Some Xylaria materials growing on the fruits of Liquidambar spp. were collected. They were identified as X. persicaria on the basis of morphological characteristics and sequence analysis of the complete ITS region (ITS1-5.8S-ITS2) of rDNA. This is the first record of this species from Korea.
DNA, Ribosomal ; Fruit* ; Korea* ; Liquidambar* ; Sequence Analysis

Four strains of Phellinus spp. was identified based on internal transcribed spacer (ITS) region of rDNA sequence analysis and morphological characteristics. Basidiocarps of all strains were effused-reflexed and hymenial surface was poroid. Hyphal system was dimitic and basidiospore was globose to ellipsoid. The amplification of ITS regions produced a DNA fragment of 500 to 780 bp in all strains examined. The determined sequences were analyzed for the reconstruction of phylogenetic tree. From these results, Phellinus sp. KM-1, KM-2, and KM-4 was identified as P. hartigii, P. baumii, and P. linteus, respectively.
DNA ; DNA, Ribosomal ; Fruiting Bodies, Fungal ; Sequence Analysis

The marine genus Marinobacterium was first identified in 1997, and a total of 18 species have been characterized so far, 10 of which have published whole-genome sequencing data. This article summarizes the characteristics of Marinobacterium genus and analyzes the genome sequencing data related to the carbon source utilization, polyhydroxyalkanoate metabolism, and aromatic compounds degradation. The Marinobacterium species possess the complete glycolysis pathway and tricarboxylic acid cycle, yet lack genes involved in xylose utilization. All strains of the Marinobacterium genus contain the genes encoding for the typeⅠand type Ⅲ polyhydroxyalkanoate synthases, suggesting that the genus may have ability of polyhydroxyalkanoate accumulation. The Marinobacterium species contain the degradation pathways of aromatic compounds. Benzene, phenol and benzoic acid can be degraded into catechol via different enzymes, subsequently catechol is converted to 3-ketoadipate through the ortho-cleavage pathway. Alternatively, catechol can be degraded into pyruvate and acetyl-CoA. The analysis of genome sequencing data of the Marinobacterium genus provides in-depth understanding of the metabolic characteristics, indicating that the genus may have certain applications in the synthesis of polyhydroxyalkanoate and the removal of marine aromatic compounds.
Alteromonadaceae ; DNA, Bacterial ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA

We analyzed the genetic diversity of Cylindrocarpon destructans isolates obtained from Korean ginseng (i.e., Panax ginseng) roots by performing virulence tests and nuclear ribosomal gene internal transcribed spacer (ITS) and mitochondrial small subunit (mt SSU) rDNA sequence analysis. The phylogenetic relationship analysis performed using ITS DNA sequences and isolates from other hosts helped confirm that all the Korean C. destructans isolates belonged to Nectria/Neonectria radicicola complex. The results of in vivo and ex vivo virulence tests showed that the C. destructans isolates could be divided into two groups according to their distinctive difference in virulence and the genetic diversity. The highly virulent Korean isolates in pathogenicity group II (PG II), together with foreign isolates from P. ginseng and P. quinquefolius, formed a single group. The weakly virulent isolates in pathogenicity group I, together with the foreign isolates from other host plants, formed another group and exhibited a greater genetic diversity than the isolates of PG II, as confirmed by the mt SSU rDNA sequence analysis. In addition, as the weakly virulent Korean isolates were genetically very similar to the foreign isolates from other hosts, they were likely to originate from hosts other than the ginseng plants.
Base Sequence ; DNA, Ribosomal ; Genetic Variation* ; Panax* ; Sequence Analysis ; Virulence*

Orchidaceous plants have symbiotic relationships with endophytic fungi, including mycorrhizal fungi, which play important roles in the seed germination and growth of the host plants. In this study, endophytic fungal communities isolated from the roots of Cephalanthera longibracteata collected from three different sites in Korea were analyzed, and it was determined whether fungal communities were preferentially correlated with the sites. The fungal isolates were identified by sequence analysis of the internal transcribed spacer regions of rDNA. In total, 30 species of endophytic fungi, including two species of mycorrhizal fungi belonging to the genus Tulasnella, were identified. Leptodontidium orchidicola showed the highest frequency and was isolated from all root samples. Species diversity and richness were not significantly different among sites. However, the community structure of the endophytic fungi significantly differed among sites, suggesting that the site characteristics affected the community composition of the endophytic fungi colonizing the roots of C. longibracteata. Our findings will aid in developing methods involving the use of symbiotic fungi for orchid conservation and restoration in native habitats.
Colon ; DNA, Ribosomal ; Ecosystem ; Fungi ; Germination ; Korea* ; Mycorrhizae ; Sequence Analysis

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.
Genome ; Genomics ; Phylogeny ; RNA, Ribosomal, 16S ; genetics ; Sequence Analysis, DNA

We report a case of Massilia varians isolated from a deep finger wound following orthopedic surgery on an immunocompetent patient. The bacterium was identified by 16S rDNA sequence analysis. This is the first case of M. varians isolated from a clinical specimen since the first report in 2008.
DNA, Ribosomal ; Fingers ; Humans ; Orthopedics ; Sequence Analysis ; Wounds and Injuries

OBJECTIVES: To identify the drop-off location of victims in drowning cases, and confirm whether it is a fatal drowning or the victim is thrown into the water after death by detecting part of 5.8S sequence and second internal transcribed spacer （ITS2） （5.8S+ITS2） of diatom rDNA in water and organs. METHODS: Two cases identified by diatom examination, which received by Nanjing Municipal Public Security Bureau Forensic Center, were taken as the research objects. The difference of the population structure of algae in water and human tissue was analysed by length polymorphism of 5.8S+ITS2 marker. RESULTS: In case 1, similar species of diatom were detected from victim's lung and liver tissues and the water sample. Two kinds of DNA fragments with length of 330 bp and 376 bp were detected from victim's lung tissue and the water sample using 5.8S+ITS2 marker, which could confirm the victim was drowning before death. In case 2, there was no diatom found in victim's lung and liver tissues. Only one kind of DNA fragment with length of 331 bp and low relative fluorescence unit （RFU） was obtained from victim's lung tissue using 5.8S+ITS2 marker, thus the victim was thrown into the water after death. CONCLUSIONS The experimental results of the two cases in present study are consistent with the actual facts and the result of the diatom microscopic examination. The difference of population structure of specific microorganism in water and human tissue can be detected by 5.8S+ITS2 marker, which can help to identify the drop-off location of victims in drowning cases, and confirm whether it is a fatal drowning or the victim is thrown into the water after death.
DNA, Ribosomal/analysis* ; Diatoms/genetics* ; Drowning/diagnosis* ; Humans ; Liver ; Lung

The paper is aimed to identify SNP in Sarcandra glabra and Chloranthus spicatus, and authenticate S. glabra from Ch. spicatus and the mixture by using PCR amplification of specific alleles. SNPs in the ITS sequences of S. glabra and Ch. spicatus were found by ClustulX 2. 1 program and Bioedit software. Primers for authentic S. glabra and Ch. spicatus was designed according to the SNP site, and ITS sequence universal primers plus to the authentic primer to construct a multi-PCR reaction system, and then optimized the PCR reaction system. Five hundred and eighty band special for S. glabra and 470 bp band special for Ch. spicatus were found by using multi-PCR reaction. The multi-PCR reaction system could be applied to identify S. glabra and Ch. spicatus's leaves.
DNA, Plant ; analysis ; genetics ; DNA, Ribosomal ; genetics ; DNA, Ribosomal Spacer ; analysis ; genetics ; Magnoliopsida ; classification ; genetics ; Plant Leaves ; genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; RNA, Ribosomal ; genetics ; RNA, Ribosomal, 18S ; genetics ; RNA, Ribosomal, 5.8S ; genetics ; Species Specificity

OBJECTIVETo identify Menthae Haplocalycis Herba and its closely related species using DNA barcoding technique.

METHODTotal genomic DNA was isolated from Mentha canadensis and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.0. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods.

RESULTThe intra-specific genetic distances of M. canadensis were ranged from 0 to 0.006, which were lower than inter-specific genetic distances between M. canadensis and its closely related species (0.071-0.231). All the three methods showed that ITS2 could discriminate M. canadensis from its closely related species correctly.

CONCLUSIONThe ITS2 region is an efficient barcode for identification of Menthae Haplocalycis Herba, which provides a scientific basis for fast and accurate identification of the herb.