title: Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR-DGGE.
abstract: Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.
authors.affiliation: Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.forename: Yaoyao
authors.initials: Y
authors.lastname: Yu
authors.forename: Zhang
authors.initials: Z
authors.lastname: Cai
authors.forename: Mark
authors.initials: M
authors.lastname: Bartlam
authors.forename: Yingying
authors.initials: Y
authors.lastname: Wang
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics*; D004275:DNA, Ribosomal / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods; D005658:Fungi / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D025341:Principal Component Analysis; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D004271:DNA, Fungal; D021901:DNA, Intergenic; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S