香菇子实体发育过程中的转录组研究

doi:10.16420/j.issn.0513-353x.2021-0660

摘要/Abstract

摘要：

对香菇子实体发育过程中不同阶段及组织（菌盖和菌柄）进行转录组测序,分析了差异表达基因、基因表达趋势、基因共表达网络及差异可变剪接事件。分析结果表明:在转色菌丝体阶段,大量碳水化合物代谢相关基因上调表达;此外,光受体等信号转导相关基因以及黑色素合成相关基因也上调表达,其可能参与到菌丝转色过程。原基形成过程可能涉及与环境因子感知、核糖体合成、真菌细胞壁重塑、蛋白质降解和染色质修饰等相关基因。与DNA复制和蛋白质降解相关的基因可能在菌盖发育过程中发挥重要作用,而糖苷水解酶基因可能在开伞过程中发挥作用。碳酸酐酶、几丁质酶、GH55家族蛋白和细胞色素P450编码基因可能在菌柄伸长过程中发挥作用。

关键词: 香菇, 子实体发育, 转录组, 时空表达, 共表达网络, 可变剪切

Abstract:

Samples from different stages and tissues（pileus and stipe of fruiting body）during the development of Lentinula edodes were collected and sequenced. By transcriptomic analyses,we identified differentially expressed genes. Then,gene expression trend,gene co-expression network and differentially alternative splicing event were analyzed. Results showed that a large number of CAZyme genes were up-regulated in mycelia browning. Genes associated with signal transduction,such as photoreceptors,and genes related to melanin biosynthesis may also be involved in mycelia browning. Primordium formation may be associated with genes involved in environmental factor sensing,ribosome biogenesis,fungal cell wall remodeling,protein degradation and chromatin modification. Genes associated with DNA replication and protein degradation may play important roles in pileus development,while genes encoding glycoside hydrolases may function in pileus opening. Genes encoding carbonic anhydrase,chitinases,GH55 and cytochrome P450s may serve the functions in stipe elongation.

Key words: Lentinula edodes, fruiting body development, transcriptome, spatiotemporal expression, co-expression network, alternative splicing

中图分类号:

S646.12

沈楠, 张荆城, 王成晨, 边银丙, 肖扬. 香菇子实体发育过程中的转录组研究[J]. 园艺学报, 2022, 49(4): 801-815.

SHEN Nan, ZHANG Jingcheng, WANG Chengchen, BIAN Yinbing, XIAO Yang. Studies on Transcriptome During Fruiting Body Development of Lentinula edodes[J]. Acta Horticulturae Sinica, 2022, 49(4): 801-815.

图/表 7

图1 用于转录组测序的香菇不同发育阶段样品 MY:转色菌丝;PR:原基;D1PI:幼嫩子实体菌盖;D1ST:幼嫩子实体菌柄;D2PI:开伞前的成熟子实体菌盖;D2ST:开伞前的成熟子实体菌柄;MFPI:开伞后的成熟子实体菌盖;MFST:开伞后的成熟子实体菌柄。下同。

Fig. 1 Samples from different development stages of Lentinula edodes for transcriptome sequencing MY:Mycelium with brown film;PR:Primordium;D1PI:Pileus of young fruiting body;D1ST:Stipe of young fruiting body;D2PI:Pileus of mature fruiting body before pileus opening;D2ST:Stipe of mature fruiting body before pileus opening;MFPI:Pileus of mature fruiting body after pileus opening;MFST:Stipe of mature fruiting body after pileus opening. The same below.

图2 香菇相邻发育阶段及同一阶段不同组织（菌盖和菌柄）之间的差异表达基因数量样品代号与图1一致。

Fig. 2 The number of DEGs between two adjacent developmental stages or tissues（pileus and stipe）at the same stage The code names of samples are consistent with those in Fig. 1.

图3 显著基因表达模式中基因显著富集的GO条目及表达量热图表达模式方框内左上角的数字代表表达模式的编号,左下角的数字代表该表达模式中的基因数量。样品代号与图1一致。

Fig. 3 The enriched GO terms and heatmap of gene expression of genes in significant profiles In the profile box,the number in the upper left corner represents the profile number and the number in the bottom left corner represents the number of genes in it. The code names of samples are consistent with those in Fig. 1.

图4 基因共表达模块与香菇各发育阶段或组织的相关性样品代号与图1一致。

Fig. 4 The relationships between gene co-expression modules and different development stages or tissues in Lentinula edodes The code names of samples are consistent with those in Fig. 1.

图5 香菇不同发育阶段或组织的差异可变剪接事件的数量（A）和差异剪接基因及差异表达基因数量（B）样品代号与图1一致。

Fig. 5 The number of DASEs（A）,DSGs and DEGs（B）between adjacent stages or tissues at the same stage The code names of samples are consistent with those in Fig. 1.

表1 相邻阶段或同一阶段不同组织间同时发生差异表达和差异可变剪接的部分基因

Table1 Part genes both differentially expressed and spliced at adjacent stages or different tissues at the same stage

样品	功能 Function	基因编号	基因功能注释
Sample	功能 Function	Gene ID	Gene annotation
MY vs. PR	碳水化合物代谢相关 Related to carbohydrate metabolism	jgi.p\|Lenedo1\|1049584	糖苷水解酶家族10蛋白
			Glycoside hydrolase family 10 protein
		jgi.p\|Lenedo1\|1114896	内切葡聚糖酶V类似蛋白
			Endoglucanase V-like protein
		jgi.p\|Lenedo1\|1038064	糖苷水解酶家族61蛋白
			Glycoside hydrolase family 61 protein
		jgi.p\|Lenedo1\|1159040	糖苷水解酶家族95蛋白
			Glycoside hydrolase family 95 protein
		jgi.p\|Lenedo1\|1158159	糖苷水解酶家族10蛋白
			Glycoside hydrolase family 10 protein
		jgi.p\|Lenedo1\|464359	糖苷水解酶 Glycoside hydrolase
		jgi.p\|Lenedo1\|1073151	糖苷水解酶家族18蛋白
			Glycoside hydrolase family 18 protein
	环境因子感知及信号转导相关 Related to environmental factor perception and signaling	jgi.p\|Lenedo1\|1035471	Rheb小单体GTPase Rheb small monomeric gtpase
		jgi.p\|Lenedo1\|1083501	COP9信号小体复合亚基4
			COP9 signalosome complex subunit 4
		jgi.p\|Lenedo1\|557311	假定水通道蛋白4 Putative aquaporin 4
	细胞壁相关 Related to cell wall	jgi.p\|Lenedo1\|1053705	扩展蛋白 Expansin
	蛋白合成与降解相关 Related to protein synthesis and degradation	jgi.p\|Lenedo1\|1100937	酸性蛋白酶 Acid protease
		jgi.p\|Lenedo1\|1060434	40S核糖体蛋白 S7 40S ribosomal protein S7
		jgi.p\|Lenedo1\|607412	核糖体蛋白L4 Ribosomal protein L4
		jgi.p\|Lenedo1\|1042368	三肽基肽酶A Tripeptidyl peptidase A
		jgi.p\|Lenedo1\|1039990	26S蛋白酶体亚基 P45 26S proteasome subunit P45
		jgi.p\|Lenedo1\|1092580	泛素结合酶E2 Ubiquitin-conjugating enzyme E2
		jgi.p\|Lenedo1\|81445	肽酶s41家族蛋白 Peptidase s41 family protein
		jgi.p\|Lenedo1\|1033416	核糖体蛋白L28e Ribosomal protein L28e
	其他功能 Other functions	jgi.p\|Lenedo1\|1059083	细胞色素P450 Cytochrome P450
		jgi.p\|Lenedo1\|1066578	细胞色素P450 Cytochrome p450
PR vs. D1ST		jgi.p\|Lenedo1\|717494	MFS转运蛋白 MFS general substrate transporter

表1 相邻阶段或同一阶段不同组织间同时发生差异表达和差异可变剪接的部分基因

Table1 Part genes both differentially expressed and spliced at adjacent stages or different tissues at the same stage

样品	功能 Function	基因编号	基因功能注释
Sample	功能 Function	Gene ID	Gene annotation
MY vs. PR	碳水化合物代谢相关 Related to carbohydrate metabolism	jgi.p\|Lenedo1\|1049584	糖苷水解酶家族10蛋白
			Glycoside hydrolase family 10 protein
		jgi.p\|Lenedo1\|1114896	内切葡聚糖酶V类似蛋白
			Endoglucanase V-like protein
		jgi.p\|Lenedo1\|1038064	糖苷水解酶家族61蛋白
			Glycoside hydrolase family 61 protein
		jgi.p\|Lenedo1\|1159040	糖苷水解酶家族95蛋白
			Glycoside hydrolase family 95 protein
		jgi.p\|Lenedo1\|1158159	糖苷水解酶家族10蛋白
			Glycoside hydrolase family 10 protein
		jgi.p\|Lenedo1\|464359	糖苷水解酶 Glycoside hydrolase
		jgi.p\|Lenedo1\|1073151	糖苷水解酶家族18蛋白
			Glycoside hydrolase family 18 protein
	环境因子感知及信号转导相关 Related to environmental factor perception and signaling	jgi.p\|Lenedo1\|1035471	Rheb小单体GTPase Rheb small monomeric gtpase
		jgi.p\|Lenedo1\|1083501	COP9信号小体复合亚基4
			COP9 signalosome complex subunit 4
		jgi.p\|Lenedo1\|557311	假定水通道蛋白4 Putative aquaporin 4
	细胞壁相关 Related to cell wall	jgi.p\|Lenedo1\|1053705	扩展蛋白 Expansin
	蛋白合成与降解相关 Related to protein synthesis and degradation	jgi.p\|Lenedo1\|1100937	酸性蛋白酶 Acid protease
		jgi.p\|Lenedo1\|1060434	40S核糖体蛋白 S7 40S ribosomal protein S7
		jgi.p\|Lenedo1\|607412	核糖体蛋白L4 Ribosomal protein L4
		jgi.p\|Lenedo1\|1042368	三肽基肽酶A Tripeptidyl peptidase A
		jgi.p\|Lenedo1\|1039990	26S蛋白酶体亚基 P45 26S proteasome subunit P45
		jgi.p\|Lenedo1\|1092580	泛素结合酶E2 Ubiquitin-conjugating enzyme E2
		jgi.p\|Lenedo1\|81445	肽酶s41家族蛋白 Peptidase s41 family protein
		jgi.p\|Lenedo1\|1033416	核糖体蛋白L28e Ribosomal protein L28e
	其他功能 Other functions	jgi.p\|Lenedo1\|1059083	细胞色素P450 Cytochrome P450
		jgi.p\|Lenedo1\|1066578	细胞色素P450 Cytochrome p450
PR vs. D1ST		jgi.p\|Lenedo1\|717494	MFS转运蛋白 MFS general substrate transporter

图6 香菇子实体发育模式图样品简称与图1一致。

Fig. 6 A model for the fruiting body development of Lentinula edodes The code names of samples are consistent with those in Fig. 1.

参考文献 65

[1]	Almási E, Sahu N, Krizsán K, Bálint B, Kovács G M, Kiss B, Cseklye J, Drula E, Henrissat B, Nagy I, Chovatia M, Adam C, LaButti K, Lipzen A, Riley R, Grigoriev I V, Nagy L G. 2019. Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae. New Phytologist, 224 (2):902-915. doi: 10.1111/nph.16032 pmid: 31257601
[2]	Anders S, Pyl P T, Huber W. 2015. HTSeq-a Python framework to work with high-throughput sequencing data. Bioinformatics, 31 (2):166-169. doi: 10.1093/bioinformatics/btu638 pmid: 25260700
[3]	Arima T, Yamamoto M, Hirata A, Kawano S, Kamada T. 2004. The eln3 gene involved in fruiting body morphogenesis of Coprinus cinereus encodes a putative membrane protein with a general glycosyltransferase domain. Fungal Genetics and Biology, 41 (8):805-812. doi: 10.1016/j.fgb.2004.04.003 URL
[4]	Attaran Dowom S, Rezaeian S, Pourianfar H R. 2019. Agronomic and environmental factors affecting cultivation of the winter mushroom or enokitake:achievements and prospects. Applied Microbiology and Biotechnology, 103 (6):2469-2481. doi: 10.1007/s00253-019-09652-y URL
[5]	Bahn Y S, Mühlschlegel F A. 2006. CO₂ sensing in fungi and beyond. Current Opinion in Microbiology, 9 (6):572-578. doi: 10.1016/j.mib.2006.09.003 URL
[6]	Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic:a flexible trimmer for Illumina sequence data. Bioinformatics, 30 (15):2114-2120. doi: 10.1093/bioinformatics/btu170 URL
[7]	Boulianne R P, Liu Y, Aebi M., Lu B, Kües U. 2000. Fruiting body development in Coprinus cinereus:regulated expression of two galectins secreted by a non-classical pathway. Microbiology, 146:1841-1853. doi: 10.1099/00221287-146-8-1841 URL
[8]	Cary J W, Harris-Coward P Y, Ehrlich K C, Di Mavungu J D, Malysheva S V, De Saeger S, Dowd P F, Shantappa S, Martens S L, Calvo A M. 2014. Functional characterization of a veA-dependent polyketide synthase gene in Aspergillus flavus necessary for the synthesis of asparasone,a sclerotium-specific pigment. Fungal Genetics and Biology, 64:25-35. doi: 10.1016/j.fgb.2014.01.001 URL
[9]	Cheawchanlertfa P, Cheevadhanarak S, Tanticharoen M, Maresca B, Laoteng K. 2011. Up-regulated expression of desaturase genes of Mucor rouxii in response to low temperature associates with pre-existing cellular fatty acid constituents. Molecular Biology Reports, 38 (5):3455-3462. doi: 10.1007/s11033-010-0455-x pmid: 21104442
[10]	Chen C, Chen H, Zhang Y, Thomas H R, Frank M H, He Y, Xia R. 2020. TBtools:an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13 (8):1194-1202. doi: 10.1016/j.molp.2020.06.009 URL
[11]	Eisenman H C, Casadevall A. 2012. Synthesis and assembly of fungal melanin. Applied Microbiology and Biotechnology, 93 (3):931-940. doi: 10.1007/s00253-011-3777-2 pmid: 22173481
[12]	Ernst J, Bar-Joseph Z. 2006. STEM:a tool for the analysis of short time series gene expression data. BMC Bioinformatics, 7:191. doi: 10.1186/1471-2105-7-191 URL
[13]	Fang S M, Hou X, Qiu K H, He R, Feng X S, Liang X L. 2020. The occurrence and function of alternative splicing in fungi. Fungal Biology Reviews, 34 (4):178-188. doi: 10.1016/j.fbr.2020.10.001 URL
[14]	Gehrmann T, Pelkmans J F, Lugones L G, Wösten H A B, Abeel T, Reinders M J T. 2016. Schizophyllum commune has an extensive and functional alternative splicing repertoire. Scientific Reports, 6 (1):33640. doi: 10.1038/srep33640 URL
[15]	Grützmann K, Szafranski K, Pohl M, Voigt K, Petzold A, Schuster S. 2014. Fungal alternative splicing is associated with multicellular complexity and virulence:a genome-wide multi-species study. DNA Research, 21 (1):27-39. doi: 10.1093/dnares/dst038 pmid: 24122896
[16]	Huang X, Zhang R, Qiu Y, Wu H, Xiang Q, Yu X, Zhao K, Zhang X, Chen Q, Penttinen P, Gu Y. 2020. RNA-seq profiling showed divergent carbohydrate-active enzymes(cazymes)expression patterns in Lentinula edodes at brown film formation stage under blue light induction. Frontiers in Microbiology, 11:1044. doi: 10.3389/fmicb.2020.01044 URL
[17]	Hughes B T, Espenshade P J. 2008. Oxygen-regulated degradation of fission yeast SREBP by Ofd1,a prolyl hydroxylase family member. EMBO J, 27 (10):1491-1501.
[18]	Kamada T, Sano H, Nakazawa T, Nakahori K. 2010. Regulation of fruiting body photomorphogenesis in Coprinopsis cinerea. Fungal Genetics and Biology, 47:917-921. doi: 10.1016/j.fgb.2010.05.003 URL
[19]	Kim D, Langmead B, Salzberg S L. 2015. HISAT:a fast spliced aligner with low memory requirements. Nature Methods, 12 (4):357-360. doi: 10.1038/NMETH.3317
[20]	Kim J Y, Kim D Y, Park Y J, Jang M J. 2020. Transcriptome analysis of the edible mushroom Lentinula edodes in response to blue light. PLoS ONE, 15 (3):e0230680.
[21]	Krizsán K, Almási E, Merényi Z, Sahu N, Virágh M, Kószó T, Mondo S, Kiss B, Bálint B, Kües U, Barry K, Cseklye J, Hegedüs B, Henrissat B, Johnson J, Lipzen A, Ohm R A, Nagy I, Pangilinan J, Yan J, Xiong Y, Grigoriev I V, Hibbett D S, Nagy L G. 2019. Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi. Proceedings of the National Academy of the Sciences of the United States of America, 116 (15):7409-7418.
[22]	Langfelder P, Horvath S. 2008. WGCNA:an R package for weighted correlation network analysis. BMC Bioinformatics, 9:559. doi: 10.1186/1471-2105-9-559 pmid: 19114008
[23]	Luan R, Liang Y, Chen Y, Liu H, Jiang S, Che T, Wong B, Sun H. 2010. Opposing developmental functions of Agrocybe aegerita galectin(AAL) during mycelia differentiation. Fungal Biology, 114 (8):599-608. doi: 10.1016/j.funbio.2010.05.001 URL
[24]	Manachère G. 1980. Conditions essential for controlled fruiting of macromycetes - a review. Transactions of the British Mycological Society, 75 (2):255-270. doi: 10.1016/S0007-1536(80)80088-X URL
[25]	Muraguchi H, Fujita T, Kishibe Y, Konno K, Ueda N, Nakahori K, Yanagi S O, Kamada T. 2008. The exp1 gene essential for pileus expansion and autolysis of the inky cap mushroom Coprinopsis cinerea(Coprinus cinereus)encodes an HMG protein. Fungal Genetics and Biology, 45 (6):890-896. doi: 10.1016/j.fgb.2007.11.004 pmid: 18164224
[26]	Muraguchi H, Kamada T. 1998. The ich1 gene of the mushroom Coprinus cinereus is essential for pileus formation in fruiting. Development, 125 (16):3133-3141. pmid: 9671586
[27]	Muraguchi H, Kamada T. 2000. A mutation in the eln2 gene encoding a cytochrome P 450 of Coprinus cinereus affects mushroom morphogenesis. Fungal Genetics and Biology, 29 (1):49-59. pmid: 10779399
[28]	Muraguchi H, Umezawa K, Niikura M, Yoshida M, Kozaki T, Ishii K, Sakai K, Shimizu M, Nakahori K, Sakamoto Y, Choi C, Ngan C Y, Lindquist E, Lipzen A, Tritt A, Haridas S, Barry K, Grigoriev I V, Pukkila P J. 2015. Strand-specific RNA-seq analyses of fruiting body development in Coprinopsis cinerea. PLoS ONE, 10 (10):e0141586.
[29]	Nagy L G, Kovács G M, Krizsán K. 2018. Complex multicellularity in fungi:evolutionary convergence,single origin,or both?Biological Reviews of the Cambridge Philosophical Society, 93 (4):1778-1794.
[30]	Nehls U, Dietz S. 2014. Fungal aquaporins:cellular functions and ecophysiological perspectives. Applied Microbiology and Biotechnology, 98 (8):8835-8851. doi: 10.1007/s00253-014-6049-0 URL
[31]	Ohm R A, Aerts D, Wösten H A B, Lugones L G. 2013. The blue light receptor complex WC-1/ 2 of Schizophyllum commune is involved in mushroom formation and protection against phototoxicity. Environmental Microbiology, 15 (3):943-955. doi: 10.1111/j.1462-2920.2012.02878.x URL
[32]	Ohm R A, de Jong J F, Lugones L G, Aerts A, Kothe E, Stajich J E, de Vries R P, Record E, Levasseur A, Baker S E, Bartholomew K A, Coutinho P M, Erdmann S, Fowler T J, Gathman A C, Lombard V, Henrissat B, Knabe N, Kues U, Lilly W W, Lindquist E, Lucas S, Magnuson J K, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze F W M R, vanKuyk P A, Horton J S, Grigoriev I V, Wösten H A B. 2010. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology, 28 (9):957-963. doi: 10.1038/nbt.1643
[33]	Pe P P W, Naing A H, Chung M Y, Park K I, Kim C K. 2019. The role of antifreeze proteins in the regulation of genes involved in the response of Hosta capitata to cold. 3 Biotech, 9 (9):335.
[34]	Pelkmans J F, Lugones L G, Wösten H A B. 2016. Fruiting body formation in basidiomycetes//Wendland J. Growth,differentiation and sexuality. The mycota(A comprehensive treatise on fungi as experimental systems for basic and applied research),Vol 1. Switzerland:Springer:387-405.
[35]	Pelkmans J F, Patil M B, Gehrmann T, Reinders M J T, Wösten H A B, Lugones L G. 2017. Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth. Scientific Reports, 7:310. doi: 10.1038/s41598-017-00483-3 pmid: 28331193
[36]	Perez Di Giorgio J, Soto G, Alleva K, Jozefkowicz C, Amodeo G, Muschietti J P, Ayub N D. 2014. Prediction of aquaporin function by integrating evolutionary and functional analyses. The Journal of Membrane Biology, 247 (2):107-125. doi: 10.1007/s00232-013-9618-8 URL
[37]	Pöggeler S, Nowrousian M, Teichert I, Beier A, Kück U. 2018. Fruiting-body development in ascomycetes//Kües U,Fischer R. Growth,differentiation and sexuality. The mycota(A comprehensive treatise on fungi as experimental systems for basic and applied research),Vol 1. Berlin:Springer:325-355.
[38]	Purschwitz J, Muller S, Kastner C, Schoser M, Haas H, Espeso E A, Atoui A, Calvo A M, Fischer R. 2008. Functional and physical interaction of blue- and red-light sensors in Aspergillus nidulans. Current Biology, 18 (4):255-259 doi: 10.1016/j.cub.2008.01.061 pmid: 18291652
[39]	Rio D C, Ares M, Hannon G J, Nilsen T W. 2010. Purification of RNA using TRIzol(TRI Reagent). Cold Spring Harb Protoc,doI: 10.1101/pdb.prot5439.
[40]	Robinson C H. 2001. Cold adaptation in Arctic and Antarctic fungi. New Phytologist, 151 (2):341-353. doi: 10.1046/j.1469-8137.2001.00177.x URL
[41]	Robinson M D, McCarthy D J, Smyth G K. 2010. edgeR:a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26 (1):139-140. doi: 10.1093/bioinformatics/btp616 pmid: 19910308
[42]	Royse D J, Baars J, Tan Q. 2017. Current overview of mushroom production in the world:technology and applications//Diego C Z,Pardo-Giménez A. Edible and medicinal mushrooms:technology and applications. Hoboken:Wiley:5-13.
[43]	Sakamoto Y, Minato K, Nagai M, Mizuno M, Sato T. 2005. Characterization of the Lentinula edodes exg2 gene encoding a lentinan-degrading exo-β-1,3-glucanase. Current Genetics, 48 (3):195-203. pmid: 16133343
[44]	Sakamoto Y, Nakade K, Sato S, Yoshida K, Miyazaki K, Natsume S, Konno N. 2017. Lentinula edodes genome survey and postharvest transcriptome analysis. Applied and Environmental Microbiology, 83 (10):e02990-16.
[45]	Sano H, Kaneko S, Sakamoto Y, Sato T, Shishido K. 2009. The basidiomycetous mushroom Lentinula edodes white collar-2 homolog PHRB,a partner of putative blue-light photoreceptor PHRA,binds to a specific site in the promoter region of the L. edodes tyrosinase gene. Fungal Genetics and Biology, 46 (4):333-341. doi: 10.1016/j.fgb.2009.01.001 URL
[46]	Shimoda C, Uehira M, Kishida M, Fujioka H, Iino Y, Watanabe Y, Yamamoto M. 1987. Cloning and analysis of transcription of the mei2 gene responsible for initiation of meiosis in the fission yeast Schizosaccharomyces pombe. Journal of Bacteriology, 169 (1):93-96. pmid: 3025190
[47]	Showalter A M. 1993. Structure and function of plant cell wall proteins. Plant Cell, 5 (1):9-23. pmid: 8439747
[48]	Song H Y, Kim D H, Kim J M. 2018. Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes. Scientific Reports, 8 (1):8983.
[49]	Song Linli, Xing Xiaoke, Guo Shunxing. 2018. Morphological process and regulation mechanisms of fruiting body differentiation in macrofungi:a review. Mycosystema, 37:671-684. (in Chinese)
	宋林丽, 邢晓科, 郭顺星. 2018. 大型真菌子实体发生的形态学过程及调控机制. 菌物学报, 37:671-684.
[50]	Tang L H, Jian H H, Song C Y, Bao D P, Shang X D, Wu D Q, Tan Q, Zhang X H. 2013. Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes. Applied Microbiology and Biotechnology, 97 (11):4977-4989. doi: 10.1007/s00253-013-4832-y URL
[51]	Tao Y X, Chen R L, Yan J J, Long Y, Tong Z J, Song H B, Xie B G. 2019. A hydrophobin gene,Hyd9,plays an important role in the formation of aerial hyphae and primordia in Flammulina filiformis. Gene, 706 (20):84-90. doi: 10.1016/j.gene.2019.04.067 URL
[52]	Tao Y X, Xie B G, Yang Z Y, Chen Z H, Chen B Z, Deng Y J, Jiang Y J, Peer A F. 2013. Identification and expression analysis of a new glycoside hydrolase family 55 exo-β-1,3-glucanase-encoding gene in Volvariella volvacea suggests a role in fruiting body development. Gene, 527 (1):154-160. doi: 10.1016/j.gene.2013.05.071 URL
[53]	Turner E M. 1977. Development of excised sporocarps of Agaricus bisporus and its control by CO₂. Transactions of the British Mycological Society, 69 (2):183-186. doi: 10.1016/S0007-1536(77)80035-1 URL
[54]	Vetchinkina E, Kupryashina M, Gorshkov V, Ageeva M, Gogolev Y, Nikitina V. 2017. Alteration in the ultrastructural morphology of mycelial hyphae and the dynamics of transcriptional activity of lytic enzyme genes during basidiomycete morphogenesis. Journal of Microbiology, 55 (4):280-288. doi: 10.1007/s12275-017-6320-z pmid: 28124773
[55]	Wang Q, Guo M, Xu R, Zhang J, Bian Y, Xiao Y. 2019. Transcriptional changes on blight fruiting body of Flammulina velutipes caused by two new bacterial pathogens. Frontiers in Microbiology, 10:2845. doi: 10.3389/fmicb.2019.02845 URL
[56]	Wang Y, Zeng X, Liu W. 2018. De novo transcriptomic analysis during Lentinula edodes fruiting body growth. Gene, 641:326-334. doi: 10.1016/j.gene.2017.10.061 URL
[57]	Wang Zhuo ren, Liu Qi yan, Xiao Yang, Wu Qian, Bian Yin bing. 2010. Grey correlational and ISSR analyses of Lentinula edodes hybrids. Mycosystema, 29 (2):267-272. (in Chinese)
	王卓仁, 刘启燕, 肖扬, 吴茜, 边银丙. 2010. 香菇单孢杂交子代群体灰色关联度和ISSR分析. 菌物学报, 29 (2):267-272.
[58]	Wösten H A B, van Wetter M A, Lugones L G, van der Mei H C, Busscher H J, Wessels J G H. 1999. How a fungus escapes the water to grow into the air. Current Biology, 9 (2):85-88. pmid: 10021365
[59]	Wu W, Zong J, Wei N, Cheng J, Zhou X, Cheng Y, Chen D, Guo Q, Zhang B, Feng Y. 2018. CASH:a constructing comprehensive splice site method for detecting alternative splicing events. Briefings in Bioinformatics, 19 (5):905-917. doi: 10.1093/bib/bbx034 URL
[60]	Yoo S I, Lee H Y, Markkandan K, Moon S, Ahn Y J, Ji S, Ko J, Kim S J, Ryu H, Hong C P. 2019. Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes. BMC Genomics, 20 (1):121. doi: 10.1186/s12864-019-5509-4 URL
[61]	Yu G, Wang L G, Han Y, He Q Y. 2012. clusterProfiler:an R package for comparing biological themes among gene clusters. Omics-A Journal of Integrative Biology, 16 (5):284-287. doi: 10.1089/omi.2011.0118 URL
[62]	Zerai D B, Fitzsimmons K M,and Collier R J. 2010. Transcriptional response of delta-9-desaturase gene to acute and chronic cold stress in Nile Tilapia,Oreochromis niloticus. Journal of the World Aquaculture Society, 41 (5):800-806. doi: 10.1111/j.1749-7345.2010.00422.x URL
[63]	Zhang J C, Shen N, Li C, Xiang X J, Liu G L, Gui Y, Patev S, Hibbett D S, Barry K, Andreopoulos W, Lipzen A, Riley R, He G F, Yan M, Grigoriev I V, Kwan H S, Cheung M K, Bian Y B, Xiao Y. 2021. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. Journal of Advanced Research,doi: 10.1016/j.jare.2021.09.008.
[64]	Zhao Chunqiao, Xie Fang, Wu Pingmin. 2021. Advance in researching the effects of environmental factors on sexual development of edible fungus. Chinese Agricultural Science Bulletin, 30:87-92. (in Chinese)
	赵春巧, 谢放, 吴萍民. 2014. 环境因素对食用菌有性发育影响的研究进展. 中国农学通报, 30:87-92.
[65]	Zhou J, Kang L, Liu C, Niu X, Wang X, Liu H, Zhang W, Liu Z, Latge J P, Yuan S. 2019. Chitinases play a key role in stipe cell wall extension in the mushroom Coprinopsis cinerea. Applied and Environmental Microbiology, 85 (15):e00532-19.