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2.
Article in English | WPRIM | ID: wpr-764986

ABSTRACT

We analyzed Clonorchis sinensis ancient DNA (aDNA) acquired from the specimens of the Joseon mummies. The target regions were cytochrome C oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), nicotinamide adenine dinucleotide hydrogen (NADH) dehydrogenase subunits 2 (NAD2) and 5 (NAD5). The sequences of C. sinensis aDNA was completely or almost identical to modern C. sinensis sequences in GenBank. We also found that ITS1, NAD2 and NAD5 could be good markers for molecular diagnosis between C. sinensis and the other trematode parasite species. The current result could improve our knowledge about genetic history of C. sinensis.


Subject(s)
Clonorchis sinensis , Cytochromes c , Cytochromes , Databases, Nucleic Acid , Diagnosis , DNA , Electron Transport Complex IV , Hydrogen , Mummies , NAD , Niacinamide , Oxidoreductases , Parasites , Republic of Korea
3.
Article in English | WPRIM | ID: wpr-761778

ABSTRACT

Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.


Subject(s)
Asian Continental Ancestry Group , Base Sequence , China , Databases, Nucleic Acid , DNA, Mitochondrial , Haplotypes , Humans , Japan , Korea , Mitochondria , Spirometra , Trees
4.
Article in English | WPRIM | ID: wpr-761719

ABSTRACT

Cryptosporidium is a common intestinal protozoan that can lead to diarrhea in humans and dogs. The predominant species of infection are C. hominis and C. parvum in humans, and C. canis in dogs. However, C. canis can infect immunocompromised humans. Considering the close contact with humans, dogs have the potential to be reservoirs for human cryptosporidiosis. Breeding kennels are the major supply source of puppies for pet shops. The present study is to determine the molecular prevalence and characteristics of Cryptosporidium spp. found in breeding kennel dogs. A total of 314 fecal samples were collected from young and adult dogs kept in 5 breeding kennels. A polymerase chain reaction targeting the small subunit rRNA gene was employed for the detection of Cryptosporidium spp. To determine the species, the DNA sequences were compared to GenBank data. Overall, 21.0% of the fecal samples were positive for Cryptosporidium spp. infection. Cryptosporidium spp. was detected in all 5 facilities. A sequencing analysis demonstrated that all isolates shared 99–100% similarity with C. canis. The results suggest that Cryptosporidium spp. infection is present at a high-level in breeding kennel dogs. However, because dominant species in this survey was C. canis, the importance of breeding kennel dogs as reservoirs for Cryptosporidium spp. transmission to humans is likely to be low in Japan.


Subject(s)
Adult , Animals , Base Sequence , Breeding , Cryptosporidiosis , Cryptosporidium , Databases, Nucleic Acid , Diarrhea , Dogs , Genes, rRNA , Humans , Japan , Polymerase Chain Reaction , Prevalence
5.
Article in Korean | WPRIM | ID: wpr-759865

ABSTRACT

Forensic science is an academic field that utilizes scientific knowledge and the conducting of research in legal procedures. Recently, legal science has been receiving more attention since the use of DNA identification started, especially in criminal procedures, in accordance with the development of human genetics. DNA identification has been used to identify criminals by analyzing humanoriginated biological materials obtained from crime scenes, and, more recently, the breadth and effectiveness of their use has been increasing with the operation of DNA databases. The Korean government regulates the operation and utilization of the DNA database through the “Act on Use and Protection of DNA Identification Information.” Meanwhile, the actual study of human genetics is regulated by the “Bioethics and Safety Act.” Professional areas, such as forensic science, are not areas where regulation by the laws is appropriate. However, the core part of behavior has to be ruled by the laws, considering the impact of scientific achievements on society and individuals when they are utilized. Since most scientific research and performance utilization belong in the scientific and technological domains, regulation through experts' autonomous guidelines is more appropriate. For the regulation of biomedical research through ethical guidelines, some requirements should be satisfied: the ethical guideline should be made by suitable professionals; the ethical guideline should be scientifically and ethically reliable; the ethical guideline should be enforced by a trustworthy institution; and most importantly, the scientist community should be trustworthy.


Subject(s)
Crime , Criminals , Databases, Nucleic Acid , DNA , Forensic Sciences , Genetics, Medical , Humans , Jurisprudence
6.
Article in English | WPRIM | ID: wpr-742302

ABSTRACT

In a population-based study with 4 years of follow up, we evaluated the prevalence of Coxiella burnetii in cattle on Ulleung Island, Korea. In this study, the rates of C. burnetii infection in cattle on Ulleung Island were determined by PCR and were found to be 0.3–1.0% in the period 2011–2014. All 17 C. burnetii partial 16S rRNA gene sequences from PCR-positive cattle were identical and 2 geographic representatives were included in our analysis. The nucleotide sequences of the 2 samples showed high (98.4–100%) identity with C. burnetii sequences obtained from the GenBank. In this long-term tracking study, the number of cattle positive for C. burnetii on Ulleung Island was low. To prevent the transmission of C. burnetii on Ulleung Island, control strategy should include biosecurity improvement in surveillance, livestock management, administering suitable tests before purchasing animals to detect C. burnetii shedders, and restricting movements between herds.


Subject(s)
Animals , Base Sequence , Cattle , Coxiella burnetii , Coxiella , Databases, Nucleic Acid , Follow-Up Studies , Genes, rRNA , Korea , Livestock , Phylogeny , Polymerase Chain Reaction , Prevalence
7.
Article in Spanish | LILACS | ID: biblio-1102169

ABSTRACT

La tecnología diagnóstica conocida como NGS por sus siglas en inglés, o Secuenciación de nueva generación, es relativamente nueva, y se está implementando en algunos hospitales de Panamá. Esta tecnología ha demostrado ser una herramienta muy eficiente para la detección de alteraciones genómicas o exómicas, tanto para la clínica como para la investigación. Dada la complejidad de esta prueba, requiere una infraestructura y un número importante de recursos humanos capacitados para poder implementar esta prueba. El propósito de este documento es establecer un marco de referencia para los procedimientos administrativos en cuanto a la realización de las pruebas de secuenciación por metodología NGS. Además, que el mismo sirva de guía para el establecimiento adecuado de programas internos de control y evaluación de calidad de esta tecnología en nuestro país y la región


The technology known as Next­Generation sequencing is relatively new, and it is been implemented in some Panamanian hospitals. It has demonstrated to be a very efficient tool to identify genomic and exomic variants in a clinical setting, as well for research purposes. Because of its complexity, it requires an important infrastructure and a significant number of trained health­care professionals to carry out this test. The purpose of this document is to establish a frame for the administrative and tec hnical aspects for NGS in a clinical setting. Moreover, it will serve as a guide to establish quality control procedures that the technology requires in our country and the region.


Subject(s)
Organization and Administration/standards , Molecular Biology/organization & administration , Kinetics , Databases, Nucleic Acid , Pathology, Molecular , Whole Genome Sequencing , Access to Essential Medicines and Health Technologies
8.
Article in English | WPRIM | ID: wpr-715741

ABSTRACT

BACKGROUND: The number of immigrants with tuberculosis (TB) increases each year in South Korea. Determining the transmission dynamics based on whole genome sequencing (WGS) to cluster the strains has been challenging. METHODS: WGS, annotation refinement, and orthology assignment for the GenBank accession number acquisition were performed on two clinical isolates from Chinese immigrants. In addition, the genomes of the two isolates were compared with the genomes of Mycobacterium tuberculosis isolates, from two native Korean and five native Chinese individuals using a phylogenetic topology tree based on the Multiple Alignment of Conserved Genomic Sequence with Rearrangements (Mauve) package. RESULTS: The newly assigned accession numbers for two clinical isolates were CP020381.2 (a Korean-Chinese from Yanbian Province) and CP022014.1 (a Chinese from Shandong Province), respectively. Mauve alignment classified all nine TB isolates into a discriminative collinear set with matched regions. The phylogenetic analysis revealed a rooted phylogenetic tree grouping the nine strains into two lineages: (1) strains from Chinese individuals and (2) strains from Korean individuals. CONCLUSION: Phylogenetic trees based on the Mauve alignments were supposed to be useful in revealing the dynamics of TB transmission from immigrants in South Korea, which can provide valuable information for scaling up the TB screening policy for immigrants.


Subject(s)
Asian Continental Ancestry Group , Databases, Nucleic Acid , Emigrants and Immigrants , Genome , Humans , Korea , Mass Screening , Mycobacterium tuberculosis , Mycobacterium , Trees , Tuberculosis
9.
Article in English | WPRIM | ID: wpr-758870

ABSTRACT

Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.


Subject(s)
Agriculture , Animals , Cattle , Computer Simulation , Dairy Products , Databases, Nucleic Acid , Drug Resistance, Microbial , Female , Foodborne Diseases , Humans , Mastitis, Bovine , Methods , Molecular Epidemiology , Prophages , Staphylococcus aureus , Staphylococcus
10.
Mycobiology ; : 254-259, 2018.
Article in English | WPRIM | ID: wpr-729773

ABSTRACT

Okra (Abelmoschus esculentus (L.) Moench) has gained more popularity as an economically significant plant for its nutritional and medicinal value, especially in China. During 2014–2016, the root disease of okra was discovered in four okra commercial fields surveyed in China. A fungul was isolated from the infected tissues, and was identified by Verticillium dahliae based on morphological characteristics. Pathogenicity test demonstrated that the fungus was pathogenic on okra, and fulfilled Koch’s postulates. The analysis of three sequences revealed 99–100% identity with the reported V. dahliae strain in GenBank. Neighbor-joining analysis of the gene sequences revealed that the representative isolates were clustered with V. dahliae. To the best of our knowledge, this is the first report of Verticillium wilt of okra in China.


Subject(s)
Abelmoschus , China , Dahlia , Databases, Nucleic Acid , Fungi , Plants , Sequence Analysis , Verticillium , Virulence
11.
Article in English | WPRIM | ID: wpr-742273

ABSTRACT

Trichuris suis infection in pigs is ubiquitous in intensive and extensive farms, which causes potential threat to human health. The objective of this research was to investigate the prevalence of T. suis in pigs in Hunan province. Total 2,267 fresh fecal samples distributed in 28 pig farms from 7 different administrative regions (Hunan province) were evaluated for the existence of T. suis eggs using saturated NaCl floating method. The average infection rate of T. suis in pigs was 8.91% in Hunan province. To determine genetic variation of the gained T. suis isolates in the present study, the internal transcribed spacer (ITS) regions from nuclear ribosomal DNA (rDNA) of 7 T. suis isolates were cloned and analyzed. Nucleotide diversities were 1.0–3.5% and 0–3.8% for ITS-1 and ITS-2, respectively. Phylogenetic analyses indicated that all isolates collected in the present study and T. suis available in Genbank generated a monophyletic clade. The present investigation revealed high infection rates of T. suis in pigs in Hunan province, which shed light on making effective measures to prevent and control T. suis infection in pigs in Hunan province.


Subject(s)
Agriculture , China , Clone Cells , Databases, Nucleic Acid , DNA, Ribosomal , Eggs , Genetic Variation , Humans , Methods , Ovum , Prevalence , Swine , Trichuris
12.
Mycobiology ; : 160-171, 2017.
Article in English | WPRIM | ID: wpr-729299

ABSTRACT

Larvae of Bradysia agrestis, an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of B. agrestis; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus Cladosporium, and the bacterial genera Bacillus and Rhodococcus. According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector B. agrestis than other genera identified. Some cutaneous bacterial genera (e.g., Pseudomonas) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via B. agrestis. This study provides comprehensive information regarding the cutaneous microflora of B. agrestis, which can help in the control of such pests for crop management.


Subject(s)
Bacillus , Biodiversity , Cladosporium , Databases, Nucleic Acid , Genes, rRNA , Insect Vectors , Insecta , Korea , Larva , Plants , Rhodococcus
13.
Article in English | WPRIM | ID: wpr-109774

ABSTRACT

The spike gene of porcine epidemic diarrhea virus (PEDV) was sequenced from 55 South China field strains isolated from pigs with symptoms of diarrhea. The sequences were compared within the set of field strains as well as with reference strains available in GenBank. Within the 55 South China PEDV field strains, the deduced amino acid sequence identities ranged from 93.8% to 99.9 % and ranged from 90.7% to 99.5% when compared with the foreign reference strains in GenBank. Our phylogenetic analysis showed that 10 of the 55 South China PEDV strains belonged to G1b and 45 belonged to G2b.


Subject(s)
Amino Acid Sequence , China , Databases, Nucleic Acid , Diarrhea , Porcine epidemic diarrhea virus , Sequence Analysis , Swine
14.
Article in English | WPRIM | ID: wpr-50238

ABSTRACT

Psychrobacter sanguinis has been described as a Gram-negative, aerobic coccobacilli originally isolated from environments and seaweed samples. To date, 6 cases of P. sanguinis infection have been reported. A 53-year-old male was admitted with a generalized tonic seizure lasting for 1 minute with loss of consciousness and a mild fever of 37.8℃. A Gram stain revealed Gram-negative, small, and coccobacilli-shaped bacteria on blood culture. Automated microbiology analyzer identification using the BD BACTEC FX (BD Diagnostics, Germany) and VITEK2 (bioMérieux, France) systems indicated the presence of Methylobacterium spp., Aeromonas salmonicida, and the Moraxella group with low discrimination. The GenBank Basic Local Alignment Search Tool and an Ez-Taxon database search revealed that the 16S rRNA gene sequence of the isolate showed 99.30% and 99.88% homology to 859 base-pairs of the corresponding sequences of P. sanguinis, respectively (GenBank accession numbers JX501674.1 and HM212667.1). To the best of our knowledge, this is the first human case of P. sanguinis bacteremia in Korea. It is notable that we identified a case based on blood specimens that previously had been misidentified by a commercially automated identification analyzer. We utilized 16S rRNA gene sequencing as a secondary method for correctly identifying this microorganism.


Subject(s)
Aeromonas salmonicida , Bacteremia , Bacteria , Databases, Nucleic Acid , Discrimination, Psychological , Fever , Genes, rRNA , Humans , Korea , Male , Methods , Methylobacterium , Middle Aged , Moraxella , Psychrobacter , RNA, Ribosomal, 16S , Seaweed , Seizures , Unconsciousness
15.
Article in English | WPRIM | ID: wpr-69359

ABSTRACT

The prevalence of Centrocestus formosanus metacercariae was investigated in ornamental fish purchased from a pet shop in Chiang Mai, Thailand, including Carassius auratus (goldfish), Cyprinus carpio (Koi), Poecilia latipinna (Sailfin Molly), Danio rerio (Zebrafish), and Puntigrus tetrazona (Tiger barb). The parasite species was identified by the morphology of worms as well as by a molecular approach using ITS2. The results showed that 50 (33.3%) of 150 fish examined were infected with the metacercariae. The highest prevalence was found in C. auratus (83.3%), and the highest intensity was noted in C. carpio (70.8 metacercariae/fish). The most important morphological character was the presence of 32–34 circumoral spines on the oral sucker. The phylogenetic studies using the rRNA ITS2 region revealed that all the specimens of C. formosanus in this study were grouped together with C. formosanus in GenBank database. This is the first report on ornamental fish, C. carpio, P. latipinna, D. rerio, and P. tetrazona, taking the role of second intermediate hosts of C. formosanus in Thailand. Prevention and control of metacercarial infection in ornamental fish is urgently needed.


Subject(s)
Carps , Databases, Nucleic Acid , Goldfish , Metacercariae , Parasites , Poecilia , Prevalence , Spine , Thailand , Zebrafish
16.
Article in English | WPRIM | ID: wpr-168697

ABSTRACT

Fasciola hepatica is a trematode that causes zoonosis, mainly in cattle and sheep, and occasionally in humans. Few recent studies have determined the infection status of this fluke in Korea. In August 2015, we collected 402 samples of freshwater snails at Hoenggye-ri (upper stream) and Suha-ri (lower stream) of Song-cheon (stream) in Daegwalnyeong-myeon, Pyeongchang-gun in Gangwon-do (Province) near many large cattle or sheep farms. F. hepatica infection was determined using PCR on the nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 402 samples, F. hepatica 1TS-2 marker was detected in 6 freshwater snails; thus, the overall prevalence in freshwater snails was 1.5%. The prevalence varied between collection areas, ranging from 0.0% at Hoenggye-ri to 2.9% at Suha-ri. However, F. gigantica ITS-2 was not detected in the 6 F. hepatica-positive samples by PCR. The nucleotide sequences of the 6 F. hepatica ITS-2 PCR-positive samples were 99.4% identical to the F. hepatica ITS-2 sequences in GenBank, whereas they were 98.4% similar to F. gigantica ITS-2 sequences. These results indicated that the prevalence of F. hepatica in snail intermediate hosts was 1.5% in Gangwon-do, Korea; however the prevalence varied between collection areas. These results may help us to understand F. hepatica infection status in natural environments.


Subject(s)
Agriculture , Animals , Base Sequence , Cattle , Databases, Nucleic Acid , Fasciola hepatica , Fasciola , Fresh Water , Humans , Korea , Polymerase Chain Reaction , Prevalence , Ranunculaceae , Sheep , Snails , Trematoda
17.
Article in English | WPRIM | ID: wpr-168670

ABSTRACT

The present study was performed to analyze molecularly the phylogenetic positions of human-infecting Trichostrongylus species in Mazandaran Province, Iran, which is an endemic area for trichostrongyliasis. DNA from 7 Trichostrongylus infected stool samples were extracted by using in-house (IH) method. PCR amplification of ITS2-rDNA region was performed, and products were sequenced. Phylogenetic analysis of the nucleotide sequence data was performed using MEGA 5.0 software. Six out of 7 isolates had high similarity with Trichostrongylus colubriformis, while the other one showed high homology with Trichostrongylus axei registered in GenBank reference sequences. Intra-specific variations within isolates of T. colubriformis and T. axei amounted to 0–1.8% and 0–0.6%, respectively. Trichostrongylus species obtained in the present study were in a cluster with the relevant reference sequences from previous studies. BLAST analysis indicated that there was 100% homology among all 6 ITS2 sequences of T. colubriformis in the present study and most previously registered sequences of T. colubriformis from human, sheep, and goat isolates from Iran and also human isolates from Laos, Thailand, and France. The ITS2 sequence of T. axei exhibited 99.4% homology with the human isolate of T. axei from Thailand, sheep isolates from New Zealand and Iran, and cattle isolate from USA.


Subject(s)
Animals , Base Sequence , Cattle , Databases, Nucleic Acid , DNA , France , Goats , Humans , Iran , Laos , Methods , New Zealand , Polymerase Chain Reaction , Sheep , Thailand , Trichostrongylus
18.
Braz. arch. biol. technol ; 60: e17160106, 2017. tab, graf
Article in Portuguese | LILACS | ID: biblio-1142496

ABSTRACT

ABSTRACT Accurate insect specimen identification is usually a crucial first step in a forensic entomological analysis. It is traditionally done by morphological classification using identification keys. However, due to sensibility limitations in the identification of animal species based only on their morphology, new methods have been developed, including species identification by DNA barcodes. The objective of this study was to identify forensically important species of Diptera in Espirito Santo state using DNA barcodes. For this, adult flies were collected in Espirito Santo, Southeast Region of Brazil. After DNA extraction, COI gene was amplified and sequenced. All sequences were matched to BOLD platform and alternatively to GenBank MegaBLAST. As result, 281 adult flies were collected and identified morphologically. From these, 36% of samples were classified as Calliphoridae, 34% of Muscidae and 30% of Sarcophagidae. Approximately 10% of all collected samples were analyzes by DNA. It was possible to identify only 35.7% of tested samples, probably due to lack of samples deposited in databases. Therefore, more efforts should be made to deposit a greater variety of dipterous in databases to allow the use of this technique in forensic routine, especially in BOLD.


Subject(s)
Animals , Diptera/classification , DNA Barcoding, Taxonomic , Brazil , Databases, Nucleic Acid , Diptera/anatomy & histology , Diptera/genetics , Forensic Entomology
19.
Mycobiology ; : 121-130, 2016.
Article in English | WPRIM | ID: wpr-729729

ABSTRACT

Recently, the Fusarium genus has been narrowed based upon phylogenetic analyses and a Fusarium-like clade was adopted. The few species of the Fusarium-like clade were moved to new, re-installed or existing genera or provisionally retained as "Fusarium." Only a limited number of reference strains and DNA marker sequences are available for this clade and not much is known about its actual species diversity. Here, we report six strains, preserved by the Belgian fungal culture collection BCCM/IHEM as a Fusarium species, that belong to the Fusarium-like clade. They showed a slow growth and produced pionnotes, typical morphological characteristics of many Fusarium-like species. Multilocus sequencing with comparative sequence analyses in GenBank and phylogenetic analyses, using reference sequences of type material, confirmed that they were indeed member of the Fusarium-like clade. One strain was identified as "Fusarium" ciliatum whereas another strain was identified as Fusicolla merismoides. The four remaining strains were shown to represent a unique phylogenetic lineage in the Fusarium-like clade and were also found morphologically distinct from other members of the Fusarium-like clade. Based upon phylogenetic considerations, a new genus, Pseudofusicolla gen. nov., and a new species, Pseudofusicolla belgica sp. nov., were installed for this lineage. A formal description is provided in this study. Additional sampling will be required to gather isolates other than the historical strains presented in the present study as well as to further reveal the actual species diversity in the Fusarium-like clade.


Subject(s)
Databases, Nucleic Acid , Fusarium , Genetic Markers , Phylogeny , Sequence Analysis
20.
Article in Chinese | WPRIM | ID: wpr-264005

ABSTRACT

<p><b>OBJECTIVE</b>To predict orthologous sequences of the GENCODE-identified 13 562 human long non-coding RNAs (lncRNA) in 16 mammalian genomes and construct a lncRNA database LongMan for lncRNA studies.</p><p><b>METHODS</b>The exon structures of a total of 13 562 human lncRNAs were analyzed using RNAfold, and their orthologous sequences were searched against 16 mammalian genomes using Infernal. The potential orthologous genes, transposons and splicing signals of human lncRNAs were predicted to construct a lncRNA database with a updating mechanism.</p><p><b>RESULTS</b>and</p><p><b>CONCLUSION</b>The lncRNA database LongMan we constructed, which currently contains 133 646 orthologous lncRNAs, provides information of the sequences, alignments, transposons, and species-specific insertions and deletions and allows database search on combinatorial conditions, graphic display and data download. As the first large-scale mammalian orthologous lncRNA database, LongMan has important values in future comparative and functional studies of lncRNAs.</p>


Subject(s)
Animals , Databases, Nucleic Acid , Exons , Humans , RNA, Long Noncoding
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