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Transcriptome Analysis Revealed Highly Expressed Genes Encoding Secondary Metabolite Pathways and Small Cysteine-Rich Proteins in the Sclerotium of Lignosus rhinocerotis

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      Abstract

      Lignosus rhinocerotis (Cooke) Ryvarden (tiger milk mushroom) has long been known for its nutritional and medicinal benefits among the local communities in Southeast Asia. However, the molecular and genetic basis of its medicinal and nutraceutical properties at transcriptional level have not been investigated. In this study, the transcriptome of L. rhinocerotis sclerotium, the part with medicinal value, was analyzed using high-throughput Illumina HiSeq TM platform with good sequencing quality and alignment results. A total of 3,673, 117, and 59,649 events of alternative splicing, novel transcripts, and SNP variation were found to enrich its current genome database. A large number of transcripts were expressed and involved in the processing of gene information and carbohydrate metabolism. A few highly expressed genes encoding the cysteine-rich cerato-platanin, hydrophobins, and sugar-binding lectins were identified and their possible roles in L. rhinocerotis were discussed. Genes encoding enzymes involved in the biosynthesis of glucans, six gene clusters encoding four terpene synthases and one each of non-ribosomal peptide synthetase and polyketide synthase, and 109 transcribed cytochrome P450 sequences were also identified in the transcriptome. The data from this study forms a valuable foundation for future research in the exploitation of this mushroom in pharmacological and industrial applications.

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      Most cited references 63

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      Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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        MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

        We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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          Mapping and quantifying mammalian transcriptomes by RNA-Seq.

          We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.
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            Author and article information

            Affiliations
            [1 ]Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
            [2 ]School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
            [3 ]Ligno Biotech Sdn. Bhd., Balakong Jaya, Selangor, Malaysia
            [4 ]Malaysian Agricultural Research and Development Institute (MARDI), Serdang, Selangor, Malaysia
            Louisiana State University Agricultural Center, UNITED STATES
            Author notes

            Competing Interests: As co-author S-TN is affiliated with Ligno Biotech Sdn. Bhd., which commercialized the tiger milk mushroom, the authors hereby declare that this does not alter their adherence to PLOS ONE policies on sharing data and materials.

            Conceived and designed the experiments: N-HT C-ST S-YF S-TN. Performed the experiments: H-YYY. Analyzed the data: H-YYY Y-HC. Contributed reagents/materials/analysis tools: N-HT C-ST S-YF S-TN. Wrote the paper: H-YYY Y-HC N-HT S-YF.

            Contributors
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            25 November 2015
            2015
            : 10
            : 11
            26606395 4659598 10.1371/journal.pone.0143549 PONE-D-15-35835

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

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            Figures: 10, Tables: 4, Pages: 25
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            Funding
            This research is supported by High Impact Research Grant UM.C/625/1/HIR/MoE/E00040-20001 and Fundamental Research Grant Scheme (FRGS) FP029-2014A from the University of Malaya/Ministry of Education, Malaysia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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            Research Article
            Custom metadata
            Raw Illumina sequencing data of L. rhinocerotis TM02 strain was submitted to NCBI Sequence Read Archive (SRA) at http://www.ncbi.nlm.nih.gov/Traces/sra with the accession number SRR1509475 under experiment SRX648275. The Whole Genome Shotgun project of L. rhinocerotis TM02 strain used in this paper is version AXZM01000000.

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