Genome Sequence of the Edible Cultivated Mushroom Lentinula Edodes (Shiitake) Reveals Insights into Lignocellulose Degradation

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 Aug 9

PMID 27500531

Citations 79

Authors

Lianfu Chen

Yuhua Gong

Yingli Cai

Wei Liu

Yan Zhou

Yang Xiao

Zhangyi Xu

Yin Liu

Xiaoyu Lei

Gangzheng Wang

Mengpei Guo

Xiaolong Ma

Yinbing Bian

Affiliations

Soon will be listed here.

Abstract

Lentinula edodes, one of the most popular, edible mushroom species with a high content of proteins and polysaccharides as well as unique aroma, is widely cultivated in many Asian countries, especially in China, Japan and Korea. As a white rot fungus with lignocellulose degradation ability, L. edodes has the potential for application in the utilization of agriculture straw resources. Here, we report its 41.8-Mb genome, encoding 14,889 predicted genes. Through a phylogenetic analysis with model species of fungi, the evolutionary divergence time of L. edodes and Gymnopus luxurians was estimated to be 39 MYA. The carbohydrate-active enzyme genes in L. edodes were compared with those of the other 25 fungal species, and 101 lignocellulolytic enzymes were identified in L. edodes, similar to other white rot fungi. Transcriptome analysis showed that the expression of genes encoding two cellulases and 16 transcription factor was up-regulated when mycelia were cultivated for 120 minutes in cellulose medium versus glucose medium. Our results will foster a better understanding of the molecular mechanism of lignocellulose degradation and provide the basis for partial replacement of wood sawdust with agricultural wastes in L. edodes cultivation.

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References

Xu H, Luo X, Qian J, Pang X, Song J, Qian G . FastUniq: a fast de novo duplicates removal tool for paired short reads. PLoS One. 2013; 7(12):e52249. PMC: 3527383. DOI: 10.1371/journal.pone.0052249. View

Castresana J . Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17(4):540-52. DOI: 10.1093/oxfordjournals.molbev.a026334. View

Han M, Thomas G, Lugo-Martinez J, Hahn M . Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol Biol Evol. 2013; 30(8):1987-97. DOI: 10.1093/molbev/mst100. View

Eastwood D, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A . The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi. Science. 2011; 333(6043):762-5. DOI: 10.1126/science.1205411. View

Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek C . Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion. Proc Natl Acad Sci U S A. 2009; 106(6):1954-9. PMC: 2644145. DOI: 10.1073/pnas.0809575106. View

Otto T, Sanders M, Berriman M, Newbold C . Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics. 2010; 26(14):1704-7. PMC: 2894513. DOI: 10.1093/bioinformatics/btq269. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y . dbCAN: a web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 2012; 40(Web Server issue):W445-51. PMC: 3394287. DOI: 10.1093/nar/gks479. View

Mitchell A, Chang H, Daugherty L, Fraser M, Hunter S, Lopez R . The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 2014; 43(Database issue):D213-21. PMC: 4383996. DOI: 10.1093/nar/gku1243. View

10.

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

11.

Martinez D, Larrondo L, Putnam N, Sollewijn Gelpke M, Huang K, Chapman J . Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol. 2004; 22(6):695-700. DOI: 10.1038/nbt967. View

12.

Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy S, Bateman A . Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 2004; 33(Database issue):D121-4. PMC: 540035. DOI: 10.1093/nar/gki081. View

13.

Nadalin F, Vezzi F, Policriti A . GapFiller: a de novo assembly approach to fill the gap within paired reads. BMC Bioinformatics. 2012; 13 Suppl 14:S8. PMC: 3439727. DOI: 10.1186/1471-2105-13-S14-S8. View

14.

Gotz S, Garcia-Gomez J, Terol J, Williams T, Nagaraj S, Nueda M . High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008; 36(10):3420-35. PMC: 2425479. DOI: 10.1093/nar/gkn176. View

15.

Gaitan-Hernandez R, Cortes N, Mata G . Improvement of yield of the edible and medicinal mushroom Lentinula edodes on wheat straw by use of supplemented spawn. Braz J Microbiol. 2014; 45(2):467-74. PMC: 4166270. DOI: 10.1590/s1517-83822014000200013. View

16.

Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire M, Geer L, Geer R . CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res. 2012; 41(Database issue):D348-52. PMC: 3531192. DOI: 10.1093/nar/gks1243. View

17.

Li L, Stoeckert Jr C, Roos D . OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003; 13(9):2178-89. PMC: 403725. DOI: 10.1101/gr.1224503. View

18.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

19.

Chen S, Xu J, Liu C, Zhu Y, Nelson D, Zhou S . Genome sequence of the model medicinal mushroom Ganoderma lucidum. Nat Commun. 2012; 3:913. PMC: 3621433. DOI: 10.1038/ncomms1923. View

20.

Park J, Park J, Jang S, Kim S, Kong S, Choi J . FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors. Bioinformatics. 2008; 24(7):1024-5. DOI: 10.1093/bioinformatics/btn058. View