De Novo Transcriptome Analysis of a Medicinal Fungi and Identification of SSR Markers

Overview

Journal Biotechnol Biotechnol Equip

Specialty Biotechnology

Date 2015 May 29

PMID 26019658

Citations 8

Authors

Yating Huang

Xiaoqiu Wu

Duan Jian

Yaguang Zhan

Guizhi Fan

Affiliations

Soon will be listed here.

Abstract

The aim of this study was to facilitate gene discovery for functional genome studies and to identify simple sequence repeat (SSR) markers for molecular-assisted selection in . The transcriptome of was sequenced using а high-throughput RNA sequencing system - the Illumina Hiseq 2000. A total of 16,383,818 clean sequencing reads, 35,532 contigs and 25,811 unigenes were postulated. Based on similarity searches with known proteins, 19,350 genes (74.97% of the unigenes) were annotated. In the present research, 19,266, 10,978 and 7831 unigenes were mapped in Nr, Swiss-Prot and clusters of orthologous groups (COG) classifications, respectively. Of all unigenes, 6845 were categorized into three functional groups, namely biological process, cellular components and molecular function and 11,088 were annotated to 108 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 1129 SSRs were identified in these unigenes. In addition, 23 candidate genes, potentially involved in sterol biosynthesis, were identified and were worthy of further investigation.

Citing Articles

Characterization and development of transcriptome-derived novel EST-SSR markers to assess genetic diversity in .

Darshan K, Aggarwal R, Bashyal B, Singh J, Saharan M, Gurjar M 3 Biotech. 2023; 13(11):379.

PMID: 37900266 PMC: 10600081. DOI: 10.1007/s13205-023-03794-7.

Transcriptome Analysis of Mycelia from Different Wood Substrates.

Chen J, Zhang Z, Wang Y, Yuan X, Wang J, Yang Y Mycobiology. 2023; 51(1):49-59.

PMID: 36846623 PMC: 9946338. DOI: 10.1080/12298093.2023.2175434.

Key metabolism pathways and regulatory mechanisms of high polysaccharide yielding in Hericium erinaceus.

Gong M, Zhang H, Wu D, Zhang Z, Zhang J, Bao D BMC Genomics. 2021; 22(1):160.

PMID: 33676419 PMC: 7937317. DOI: 10.1186/s12864-021-07480-x.

De novo transcriptome analysis of stressed blood clam (Anadara broughtonii) and identification of genes associated with hemoglobin.

Wang Y, Zhou S, Liu T, Chen M, Zhang X Genes Genomics. 2019; 42(2):189-202.

PMID: 31797313 DOI: 10.1007/s13258-019-00887-7.

RNA Sequencing Reveals Differential Gene Expression of in Response to Variable Lighting Conditions.

Pawlik A, Mazur A, Wielbo J, Koper P, Zebracki K, Kubik-Komar A Int J Mol Sci. 2019; 20(2).

PMID: 30642073 PMC: 6358801. DOI: 10.3390/ijms20020290.

References

Zhou X, Su K, Zhang Y . Applied modern biotechnology for cultivation of Ganoderma and development of their products. Appl Microbiol Biotechnol. 2011; 93(3):941-63. PMC: 7080118. DOI: 10.1007/s00253-011-3780-7. View

Huang H, Chieh S, Tso T, Chien T, Lin H, Tsai Y . Orally administered mycelial culture of Phellinus linteus exhibits antitumor effects in hepatoma cell-bearing mice. J Ethnopharmacol. 2010; 133(2):460-6. DOI: 10.1016/j.jep.2010.10.015. View

Zhu H, Sun S, Zhang S . Enhanced production of total flavones and exopolysaccharides viaVitreoscilla hemoglobin biosynthesis in Phellinus igniarius. Bioresour Technol. 2010; 102(2):1747-51. DOI: 10.1016/j.biortech.2010.08.085. View

Ye S, Hou Z, Zhang Q . Protective effects of Phellinus linteus extract against iron overload-mediated oxidative stress in cultured rat hepatocytes. Phytother Res. 2007; 21(10):948-53. DOI: 10.1002/ptr.2182. View

Mudalkar S, Golla R, Ghatty S, Reddy A . De novo transcriptome analysis of an imminent biofuel crop, Camelina sativa L. using Illumina GAIIX sequencing platform and identification of SSR markers. Plant Mol Biol. 2013; 84(1-2):159-71. DOI: 10.1007/s11103-013-0125-1. View

Zhong M, Liu B, Wang X, Liu L, Lun Y, Li X . De novo characterization of Lentinula edodes C(91-3) transcriptome by deep Solexa sequencing. Biochem Biophys Res Commun. 2012; 431(1):111-5. DOI: 10.1016/j.bbrc.2012.12.065. View

Wang W, Li C, Ge C, Lei L, Gao Y, Qian G . De-novo characterization of the soft-shelled turtle Pelodiscus sinensis transcriptome using Illumina RNA-Seq technology. J Zhejiang Univ Sci B. 2013; 14(1):58-67. PMC: 3542959. DOI: 10.1631/jzus.B1200219. View

El Enshasy H, Hatti-Kaul R . Mushroom immunomodulators: unique molecules with unlimited applications. Trends Biotechnol. 2013; 31(12):668-77. DOI: 10.1016/j.tibtech.2013.09.003. View

Wenping H, Yuan Z, Jie S, Lijun Z, Zhezhi W . De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients. Genomics. 2011; 98(4):272-9. DOI: 10.1016/j.ygeno.2011.03.012. View

10.

Lu X, Li J, Yang J, Liu X, Ma J . De novo transcriptome of the desert beetle Microdera punctipennis (Coleoptera: Tenebrionidae) using Illumina RNA-seq technology. Mol Biol Rep. 2014; 41(11):7293-303. PMC: 4204002. DOI: 10.1007/s11033-014-3615-6. View

11.

Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I . Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011; 29(7):644-52. PMC: 3571712. DOI: 10.1038/nbt.1883. View

12.

Hou R, Bao Z, Wang S, Su H, Li Y, Du H . Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PLoS One. 2011; 6(6):e21560. PMC: 3123371. DOI: 10.1371/journal.pone.0021560. View

13.

Zhang S, Sui Z, Chang L, Kang K, Ma J, Kong F . Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform. Gene. 2014; 537(2):285-93. DOI: 10.1016/j.gene.2013.12.041. View

14.

Li P, Deng W, Li T, Song B, Shen Y . Illumina-based de novo transcriptome sequencing and analysis of Amanita exitialis basidiocarps. Gene. 2013; 532(1):63-71. DOI: 10.1016/j.gene.2013.09.014. View

15.

Jeon T, Jung C, Cho J, Park D, Moon J . Identification of an anticancer compound against HT-29 cells from Phellinus linteus grown on germinated brown rice. Asian Pac J Trop Biomed. 2013; 3(10):785-9. PMC: 3761137. DOI: 10.1016/S2221-1691(13)60156-2. View

16.

Villares A, Mateo-Vivaracho L, Garcia-Lafuente A, Guillamon E . Storage temperature and UV-irradiation influence on the ergosterol content in edible mushrooms. Food Chem. 2013; 147:252-6. DOI: 10.1016/j.foodchem.2013.09.144. View

17.

Gao X, Han J, Lu Z, Li Y, He C . De novo assembly and characterization of spotted seal Phoca largha transcriptome using Illumina paired-end sequencing. Comp Biochem Physiol Part D Genomics Proteomics. 2013; 8(2):103-10. DOI: 10.1016/j.cbd.2012.12.005. View

18.

Aoki-Kinoshita K, Kanehisa M . Gene annotation and pathway mapping in KEGG. Methods Mol Biol. 2007; 396:71-91. DOI: 10.1007/978-1-59745-515-2_6. View

19.

Lin C, Lien H, Chang H, Huang C, Liu J, Chang Y . Biological evaluation of Phellinus linteus-fermented broths as anti-inflammatory agents. J Biosci Bioeng. 2014; 118(1):88-93. DOI: 10.1016/j.jbiosc.2014.01.001. View

20.

Tang Y, Zhang W, Zhong J . Performance analyses of a pH-shift and DOT-shift integrated fed-batch fermentation process for the production of ganoderic acid and Ganoderma polysaccharides by medicinal mushroom Ganoderma lucidum. Bioresour Technol. 2008; 100(5):1852-9. DOI: 10.1016/j.biortech.2008.10.005. View