Project description:Lepista nuda is a wild edible fungus that is valued for its odor and taste. Recent studies identified intraspecific morphological and genetic differences in L. nuda. Although single-nucleotide polymorphisms (SNPs) are useful for revealing intraspecific differences, the traditional methods used for investigating SNPs are time consuming and expensive, and they only locate a limited number of SNPs. This study used a "restriction-site associated DNA" (RAD) method combined with high throughput sequencing to efficiently identify a large number of SNPs in two samples of L. nuda. A total of 7 and 9 billion bp of raw data were obtained from the two collections. A total of 712 SNPs were found. These SNPs will be useful for the further analysis of the genetic variation within L. nuda. The study also confirms that the RAD method can be used to identify SNPs in a nonmodel macrofungus for which a reference genome is unavailable.
Project description:Lepista nuda is a popular wild edible mushroom that grows in China. In this study, we used ISSR and SRAP molecular markers to analyze the genetic diversity of 72 samples of L. nuda from eight populations in Northeast China. In total, six ISSR primers and five pairs of SRAP primers that produced clear and polymorphic banding profiles were selected for assessing L. nuda genetic diversity. The results revealed a high level of genetic variation among the 72 samples (94.4% polymorphism) but a low degree of gene flow among the populations. Among L. nuda populations, genetic distance was not correlated significantly with geographic distance. The antioxidant activity of the samples from each population was also tested and the result showed that all the selected samples had more than 60% DPPH scavenging activities. Nonetheless, the antioxidant activity diversity is not coincident with both the genetic diversity and the geographic distribution. The results indicate that ISSR and SRAP molecular markers are useful for studying the genetic diversity of L. nuda. The results also suggest that L. nuda populations in Northeast China require protection.
Project description:A strain LN07 with high laccase yield was identified as basidiomycete fungus Lepista nuda from which a white laccase without type I copper was purified and characterized. The laccase was a monomeric protein with a molecular mass of 56 kDa. Its N-terminal amino acid sequence was AIGPAADLHIVNKDISPDGF. Besides, eight inner peptide sequences were determined and lac4, lac5 and lac6 sequences were in the Cu(2+) combination and conservation zones of laccases. HIV-1 reverse transcriptase was inhibited by the laccase with a half-inhibitory concentration of 0.65 ?M. Cu(2+) ions (1.5 mM) enhanced the laccase production and the optimal pH and temperature of the laccase were pH 3.0 and 50 °C, respectively. The Km and Vmax of the laccase using ABTS as substrate were respectively 0.19 mM and 195 ?M. Several dyes including laboratory dyes and textile dyes used in this study, such as Methyl red, Coomassie brilliant blue, Reactive brilliant blue and so on, were decolorized in different degrees by the purified laccase. By LC-MS analysis, Methyl red was structurally degraded by the laccase. Moreover, the laccase affected the absorbance at the maximum wavelength of many pesticides. Thus, the white laccase had potential commercial value for textile finishing and wastewater treatment.
Project description:We studied the identity and function of the 528-bp gene immediately upstream of Legionella pneumophila F2310 ptsP (enzyme I(Ntr)). This gene, nudA, encoded for a Nudix hydrolase based on the inferred protein sequence. NudA had hydrolytic activity typical of other Nudix hydrolases, such as Escherichia coli YgdP, in that Ap(n)A's, in particular diadenosine pentaphosphate (Ap(5)A), were the preferred substrates. NudA hydrolyzed Ap(5)A to ATP plus ADP. Both ptsP and nudA were cotranscribed. Bacterial two-hybrid analysis showed no PtsP-NudA interactions. Gene nudA was present in 19 of 20 different L. pneumophila strains tested and in 5 of 10 different Legionella spp. other than L. pneumophila. An in-frame nudA mutation was made in L. pneumophila F2310 to determine the phenotype. The nudA mutant was an auxotroph that grew slowly in liquid and on solid media and had a smaller colony size than its parent. In addition, the mutant was more salt resistant than its parent and grew very poorly at 25 degrees C; all of these characteristics, as well as auxotrophy and slow-growth rate, were reversed by transcomplementation with nudA. The nudA mutant was outcompeted by about fourfold by the parent in competition studies in macrophages; transcomplementation almost completely restored this defect. Competition studies in guinea pigs with L. pneumophila pneumonia showed that the nudA mutant was outcompeted by its parent in both lung and spleen. NudA is of major importance for resisting stress in L. pneumophila and is a virulence factor.
Project description:Background:Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods:To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results:The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.
Project description:BACKGROUND:Most of the rice varieties are pubescent. However, the presence of trichomes is an undesirable characteristic in rice production because trichomes can cause atmospheric pollution. The use of glabrous rice varieties represents a solution to this problem. Yunnan Nuda Rice, a glabrous cultivar that constitutes approximately 20% of rice germplasms in Yunnan can provide important recourse for breeding of glabrous rice varieties. RESULTS:The "Nuda" phenotype in Yunnan Nuda Rice was found to be controlled by a single recessive allelic gene within the well-characterized GL-1 locus. A high-resolution genetic and physical map was constructed using 1,192 Nuda individuals from the F2 population that was delivered from the cross between the Yunnan Nuda variety HMK and the pubescent TN1 variety. The NUDA/GL-1 gene was mapped to a 28.5 kb region containing six annotated genes based on the Nipponbare genomic sequence. By comparing the sequences and expression patterns of different pubescent and glabrous varieties, LOC_Os05g02730, a WUSCHEL-like homeobox gene (OsWOX3B) was identified as the candidate gene. This hypothesis was confirmed by RNA interference (RNAi) and transgenic complementation. Trichome deficiency in RNAi lines was associated with increased efficiency of grain packaging but did not affect the main agronomic traits. CONCLUSION:NUDA/GL-1 locus encodes OsWOX3B gene.