灰树花菌丝体与原基转录组差异表达分析

doi:10.3969/J.ISSN.1671-9964.2016.01.013

Abstract
Figure/Table
References
Related Citation (0)

Download: PDF (1094 KB) HTML (1 KB)
Export: BibTeX | EndNote (RIS)

Abstract

The expression profiling of mycelium and primordium of Grifola frondosa was analyzed with high-throughput sequencing technology based on the Illumina Genome Analyzer platform.Totally 35788532 and 32755254 clean reads from mycelium and primordium libraries were obtained.Analysis of differentially expressed genes shows that there are 4094 genes differentially expressed between two libraries, and in the primordium library, 1886 of them are up-regulated while 2208 of them are down-regulated.There are 284 genes that are only expressed in the primordium library.With Blastnr comparison, genes differently expressed between two libraries are found to be related to acid protease and lectin, cytochrome, NADPH-P450 reductase, esterase, amine oxidase, clavaminate synthase, glycoside hydrolase.Genes only expressed in the primordium are found to be related to glucose, lipid, nucleic acids metabolism and cell and chloroplast membrane structure.Gene ontology functional enrichment analysis reveals that most genes related to mitochondrial membrane, glutamine family amino acid metabolic process, fatty acid biosynthetic process are up-regulated.Pathway enrichment analysis shows that genes related to ribosome are all up-regulated, and this indicates that when primordium is developed the cell metabolism speeds up and the protein synthesis increases.

Key words： Grifola frondosa mycelium primordium differentially expressed gene

Received: 23 April 2015 Published: 08 March 2016

Corresponding Authors: Wei-dong YUAN E-mail: akeok@126.com;ywd0507@126.com

	Service

	E-mail this article
	Add to my bookshelf
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	Wei-ke WANG
	Zu-fa ZHOU
	Qing CHEN
	Wei-dong YUAN

Cite this article:

Wei-ke WANG,Zu-fa ZHOU,Qing CHEN, et al. Analysis of Differentially Expressed Genes between Mycelium and Primordium of Grifola frondosa[J]. Journal of Shanghai Jiaotong University (Agricultural Sciences), 2016, 34(1): 74-80.

URL:

http://www.qk.sjtu.edu.cn/jsjtua/EN/10.3969/J.ISSN.1671-9964.2016.01.013 OR http://www.qk.sjtu.edu.cn/jsjtua/EN/Y2016/V34/I1/74

Concentration of RNA from mycelium and primordium of Grifola frondosa

Electropherogram of RNAs from mycelium and primordium of Grifola frondosa

1-JST mean mycelium, 2-YJ mean primordium

Distributions of tags from two libraries

基因ID Gene ID	菌丝中表达值 Expression value of mycelium	原基中表达值 Expression value of primordium	Q值 Q value	同源基因及其功能 Homologous gene and its function
unigene23873	483.4	6.0	0.023	酸性蛋白酶(gi\|392558359\|)(gb\|EIW51548.1\|) Acid protease
unigene13929	11.6	5860.5	0.037	凝集素(gi\|18478668\|)(gb\|AAL73235.1\|)
unigene30943	186.4	1.4	0.037	DUF1479结构域蛋白(gi\|392564554\|)(gb\|EIW57732.1\|) DUF1479 domain containing protein
unigene12210	8.2	2412.5	0.042	凝集素(gi\|50980806\|)(gb\|AAT91249.1\|) lectin
unigene41873	2.3	81.1	0.042	细胞色素P450(gi\|395327404\|)(gb\|EJF59804.1\|) Cytochrome P450
unigene45937	1.7	67.0	0.042	NADPH-P450还原酶(gi\|392559250\|)(gb\|EIW52435.1\|) NADPH-P450 reductase
unigene27346	223.5	5.9	0.044	IlvN结构域蛋白(gi\|395334382\|)(gb\|EJF66758.1\|) IlvN domain containing protein
unigene28323	3.5	162.9	0.044	酯酶(gi\|395328576\|)(gb\|EJF60967.1\|) esterase
unigene41874	2.1	68.9	0.044	细胞色素P450(gi\|395327404\|)(gb\|EJF59804.1\|) Cytochrome P450
unigene45936	2.2	73.6	0.044	NADPH-P450还原酶(gi\|392559250\|)(gb\|EIW52435.1\|) NADPH-P450 reductase
unigene41875	3.0	170.3	0.048	细胞色素P450(gi\|395327404\|)(gb\|EJF59804.1\|) Cytochrome P450
unigene14635	3.5	118.4	0.052	真菌疏水蛋白结构(gi\|390605204\|)(gb\|EIN14595.1\|) Fungal hydrophobin
unigene47574	248.0	1.3	0.056	胺氧化酶(gi\|392563541\|)(gb\|EIW56720.1\|) Amine oxidase
unigene19870	22.8	653.1	0.058	真菌疏水蛋白结构(gi\|395323171\|)(gb\|EJF55662.1\|) Fungal hydrophobin
unigene36089	1.8	34.7	0.058	细胞色素P450(gi\|390599619\|)(gb\|EIN09015.1\|) Cytochrome P450
unigene30525	0.8	13.6	0.06	克拉维胺合成酶(gi\|392569544\|)(gb\|EIW62717.1\|) Clavaminate synthase-like protein
unigene36088	1.5	27.1	0.06	细胞色素P450(gi\|390599619\|)(gb\|EIN09015.1\|) Cytochrome P450
unigene39627	14.6	1.0	0.061	类CDF转运蛋白(gi\|395334914\|)(gb\|EJF67290.1\|) CDF-like metal transporter
unigene30523	0.5	14.7	0.063	克拉维胺合成酶(gi\|392569544\|)(gb\|EIW62717.1\|) Clavaminate synthase-like protein
unigene2984	69.6	0.3	0.065	糖苷水解酶家族(gi\|392564918\|)(gb\|EIW58095.1\|) Glycoside hydrolase family protein

Blastnr of differently expressed genes between mycelium and primordium libraries

Blastnr comparison of genes only expressed in the primordium

基因本体条目 Gene ontology entries	分类 Classification	P值 P value	上调基因数 Up-regulated genes	下调基因数 Down-regulated genes
结合ATP ATP binding	分子功能 Molecular function	9.9E-06	74	30
酸酐水解酶活性 Hydrolase activity	分子功能 Molecular function	2.1E-07	46	5
胞内成分 Intracellular part	细胞组成 Cellular component	3.1E-07	91	24
结合过渡金属离子 Transition metal ion binding	分子功能 Molecular function	9.8E-09	102	52
线粒体膜成分 Mitochondrial membrane part	细胞组成 Cellular component	9.9E-08	6	0
结合金属离子 Metal ion binding	分子功能 Molecular function	1.6E-11	117	60
结合核酸 Nucleic acid binding	分子功能 Molecular function	8.0E-13	115	24
谷氨酰胺家族氨基酸代谢过程 Glutamine family amino acid metabolic process	生物过程 Biological process	1.4E-05	8	0
肽酶活性 Peptidase activity	分子功能 Molecular function	6.6E-11	27	25
结合阳离子 Cation binding	分子功能 Molecular function	2.9E-11	117	60
脂肪酸生物合成过程 Fatty acid biosynthetic process	生物过程 Biological process	4.8E-06	4	0
单糖分解代谢过程 Monosaccharide catabolic process	生物过程 Biological process	7.7E-06	2	5
胞内蛋白代谢过程 Cellular protein metabolic process	生物过程 Biological process	2.2E-06	41	2
小分子代谢过程 Small molecule metabolic process	生物过程 Biological process	6.7E-06	21	10
金属内肽酶活性 Metalloendopeptidase activity	分子功能 Molecular function	1.1E-06	9	1
水解酶活性 Hydrolase activity	分子功能 Molecular function	1.5E-09	120	62
结合嘌呤核苷三磷酸 Purine ribonucleoside triphosphate binding	分子功能 Molecular function	3.2E-07	95	32
氧化还原酶活性 Oxidoreductase activity	分子功能 Molecular function	1.1E-16	141	59
依赖NTP嘌呤解旋酶活性 Purine NTP-dependent helicase activity	分子功能 Molecular function	2.6E-07	17	3
单价无机阳离子跨膜运输活性 Monovalent inorganic cation transmembrane transporter activity	分子功能 Molecular function	1.1E-05	6	5

Significantly enriched GO terms of mycelium and primordium

List of pathway enrichment analysis of mycelium and primordium

[1]	汤庆莉, 张洪, 张勇, 等.灰树花胞外多糖提取工艺优化[J].核农学报, 2013, 27(11):1704-1708.
[2]	杨海, 耿传信, 周学锋.灰树花活性多糖药理研究综述[J].中国执业药师, 2012, 9(3):30-33.
[3]	张桂春, 刘玉静, 解卫海, 等.响应面法优化灰树花发酵全液多糖提取工艺及其抗肿瘤活性[J].食品科学, 2013, 34(24):30-35.
[4]	许占伍, 张引芳, 金力, 等.灰树花工厂化袋栽原基形成条件研究[J].食用菌, 2012(2):7-9.
[5]	潘辉, 李正鹏, 王瑞娟, 等.灰树花子实体发育过程研究[J].食用菌, 2010, 32(5):9-11.
[6]	Tomas Maseka, Vaclav Vopalenskya, Petra Suchomelovab, et al.Denaturing RNA electrophoresis in TAE agarose gels[J].Analytical Biochemistry, 2005, 336(1):46-50.
[7]	Shen R, Fan J B, Campbell D, et al.High-throughput SNP genotyping on universal bead arrays[J].Mutat Res, 2005, 573(1/2):70-82.
[8]	Haas B J, Papanicolaou A, Yassour M, et al.De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis[J].Nature Protocols, 2013, 8(8):1494-1512.
[9]	Mortazavi A, Williams B A, McCue K, et al.Mapping and quantifying mammalian transcriptomes by rna-seq[J].Nat Methods, 2008, 5(7):621-628.
[10]	Ye J, Fang L, Zheng H, et al.WEGO:a web tool for plotting GO annotations[J].Nucleic Acids Research, 2006, 34(2):293-297.
[11]	刘朋虎, 邓优锦, 江玉姬, 等.草菇菌丝体与原基差异表达基因分析[J].基因组学与应用生物学, 2012, 31(2):147-153.
[12]	刘芳, 王威, 谢宝贵.金针菇菌丝与原基差异表达基因分析[J].食用菌学报, 2014(1):1.