species and developing molecular markers for identifying the origin of commercial products. Comparison of the sequence divergence among two available and the current mitogenomes revealed a low but substantial number of substitutions, totaling 23 nucleotides in the whole genome. CytB and ND5 showed the highest variability with five and four variations, respectively, suggesting that these regions will be prior regions to target for subsequent biogeographic and diagnosis study. Phylogenetic reconstruction based on all available sequences of Saturniidae showed that An. yamamai is a sister to the congeneric species An. pernyi, corroborating that Antheraea is a highly supported monophyletic group. The tribe Saturniini was clearly non-monophyletic and interrupted by Attacini and Bunaeini.

• 한국수산과학회지
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• 제37권5호
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• pp.405-413
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• 2004

The previous morphology-based taxonomic frameworks within the family Syngnathidae had emphasized the significance of the male brood pouch and reproductive biology in defining the group. However, several different hypotheses had been proposed by different investigators. This study has been carried out to determine the phylogenetic relationships among 19 species belonging to the order Syngnathiformes with three Gasterosteiformes species as outgroup taxa by using the mitochondrial cytochrome b DNA sequences. Phylogenetic analyses based on neighbor-joining distance, maximum parsimony, minimum evolution and maximum likelihood method strongly supported that the family Syngnathidae, the suborder Syngnathoidei and the order Syngnathiformes were all monophyletic group. Although much of previous morphological analyses were supported by our molecular data, there were some significant discrepancies between molecular and morphological work. Such an interesting result was that the weedy seadragon (Phyllopteryx taeniolatus) strongly grouped together with the New Zealand pot-belly seahorse (Hippocampus abdominalis). Considering the markedly different brooding structure between them, this unexpected result might be explained whether by multiple independent origins of brooding structure or by hybridization between the female Hippocampus and other syngnathid species having individual membranous egg compartment. In addition, the suborder Aulostomoidei was paraphyletic group because the shrimpfish (Aeliscus strigatus), belonging to the family Centriscidae, always grouped together with the family Syngnathidae as a sister taxon.

• Plant Resources
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• 제8권2호
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• pp.135-144
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• 2005

RAPD analysis was performed to discuss the taxonomic status and phylogenetic relationships among the tribe Forsythieae and related groups. Two hundred and eighteen scorable polymorphic bands were detected from fourteen oligonucleotide primers. From the results of RAPD analysis by Nei and Li's genetic distance, each individuals of Abeliophyllum distichum showed high genetic relationships with ranging from 0.085 to 0.301, also the genus Forsythia showed from 0.042 to 0.655 among the species and populations. But, Abeliophyllum and Forsythia showed distinct dissimilarity, ranging from 0.610 to 1.258. And genetic differences among the population of Forsythia were 0.042 in F. koreana, 0.275 in F. saxatilis, 0.275 in F. ovata, 0.279 in F. nakaii, and 0.249 in F. viridissima. The UPGMA phenogram of tribe Forsythieae based on the results of RAPD analysis were presented that Abeliophyllum is distinct genus different from Forsythia. NJ tree which applied as the outgroups Fontanesia and Jasminum was derived, and it showed that tribe Forsythieae might be a monophyletic group. The genus Fontanesia was showed as sister group of tribe Forsythieae. Among the populations of taxa in Forsythia, F. koreana and F. saxatilis were more closely related, and F. ovata and F. nakaii were very closely related to F.japonica. And Fontanesia was the sister group of tribe Forsythieae.