• Title, Summary, Keyword: NOV Gene

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Taxonomic revision of the genus Herposiphonia (Rhodomelaceae, Rhodophyta) from Korea, with the description of three new species

  • Koh, Young Ho;Kim, Myung Sook
    • ALGAE
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    • v.33 no.1
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    • pp.69-84
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    • 2018
  • We examined the species diversity of Herposiphonia on Korean coasts, based on a combination of morphology and molecular analyses of the mitochondrial COI-5P DNA barcode marker and plastid rbcL gene. We report the presence of eight species including three novel species: H. donghaensis sp. nov., H. jejuinsula sp. nov., H. sparsa sp. nov., H. caespitosa, H. fissidentoides, H. insidiosa, H. parca, and H. subdisticha. Specimens were separated into eight clades in both the COI-5P and rbcL gene analyses, with 1.3-19.6 and 6.6-15% interspecific sequence divergence, respectively. These eight species are also distinguishable by several morphological characteristics such as: branching pattern (d/i pattern in H. donghaensis sp. nov. and H. sparsa sp. nov.; d/d/d/i pattern in others), shape of determinate branch (ligulate in H. fissidentoides; terete in others), number of vegetative trichoblasts (1-2 in H. insidiosa and H. sparsa sp. nov.; 3-4 in H. caespitosa; absent in others), and number of segments and pericentral cells in determinate branches. About three novel species revealed by our analyses, H. donghaensis sp. nov. is newly discovered, and H. jejuinsula sp. nov. and H. sparsa sp. nov. were previously reported in Korea as H. nuda and H. secunda, respectively. Our results show that DNA barcoding and rbcL analyses are useful for delimiting species boundaries and discovering cryptic species diversity in the genus Herposiphonia.

Genetic Polymorphisms of the Bovine NOV Gene Are Significantly Associated with Carcass Traits in Korean Cattle

  • Kim, B.S.;Kim, S.C.;Park, C.M.;Lee, S.H.;Cho, S.H.;Kim, N.K.;Jang, G.W.;Yoon, D.H.;Yang, B.S.;Hong, S.K.;Seong, H.H.;Choi, B.H.
    • Asian-Australasian Journal of Animal Sciences
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    • v.26 no.6
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    • pp.780-787
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    • 2013
  • The objective of this study was to investigate single nucleotide polymorphisms (SNPs) in the bovine nephroblastoma overexpressed (NOV) gene and to evaluate whether these polymorphisms affect carcass traits in the Korean cattle population. We resequenced to detect SNPs from 24 unrelated individuals and identified 19 SNPs within the full 8.4-kb gene, including the 1.5-kb promoter region. Of these 19 SNPs, four were selected for genotyping based on linkage disequilibrium (LD). We genotyped 429 steers to assess the associations of these four SNPs with carcass traits. Statistical analysis revealed that g.7801T>C and g.8379A>C polymorphisms in the NOV gene were associated with carcass weight (p = 0.012 and 0.008, respectively), and the g.2005A>G polymorphism was associated with the back fat thickness (BF) trait (p = 0.0001). One haplotype of the four SNPs (GGTA) was significantly associated with BF (p = 0.0005). Our findings suggest that polymorphisms in the NOV gene may be among the important genetic factors affecting carcass yield in beef cattle.

Ponticoccus gilvus gen. nov., sp. nov., a Novel Member of the Family Propionibacteriaceae from Seawater

  • Lee, Dong Wan;Lee, Soon Dong
    • Journal of Microbiology
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    • v.46 no.5
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    • pp.508-512
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    • 2008
  • A novel actinobacterium, designated strain MSW-$19^T$, was isolated from a seawater sample in Republic of Korea. Cells were aerobic, Gram-positive, non-endospore-forming, and non-motile cocci. Colonies were circular, convex, opaque, and vivid yellow in colour. A phylogenetic tree based on 16S rRNA gene sequences exhibited that the organism formed a distinct clade within the radius encompassing representatives of the family Propionibacteriaceae. The phylogenetic neighbors were the type strains of the genera Friedmanniella, Microlunatus, Micropruina, Propionicicella, and Propionicimonas. Levels of 16S rRNA gene sequence similarity between the isolate and members of the family were less than 95.3%. The cell wall peptidoglycan of the organism contained LL-diaminopimelic acid as the diagnostic diamino acid. The isolate contained MK-9($H_4$) as the predominant menaquinone, $ai-C_{15:0}$ as the major fatty acid and polar lipids including phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid. The G+C content of the DNA was 69.6 mol%. On the basis of the phenotypic and phylogenetic data presented here, the isolate is considered to represent a novel genus and species in the family Propionibacteriaceae, for which the name Ponticoccus gilvus gen. nov., sp. nov. is proposed. The type strain is strain $MSW-19^T$ (= KCTC $19476^T$= DSM $21351^T$).

Aliihoeflea aestuarii gen. nov., sp. nov., a Novel Bacterium Isolated from Tidal Flat Sediment

  • Roh, Seong Woon;Kim, Kyoung-Ho;Nam, Young-Do;Chang, Ho-Won;Kim, Min-Soo;Shin, Kee-Sun;Yoon, Jung-Hoon;Oh, Hee-Mock;Bae, Jin-Woo
    • Journal of Microbiology
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    • v.46 no.5
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    • pp.594-598
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    • 2008
  • A novel Gram-negative and rod-shaped bacterium, designated $N8^T$, was isolated from tidal flat sediment. Phylogenetic analysis based on 16S rRNA gene sequences showed that $N8^T$ strain is associated with the family Phyllobacteriaceae: two uncultured clones (98.4 and 99.8% 16S rRNA gene sequence similarity) and the genus Mesorhizobium (${\leq}97.0%$). The novel strain formed a separate clade with uncultured clones in the phylogenetic tree based on 16S rRNA gene sequences. Cellular fatty acid profiles predominately comprised $C_{18:1}$ ${\omega}7c$ and $C_{19:0}$ cyclo ${\omega}8c$. The major isoprenoid quinone is ubiquinone-10 and genomic DNA G+C content is 53.4 mol%. The polyphasic taxonomic study indicates that the novel strain $N8^T$ represents a novel species of the new genus in the family Phyllobacteriaceae, named Aliihoeflea aestuarii. The type strain is $N8^T$ (= KCTC $22052^T$= JCM $15118^T$= DSM $19536^T$).

Inhella inkyongensis gen. nov., sp. nov., a New Freshwater Bacterium in the Order Burkholderiales

  • Song, Jae-Ho;Oh, Hyun-Myung;Lee, Jung-Sook;Woo, Seung-Buhm;Cho, Jang-Cheon
    • Journal of Microbiology and Biotechnology
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    • v.19 no.1
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    • pp.5-10
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    • 2009
  • A freshwater bacterium, designated $IMCC1713^T$, was isolated from a highly eutrophic artificial pond. Cells of the strain were Gram-negative, chemoheterotrophic, poly-$\beta$-hydroxybutyrate granule containing and obligately aerobic short rods that were motile with a single polar flagellum. The 16S rRNA gene sequence similarity analysis showed that the novel strain was most closely related to the species Roseateles depolymerans (96.3%), Mitsuaria chitosanitabida (96.2%), Ideonella dechloratans (96.2%), and Pelomonas saccharophila (96.1%) in the Sphaerotilus-Leptothrix group within the order Burkholderiales. Phylogenetic trees based on 16S rRNA gene sequences indicated that the isolate formed an independent monophyletic clade within the order Burkholderiales. The relatively low DNA G+C content (57.4mol%), together with several phenotypic characteristics, differentiated the novel strain from other members of the Sphaerotilus-Leptothrix group. From the taxonomic data, therefore, the strain should be classified as a novel genus and species, for which the name Inhella inkyongensis gen. nov., sp. nov. is proposed. The type strain of the proposed species is strain $IMCC1713^T$ (=KCTC $12791^T$=NBRC $103252^T$=CCUG $54308^T$).

Granulosicoccaceae fam. nov., to Include Granulosicoccus antarcticus gen. nov., sp. nov., a Non-phototrophic, Obligately Aerobic Chemoheterotroph in the Order Chromatiales, Isolated from Antarctic Seawater

  • Lee, Ki-Young;Lee, Hong-Kum;Choi, Tae-Hwan;Kim, Kyung-Mi;Cho, Jang-Cheon
    • Journal of Microbiology and Biotechnology
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    • v.17 no.9
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    • pp.1483-1490
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    • 2007
  • A Gram-negative, motile by tuft flagella, obligately aerobic chemoorganoheterotrophic, sphere-form bacterium, designated $IMCC3135^T$, was isolated from the Antarctic surface seawater of King George Island, West Antarctica. The strain was mesophilic, neutrophilic, and requiring NaCl for growth, but neither halophilic nor halotolerant. The 16S rRNA gene sequence analysis indicated that the strain was most closely related to genera of the order Chromatiales in the class Gammaproteobacteria. The most closely related genera showed less than 90% 16S rRNA gene sequence similarity and included Thioalkalispira (89.9%), Thioalkalivibrio (88.0%-89.5%), Ectothiorhodospira (87.9%-89.3%), Chromatium (88.3%-88.9%), and Lamprocystis (87.7%-88.9%), which represent three different families of the order Chromatiales. Phylogenetic analyses showed that this Antarctic strain represented a distinct phylogenetic lineage in the order Chromatiales and could not be assigned to any of the defined families in the order. Phenotypic characteristics, including primarily non-phototrophic, non-alkaliphilic, non-halophilic, and obligately aerobic chemoheterotrophic properties, differentiated the strain from other related genera. The very low sequence similarities (<90%) and distant relationships between the strain and members of the order suggested that the strain merited classification as a novel genus within a novel family in the order Chromatiales. On the basis of these taxonomic traits, a novel genus and species is proposed, Granulosicoccus antarcticus gen. nov., sp. nov., in a new family Granulosicoccaceae fam. nov. Strain $IMCC3135^T\;(=KCCM42676^T=NBRC\;102684^T)$ is the type strain of Granulosicoccus antarcticus.

Account of montane and insular speciation in some Korean megadriles (Annelida: Oligochaeta)

  • Blakemore, Robert J.;Lee, Seunghan;Seo, Hong-Yul
    • Journal of Species Research
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    • v.4 no.1
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    • pp.1-22
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    • 2015
  • Surveys of easily accessible or moderately remote South Korean mountains has revealed several common exotic and early species-complexes [Amynthas corticis (Kinberg, 1867) with A. diffringens (Baird, 1869), A. gracilis (Kinberg, 1867) and Metaphire californica (Kinberg, 1867)], plus an unexpected number of new native taxa. Megascolecid Metaphire muuido sp. nov. and lumbricid Eisenia muuido sp. nov. are newly described from Muuido Island, Incheon. Montane taxa are parthenogenetic Amynthas tokioensis oculo sub-sp. nov. that lacks male pores but is yet comparable to both Amynthas tokioensis (Beddard, 1892) and Metaphire soulensis (Kobayashi, 1938) with its possible new synonym A. chiakensis Hong & James, 2013. Apparently unique sympatric taxa are Amynthas bangtaesan bangtaesan and A. b. confinius sup-spp. nov., Amynthas centurio sp. nov., Amynthas punicans sp. nov., Amynthas seoraksan and A. seoraksan iti sub-spp. nov. These are newly described and their DNA COI gene barcodes, where obtainable, are presented in a phylogram with outgroup Acanthodrilidae Microscolex dubius (Fletcher, 1887) from Lake Biwa Japan being a new exotic record for Asia.

Pedobacter xinjiangensis sp. nov., from the Desert, Xinjiang

  • Tang, Yali;Wang, Yang;Ji, Shanming;Zhang, Kundi;Dai, Jun;Zhang, Lei;Peng, Fang;Fang, Chengxiang
    • Journal of Microbiology and Biotechnology
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    • v.20 no.2
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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.

Acinetobacter marinus sp. novo and Acinetobacter seohaensis sp. nov., Isolated from Sea Water of the Yellow Sea in Korea

  • Yoon, Jung-Hoon;Kim, In-Gi;Oh, Tae-Kwang
    • Journal of Microbiology and Biotechnology
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    • v.17 no.11
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    • pp.1743-1750
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    • 2007
  • Two Gram-negative, nonmotile, coccobacilli, SW-$3^T$ and SW-$100^T$, were isolated from sea water of the Yellow Sea in Korea. Strains SW-$3^T$ and SW-$100^T$ contained ubiquinone-9 (Q-9) as the predominant respiratory lipoquinone and $C_{18:1}\;{\omega}9c$ and $C_{16:0}$ as the major fatty acids. The DNA G+C contents of strains SW-$3^T$ and SW- $100^T$ were 44.1 mol% and 41.9 mol%, respectively. A neighbor-joining tree based on l6S rRNA gene sequences showed that the two isolates fell within the evolutionary radiation enclosed by the genus Acinetobacter. Strains SW-$3^T$ and SW-$100^T$ exhibited a l6S rRNA gene similarity value of 95.7% and a mean DNA-DNA relatedness level of 9.2%. Strain SW-$3^T$ exhibited l6S rRNA gene sequence similarity levels of 93.5-96.9% to the validly described Acinetobacter species and fifteen Acinetobacter genomic species. Strain SW-$100^T$ exhibited l6S rRNA gene sequence similarity levels of less than 97.0% to the other Acinetobacter species except Acinetobacter towneri DSM $14962^T$ (98.0% similarity). Strains SW-$3^T$ and SW-$100^T$ exhibited mean levels of DNA-DNA relatedness of 7.3-l6.7% to the type strains of some phylogenetically related Acinetobacter species. On the basis of phenotypic, phylogenetic, and genetic data, strains SW-$3^T$ and SW-$100^T$ were classified in the genus Acinetobacter as two distinct novel species, for which the names Acinetobacter marinus sp. novo (type strain SW-$3^T$=KCTC $12259^T$=DSM $16312^T$) and Acinetobacter seohaensis sp. novo (type strain SW-$100^T$=KCTC $12260^T$=DSM $16313^T$) are proposed, respectively.