Transcriptome exploration to provide a resource for the study of Auricularia heimuer

  • Jian Zhang
  • Tingting Sun
  • Shixin Wang
  • Li ZouEmail author
Original Paper


Auriculariaheimuer, an edible jelly fungus, is in considerable demand in Asia due to its high nutritive, economic and medicinal values. RNA-Seq was used to investigate and analyze the mycelium transcriptome of A. heimuer for gene discovery. A total of 26,857 unigenes with an N50 length of 1333 bp were assembled by de novo sequencing. In addition, unigenes were annotated by publicly available databases, including gene descriptions, gene ontology (GO), clusters of orthologous group (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways, and protein family (Pfam) terms. A. heimuer was also studied for its wood degradation ability. Thirty-eight putative FOLymes (fungal oxidative lignin enzymes) and 251 CAZymes (carbohydrate-active enzymes) were located from A. heimuer transcriptome. Our study provides a comprehensive sequence resource for A. heimuer at the transcriptional level, which will lay a strong foundation for functional genomics studies and gene discovery of this promising fungus.


Auriculariaheimuer Transcriptome Carbohydrate active enzymes Lignin degradation Next-generation sequencing 


Supplementary material

11676_2019_989_MOESM1_ESM.docx (28 kb)
Supplementary file1 (DOCX 27 kb)


  1. Acharya K, Samui K, Rai M, Dutta B, Acharya R (2004) Antioxidant and nitric oxide synthase activation properties of Auricularia auricula. Indian J Exp Biol 42:538–540Google Scholar
  2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37:D233–238CrossRefGoogle Scholar
  3. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRefGoogle Scholar
  4. Fan XZ, Zhou Y, Xiao Y, Xu ZY, Bian YB (2014) Cloning, expression and phylogenetic analysis of a divergent laccase multigene family in Auricularia auricula-judae. Microbiol Res 169:453–462CrossRefGoogle Scholar
  5. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230CrossRefGoogle Scholar
  6. Hatakka and Hamm (2011) Hatakka A, Hammel KE (2011) Fungal biodegradation of lignocelluloses. Mycota. Industrial applications, 2nd edn. Springer, Berlin, pp 319–340Google Scholar
  7. Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280:309–316CrossRefGoogle Scholar
  8. Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. In: Proceedings international conference on intelligent systems for molecular biology, pp 138–148.Google Scholar
  9. Lonowicz A, Matuszewska A, Luterek J, Ziegenhagen D, Wasilewska MW, Cho NS, Hofrichter M, Rogalski J (1999) Biodegradation of lignin by white rot fungi. Fungal Genet Biol 27:175–185CrossRefGoogle Scholar
  10. Lvasseur A, Piumi F, Coutinho PM, Rancurel C, Asther M, Delattre M, Henrissat B, Pontarotti P, Asther M, Record E (2008) FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genet Biol 45:638–645CrossRefGoogle Scholar
  11. Li RQ, Zhu HM, Ruan J, Qian WJ, Fang XD, Shi ZB, Li YR, Li ST, Gao S, Kristiansen K, Li SG, Yang HM, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272CrossRefGoogle Scholar
  12. Li XB, Luo J, Yan TL, Xiang L, Jin F, Qin DH, Sun CB, Xie M (2013) Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PLoS ONE 8:e85480CrossRefGoogle Scholar
  13. Liu L, Li YH, Li SL, Ni H, He YM, Pong R, Lin DN, Lu LH, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:251364Google Scholar
  14. MacLean D, Jones JD, Studholme DJ (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat Rev Microbiol 7:287–296CrossRefGoogle Scholar
  15. Martinez D, Larrondo LF, PutnamN Gelpke MDS, Huang K, Chapman J (2004) Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol 22:695–700CrossRefGoogle Scholar
  16. Metzker ML (2010) Sequencing technologies - the next generation. Nat Rev Genet 11:31–46CrossRefGoogle Scholar
  17. Misaki A, Kakuta M, Sasaki T, Tanaka M, Miyaji H (1981) Studies on interrelation of structure and antitumor effects of polysaccharides: antitumor action of periodate-modified, branched-beta-D-glucan of Auricularia auricula-judae, and other polysaccharides containing-glycosidic linkages. Carbohydr Res 92:115–129CrossRefGoogle Scholar
  18. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res-NAR 35:182–185CrossRefGoogle Scholar
  19. Munk L, Sitarz AK, Kalyani DC, Mikkelsen JD, Meyer AS (2015) Can laccases catalyze bond cleavage in lignin? Biotechnol Adv 33:13–24CrossRefGoogle Scholar
  20. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27:29–34CrossRefGoogle Scholar
  21. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467CrossRefGoogle Scholar
  22. Ukai S, Kiho T, Hara C, Kuruma I, Tanaka Y (1983) Polysaccharides in fungi XIV. Anti-inflammatory effect of the polysaccharides from the fruit bodies of several fungi. J Pharmacobio-Dyn 6:983–990CrossRefGoogle Scholar
  23. Wang M, Gu BL, Huang J, Jiang S, Chen YJ, Yin YL, Pan YF, Yu GJ, Li YM, Wong BHC, Liang Y, Sun H (2013) Transcriptome and proteome exploration to provide a resource for the study of Agrocybe aegerita. PLoS ONE 2:e56686CrossRefGoogle Scholar
  24. Wang F, Li DL, Wang ZY, Dong AR, Liu LH, Wang BY, Chen QL, Liu XH (2014) Transcriptomic Analysis of the Rice White Tip Nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae). PLoS ONE 9:e91591CrossRefGoogle Scholar
  25. Yang Y, Xu M, Luo QF, Wang J, Li HG (2014) De novo transcriptome analysis of Liriodendron chinense petals and leaves by Illumina sequencing. Gene 534:155–162CrossRefGoogle Scholar
  26. Ye J, Fang L, Zheng HK, Zhang Y, Chen J, Zhang ZJ, Wang J, Li ST, Li RQ, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–297CrossRefGoogle Scholar
  27. Yin YL, Yu GJ, Chen YJ, Jiang S, Wang M, Jin YX, Lan XQ, Liang Y, Sun H (2012) Genome-wide transcriptome and proteome analysis on different developmental stages of Cordyceps militaris. PLoS ONE 7:e51853CrossRefGoogle Scholar
  28. Yoon SJ, Yu MA, Pyun YR, Hwang JK, Chu DC, Juneja LR, Mourao PAS (2003) The nontoxic mushroom Auricularia auricula contains a polysaccharide with anticoagulant activity mediated by antithrombin. Thromb Res 112:151–158CrossRefGoogle Scholar
  29. Yu GJ, Wang M, Huang J, Yin YL, Chen YJ, Jiang S, Jin YX, Lan XQ, Wong BH, Liang Y, Sun H (2012) Deep insight into the Ganoderma lucidum by comprehensive analysis of its transcriptome. PLoS ONE 7:e44031CrossRefGoogle Scholar
  30. Yuan Z, He P, Cui J, Takeuchi H (1998) Hypoglycemic effect of water-soluble polysaccharide from Auricularia auricula-judae Quel. on genetically diabetic KK-Ay mice. Biosci Biotechnol Biochem 62:1898–1903CrossRefGoogle Scholar
  31. Yuan Y, Wu F, Si J, Zhao YF, Dai YC (2019) Whole genome sequence of Auricularia heimuer (Basidiomycota, Fungi), the third most important cultivated mushroom worldwide. Genomics 111:50–58CrossRefGoogle Scholar
  32. Zeng WC, Zhang Z, Gao H, Jia LR, Chen WY (2012) Characterization of antioxidant polysaccharides from Auricularia auricula using microwave-assisted extraction. Carbohydr Polym 89:694–700CrossRefGoogle Scholar
  33. Zhang H, Wang ZY, Yang L, Yang X, Wang X, Zhang Z (2011) In Vitro Antioxidant Activities of Sulfated Derivatives of Polysaccharides Extracted from Auricularia auricula. Int J Mol Sci 12:3288–3302CrossRefGoogle Scholar
  34. Zhong MT, Liu B, Wang XL, Liu L, Lun YZ, Li XY, Ning AH, Cao J, Huang M (2013) De novo characterization of Lentinula edodes C91–3 transcriptome by deep Solexa sequencing. Biochem Biophys Res Commun 431:111–115CrossRefGoogle Scholar
  35. Zou L, Sun TT, Li DL, Tan Y, Zhang GY, Wang F, Zhang J (2016) De novo transcriptome analysis of Inonotus baumii by RNA-seq. J Biosci Bioeng 121:380–384CrossRefGoogle Scholar

Copyright information

© Northeast Forestry University 2019

Authors and Affiliations

  1. 1.College of ForestryNortheast Forestry UniversityHarbinPeople’s Republic of China
  2. 2.Department of Food EngineeringHarbin UniversityHarbinPeople’s Republic of China

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