Dataset Information

Identification of SNPs in a nonmodel macrofungus (Lepista nuda, Basidiomycota) through RAD sequencing.

ABSTRACT: 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.

SUBMITTER: Ye F

PROVIDER: S-EPMC5063826 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Identification of SNPs in a nonmodel macrofungus (Lepista nuda, Basidiomycota) through RAD sequencing.

Ye Fei F Yu Xiao-Dan XD Wang Qing Q Zhao Peng P

SpringerPlus 20161013 1

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 thr ...[more]

PMID: 27795935

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Project description:Laying performance is an important economical trait of goose production. As laying performance is of low heritability, it is of significance to develop a marker-assisted selection (MAS) strategy for this trait. Definition of sequence variation related to the target trait is a prerequisite of quantitating MAS, but little is presently known about the goose genome, which greatly hinders the identification of genetic markers for the laying traits of geese. Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available. In the present study, we developed a pooled RAD sequencing strategy for detecting geese laying-related SNP. Two DNA pools were constructed, each consisting of equal amounts of genomic DNA from 10 individuals with either high estimated breeding value (HEBV) or low estimated breeding value (LEBV). A total of 139,013 SNP were obtained from 42,291,356 sequences, of which 18,771,943 were for LEBV and 23,519,413 were for HEBV cohorts. Fifty-five SNP which had different allelic frequencies in the two DNA pools were further validated by individual-based AS-PCR genotyping in the LEBV and HEBV cohorts. Ten out of 55 SNP exhibited distinct allele distributions in these two cohorts. These 10 SNP were further genotyped in a goose population of 492 geese to verify the association with egg numbers. The result showed that 8 of 10 SNP were associated with egg numbers. Additionally, liner regression analysis revealed that SNP Record-111407, 106975 and 112359 were involved in a multiplegene network affecting laying performance. We used IPCR to extend the unknown regions flanking the candidate RAD tags. The obtained sequences were subjected to BLAST to retrieve the orthologous genes in either ducks or chickens. Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2). Collectively, our data suggests that 8 SNP and 5 genes might be promising candidate markers or targets for marker-assisted selection of egg numbers in geese.

Project description:Mushrooms have been consumed for centuries and have recently gained more popularity as an important source of nutritional and pharmaceutical compounds. As part of the valorization of mushroom species in northern Morocco, the current study aimed to investigate the chemical compositions and antioxidant properties of two wild edible mushrooms, Paralepista flaccida and Lepista nuda. Herein, the bioactive compounds were determined using spectrophotometer methods, and results showed that the value of total phenolic content (TPC) was found to be higher in P. flaccida (32.86 ± 0.52 mg) than in L. nuda (25.52 ± 0.56 mg of gallic acid equivalents (GAEs)/mg of dry methanolic extract (dme)). On the other hand, the value of total flavonoid content (TFC) was greater in L. nuda than in P. flaccida, with values of 19.02 ± 0.80 and 10.34 ± 0.60 mg of (+)-catechin equivalents (CEs)/g dme, respectively. Moreover, the ascorbic acid, tannin, and carotenoids content was moderate, with a non-significant difference between the two samples. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis allowed the identification and quantification of thirteen individual phenolic compounds in both P. flaccida and L. nuda, whereas p-Hydroxybenzoic acid was recognized as the major compound detected, with values of 138.50 ± 1.58 and 587.90 ± 4.89 µg/g of dry weight (dw), respectively. The gas chromatography-mass spectrometry (GC-MS) analysis of methanolic extracts of P. flaccida and L. nuda revealed the presence of sixty-one and sixty-six biomolecules, respectively. These biomolecules can mainly be divided into four main groups, namely sugars, amino acids, fatty acids, and organic acids. Moreover, glycerol (12.42%) and mannitol (10.39%) were observed to be the main chemical compositions of P. flaccida, while L. nuda was predominated by linolelaidic acid (21.13%) and leucine (9.05%). L. nuda showed a strong antioxidant property, evaluated by DPPH (half maximal effective concentration (EC50) 1.18-0.98 mg/mL); β-carotene bleaching (EC50 0.22-0.39 mg/mL); and reducing power methods (EC50 0.63-0.48 mg/mL), respectively. These findings suggested that both mushrooms are potential sources of various biomolecules, many of which possess important biological activities which are interesting for the foods and pharmaceuticals industry.

Dataset Information

Identification of SNPs in a nonmodel macrofungus (Lepista nuda, Basidiomycota) through RAD sequencing.

Publications

Identification of SNPs in a nonmodel macrofungus (<i>Lepista nuda</i>, Basidiomycota) through RAD sequencing.

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