ABSTRACT
The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological information-based database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources, such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.
Subject(s)
Humans , Asian People , Biotechnology , Brassica , Computational Biology , Genome , Genomics , Information Centers , Proteomics , Systems BiologyABSTRACT
Molecular approaches, internal transcribed spacer(ITS) sequences of ribosomal DNA, and Universal Rice Primer Polymerase Chain Reaction(URP-PCR) were used to investigate the genetic diversity, taxonomic complexity, and relationships of Trichoderma species in mushroom farms. Forty-one isolates of 13 Trichoderma spp. were used in this study and clustered into eight groups. The DNA fingerprint patterns and ITS1 region sequence alignment data showed similar results, but not in some species, such as T. virens, T. atroviride, T. harzianum, and T. aureoviride. Results of this study have proven that the morphology-based taxonomic system has some limitations in terms of classification. The data obtained in this study would be a good index for classifying indistinguishable Trichoderma strains.
Subject(s)
Agaricales , Classification , DNA Fingerprinting , DNA , DNA, Ribosomal , Genetic Variation , Korea , Sequence Alignment , TrichodermaABSTRACT
In order to investigate biodiversity and establish identification system for Phytophthora spp. in Korea, a variety of band pattern was produced by using the URP (universal rice primer). The fingerprint patterns of Phytophthora spp. showed many common and variable fragments according to their isolates in distinct genotypes. In particular, P. drechsleri was classified into four distinct types (I to IV). P. drechsleri (KACC 40498 and KACC 40499) and P. cryptogea (KACC 40413) appeared to have almost equal bands despite their being different species. Ninety isolates of Phytophthora spp. were clustered into 13 groups based on UPGMA (unweighted pair group method with arithmetic means) analysis. These DNA fingerprinting data would be helpful for inter- and intra-species identification of Phytophthora species.
Subject(s)
Biodiversity , Dermatoglyphics , DNA Fingerprinting , DNA , Genotype , Korea , PhytophthoraABSTRACT
This study was carried out to develop specific primers for PCR detection of Phellinus linteus. Diverse genomes of 15 Phellinus spp. including five Phellinus linteus isolates were fingerprinted by Primer Universal rice primer (URP)1F. The URP-PCR pattern differentiated P. linteus isolates from other phellinus spp. A polymorphic band (2.8 kb), which is unique for P. linteus isolates, was isolated and sequenced. Twenty four-oligonucleotide primer pairs were designed based on information of DNA sequence. The primer set (PLSPF2/PLSPR1) amplified single band (2.2 kb) of expected size with genomic DNA from seven Phellinus linteus, but not with that of other Phellinus species tested. The primers could be used identically in both DNA samples from mycelium and fruit bodies. This specific primers could offer a useful tool for detecting and identifying P. linteus rapidly.
Subject(s)
Base Sequence , Dermatoglyphics , DNA , Fruit , Genome , Mycelium , Polymerase Chain ReactionABSTRACT
URP primers of 20 mer derived from repetitive sequence of rice were used to assess genetic variation of oyster mushroom consisting of 10 cultivars of Pleurotus ostreatus, two cultivars of P. florida and two cultivars of P. sajor-caju which were registered in Korea. URP2F and URP38F primers produced cultivar-specific PCR polymorphic bands in the Pleurotus species. UPGMA cluster analysis using the URP-PCR data showed that 14 Pleurotus cultivars are genetically clustered into large three groups. The URP-PCR data provided important information for more efficient breeding strategies of Pleurotus cultivars.
Subject(s)
Breeding , Dermatoglyphics , Florida , Genetic Variation , Korea , Ostreidae , Pleurotus , Polymerase Chain Reaction , Repetitive Sequences, Nucleic AcidABSTRACT
Based on the rDNA ITS sequences data, specific primer set for PCR detection of wood-decaying fungus Phellinus linteus was designed. The length of PCR products using designed primer set(SHF and SHR) was about 540 bp. Among 11 species, 17 isolates of Phellinus spp. including Phellinus linteus, P. pomaceus, P. spiculosus, P. baumi, P. pini, P. igniarius, P. gilvus, P. biscuspidatus, P. weirii, P. johnsonianus, P. robutus, and P. igniarius, seven isolates of Phellinus linteus showed about 540 bp-sized single band. This molecular technique could offer a useful tool for detecting and identifying Phellinus linteus.