Journal of Microbiology

Research Support, Non-U.S. Gov'ts

Species Delimitation of Three Species within the Russula Subgenus Compacta in Korea: R. eccentrica, R. nigricans, and R. subnigricans: Myung Soo Park , Hyun Lee , Seung-Yoon Oh , Paul Eunil Jung , Soon Ja Seok , Jonathan J. Fong , Young Woon Lim; J. Microbiol. 2014;52(8):631-638. Published online July 4, 2014; DOI: https://doi.org/10.1007/s12275-014-4168-z

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Abstract: Distinguishing individual Russula species can be very difficult due to extensive phenotypic plasticity and obscure morphological and anatomical discontinuities. In this study, we use the internal transcribed spacer (ITS) and 28S nuclear ribosomal large subunit (LSU) markers to identify and study the genetic diversity of species in the Russula subgenus Compacta in Korea. We focus on two morphologically similar species that are often misidentified for each other: R. nigricans and R. subnigricans. Based on molecular phylogenetic analyses, we identify three subgroups of R. nigricans, with two from Asia and one from Europe/North America. Surprisingly, we find Korean R. subnigricans are more closely related to R. eccentrica from North America than the type specimen of R. subnigricans from Japan. These molecular data, along with habitat data, reveal that Korean R. subnigricans had previously been misclassified and should now be recognized as R. eccentrica. Both ITS and LSU exhibit high interspecific and low intraspecific variation for R. eccentrica, R. nigricans, and R. subnigricans. These markers provide enough resolutional power to differentiate these species and uncover phylogeographic structure, and will be powerful tools for future ecological studies of Russula.

A Real-Time qPCR Assay to Quantify Ophiocordyceps sinensis Biomass in Thitarodes Larvae: Wei Lei , Shaosong Li , Qingyun Peng , Guren Zhang , Xin Liu; J. Microbiol. 2013;51(2):229-233. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2241-7

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Abstract: Ophiocordyceps sinensis, an entomogenous fungus parasitic in the larvae of moths (Lepidoptera), is one of the most valuable medicinal fungi, and it only distributed naturally on the Tibetan Plateau. The parasitical amount of O. sinensis in various tissues of the host Thitarodes larvae has an important role in study the occurrence and developmental mechanisms of O. sinensis, but there no an effective method to detect the fungal anamorph. A real-time quantitative PCR (qPCR) system, including a pair of species-specific ITS primers and its related program, was developed for O. sinensis assay with high reliability and efficiency. A calibration curve was established and exhibited a very good linear correlation between the fungal biomass and the CT values (R2=0.999419) by the qPCR system. Based on this method, O. sinensis was detected rapidly in four tissues of its host caterpillars, and the results were shown as following: the maximum content of O. sinensis parasitized in the fat-body, and next came bodywall; both of them were much larger than that observed in the haemolymph and intestinal-wall. Taken together, these
results
show that qPCR assays may become useful tools for study on developmental mechanism of O. sinensis.

NOTE] A Rapid PCR-Based Approach for Molecular Identification of Filamentous Fungi: Yuanyuan Chen , Bernard A. Prior , Guiyang Shi , Zhengxiang Wang; J. Microbiol. 2011;49(4):675-679. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0525-3

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13 Citations

Abstract: In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal with a large number of filamentous fungal isolates in the same batch, was established. The filamentous fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted DNA also can be used to amplify other protein-coding genes for fungal identification. This method can be used for rapid systematic identification of filamentous fungal isolates.

PCR-RFLP and Sequence Analysis of the rDNA ITS Region in the Fusarium spp.: Lee , Young-Mi , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2000;38(2):66-73.

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Abstract: To investigate the genetic relationship among 12 species belonging to the Fusarium section Martiella, Dlaminia, Gibbosum, Arthrosporiella, Liseola and Elegans, the internal transcribed spacer (ITS) regions of ribosomal DNA (rDNA) were amplified with primer pITS1 and pITS4 using the polymerase chain reaction (PCR). After the amplified products were digested with 7 restriction enzymes, restriction fragment length polymorphism (RFLP) patterns were analyzed. The partial nucleotide sequences of the ITS region were determined and compared. Little variation was observed in the size of the amplified product having sizes of 550bp or 570bp. Based on the RFLP analysis, the 12 species studied were divided into 5 RFLP types. In particular, strains belonging to the section Martiella were separated into three RFLP types. Interestingly, the RFLP type of F. solani f. sp. piperis was identical with that of isolates belonging to the section Elegans. In the dendrogram derived from RFLP analysis of the ITS region, the Fusarium spp. examined were divided into two major groups. In general, section Martiella excluding F. solani f. sp. piperis showed relatively low similarity with the other section. The dendrogram based on the sequencing analysis of the ITS2 region also gave the same results as that of the RFLP analysis. As expected, 5.8S, a coding region, was highly conserved, whereas the ITS2 region was more variable and informative. The difference in the ITS2 region between the length of F. solani and its formae speciales excluding F. solani f. sp. piperis and that of other species was caused by the insertion/deletion of nucleotides in positions 143-148 and 179-192.

PCR-DGGE and PCR-RFLP Analyses of the Internal Transcribed Spacer (ITS) of Ribosomal DNA in the Genus Rhizopus: You-Jung Park , Yong-Keel Choi , Byung-Re Min; J. Microbiol. 2003;41(2):157-160.

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Abstract: To estimate genetic relationships within the genus Rhizopus, genetic variations in 20 strains were investigated by DGGE and PCR-RFLP of rDNA ITS region (ITS1, ITS2, 5.8S). The size of the amplified products showed the interspecific polymorphisms, 650 bp, 700 bp, and 900 bp. The DGGE approach allowed the separation of PCR amplicons of the same length according to their sequence variations. When the rDNA ITS region was digested with six restriction enzymes, 20 strains were classified into five RFLP haplotypes. The range of similarity between the 20 strains by PCR-RFLP was 42.3-100%. Based on the results of DGGE and PCR-RFLP, the 20 strains were divided into four groups, R. oryzae, R. stolonifer, R. microsporus and R. homothallicus. Further study of R. homothallicus is required.

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