松乳菇子实体两个发育时期的转录组分析

doi:10.3969/j.issn.1004-1524.2020.02.18

浙江农业学报 ›› 2020, Vol. 32 ›› Issue (2): 337-347.DOI: 10.3969/j.issn.1004-1524.2020.02.18

松乳菇子实体两个发育时期的转录组分析

宋志强¹, 丁祥², 唐贤¹, 朱淼¹, 侯怡铃^1,*

1.西华师范大学生命科学学院,西南野生动植物资源保护教育部重点实验室,四川南充 637009;
2.西华师范大学环境科学与工程学院,四川南充 637009

收稿日期:2019-05-10 出版日期:2020-02-25 发布日期:2020-03-13
通讯作者: *侯怡铃,E-mail:starthlh@126.com
作者简介:宋志强(1995—),男,安徽淮北人,硕士研究生,主要从事细胞生物学研究。E-mail:1484655071@qq.com
基金资助:
四川省科技厅应用基础重点项目(2018JY0087); 四川省科技厅重点研发项目(2018NZ0055); 南充市科技局项目(16YFZJ0043)

Transcriptome analysis of fruiting bodies of Lactarius deliciosus at two developmental stages

SONG Zhiqiang¹, DING Xiang², TANG Xian¹, ZHU Miao¹, HOU Yiling^1,*

1. Key Laboratory of Southwest China Wildlife Resources Conservation, Ministry of Education, College of Life Sciences, China West Normal University, Nanchong 637009, China;
2. College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China

Received:2019-05-10 Online:2020-02-25 Published:2020-03-13

摘要/Abstract

摘要： 以松乳菇子实体为研究材料,采用de novo测序对松乳菇子实体进行测序与生物信息学分析,探究松乳菇子实体生长发育过程中幼菇期(LDG-1)和成熟期(LDG-2)基因表达的差异,并探寻影响松乳菇生长发育相关的主要基因和代谢通路。测序结果显示,共获得7.44G(LDG-1)和7.21G(LDG-2)的分析数据(clean reads)。KOG功能注释结果显示,松乳菇在幼菇期(LDG-1)和成熟期(LDG-2)具有全面而复杂的基因功能类别。GO富集结果提示,松乳菇在不同生长阶段(LDG-1和LDG-2)的生物代谢功能存在一定的差异。基因表达水平与聚类分析显示,ATP酶、多功能伴侣蛋白等家族基因为LDG-1和LDG-2主要高表达基因,在能量代谢与参与调控细胞周期中起重要作用。分析差异表达基因发现,相较于LDG-1期,LDG-2期有16 789个差异表达基因,其中7 635个基因上调,9 154个基因下调。差异表达基因KEGG富集通路分析结果显示,氧化磷酸化途径是松乳菇幼菇期生长发育过程中能量代谢的关键途径。进一步分析显示,MAPK信号通路是影响松乳菇子实体发育的关键信号通路,在促进松乳菇子实体进行有性生殖和调控菌丝体的极性生长中起重要作用。

关键词: 松乳菇, de novo测序, 差异表达基因, 氧化磷酸化, MAPK信号通路

Abstract: In this study, the fruiting bodies of Lactarius deliciosus were sequenced by de novo sequencing and bioinformatics analysis. The differences of gene expression between young mushroom (LDG-1) and mature mushroom (LDG-2) during the growth and development of fruiting bodies of Lactarius deliciosus were explored, and the main genes and metabolic pathways related to the growth and development of Lactarius deliciosus were also studied. The sequencing results showed that a total of 7.44G (LDG-1) and 7.21G (LDG-2) clean reads were obtained. The results of KOG functional annotation showed that Lactarius deliciosus had comprehensive and complex gene functional categories at LDG-1 and LDG-2. The results of GO enrichment indicated that there were some differences in the bio-metabolic functions of Lactarius deliciosus at different growth stages (LDG-1 and LDG-2). The analysis of gene expression level and cluster showed that the main high-expression genes were ATPase, multifunctional chaperone family genes, etc., which played an important role in energy metabolism and cell cycle regulation. Analysis of differentially expressed genes showed that compared with LDG-1, there were 16 789 differentially expressed genes in LDG-2, in which 7 635 genes were up-regulated and 9 154 genes were down-regulated. KEGG pathway enrichment of differential expression gene results showed that oxidative phosphorylation was the key pathway of energy metabolism during the growth and development of Lactarius deliciosus. Further analysis showed that MAPK signaling pathway was the key signaling pathway affecting the development of fruiting body of Lactarius deliciosus, which plays an important role in promoting sexual reproduction and regulating polar growth of mycelium of fruiting body of Lactarius deliciosus.

Key words: Lactarius deliciosus, de novo sequencing, differentially expressed genes, oxidative phosphorylation, MAPK signaling pathway

中图分类号:

S646

宋志强, 丁祥, 唐贤, 朱淼, 侯怡铃. 松乳菇子实体两个发育时期的转录组分析[J]. 浙江农业学报, 2020, 32(2): 337-347.

SONG Zhiqiang, DING Xiang, TANG Xian, ZHU Miao, HOU Yiling. Transcriptome analysis of fruiting bodies of Lactarius deliciosus at two developmental stages[J]. , 2020, 32(2): 337-347.

参考文献

[1] 耿妍, 陈玲玲, 鲁焕, 等. de novo转录组学分析华南地区入侵植物五爪金龙代谢特征[J]. 热带亚热带植物学报, 2016, 24(2): 128-142.
GENG Y, CHEN L L, LU H, et al.Metabolic characteristics of invasive plant Ipomoea cairica in South China by de novo transcriptomics[J]. Journal of Tropical and Subtropical Botany, 2016, 24(2): 128-142. (in Chinese with English abstract)
[2] 李帆, 陈利丁, 艾柳英, 等. 刺芹侧耳不同发育时期的转录组差异分析[J]. 菌物学报, 2018, 37(12): 1586-1597.
LI F, CHEN L D, AI L Y, et al.Comparative transcriptomics analyses of Pleurotus eryngii at different developmental stages[J]. Mycosystema, 2018, 37(12): 1586-1597. (in Chinese with English abstract)
[3] 吴小梅, 张昕, 李南羿. 双孢蘑菇子实体不同发育时期的转录组分析[J]. 菌物学报, 2017, 36(2): 193-203.
WU X M, ZHANG X, LI N Y.Transcriptome analysis of Agaricus bisporus fruiting at different stages[J]. Mycosystema, 2017, 36(2): 193-203. (in Chinese with English abstract)
[4] 陈志宏, 陶永新, 陈炳智, 等. 与草菇菌柄伸长相关的bZIP转录因子基因克隆与表达分析[J]. 基因组学与应用生物学, 2014, 33(3): 585-590.
CHEN Z H, TAO Y X, CHEN B Z, et al.Cloning and expression analysis of a bZIP transcription factor gene involved in stipe elongation in Volvariella volvacea[J]. Genomics and Applied Biology, 2014, 33(3): 585-590.(in Chinese with English abstract)
[5] 申进文, 粱思思, 邱立友, 等. 糙皮侧耳子实体发育相关基因fst3的克隆及分析[J]. 食用菌学报, 2015, 22(1): 15-20.
SHEN J W, LIANG S S, QIU L Y, et al.Cloning and expression of a fst3 gene from Pleurotus ostreatus[J]. Acta Edulis Fungi, 2015, 22(1): 15-20.(in Chinese with English abstract)
[6] 杨明毅, 徐虹. 松乳菇的研究与开发[J]. 中国野生植物资源, 2001, 20(2): 29-30.
YANG M Y, XU H.Research and development of Lactarius deliciosus[J]. Chinese Wild Plant Resources, 2001, 20(2): 29-30. (in Chinese)
[7] 王艺, 丁贵杰. 外生菌根对马尾松幼苗生长的影响[J]. 中南林业科技大学学报, 2011, 31(4): 74-78.
WANG Y, DING G J.Effects of exogenous mycorrhiza on growth of Pinus massoniana seedlings[J]. Journal of Central South University of Forestry & Technology, 2011, 31(4): 74-78.(in Chinese with English abstract)
[8] 熊涛, 肖满. 松乳菇研究进展[J]. 食品与发酵工业, 2005, 31(5): 84-86.
XIONG T, XIAO M.Research progress of Lactarius deliciosus[J]. Food and Fermentation Industries, 2005, 31(5): 84-86. (in Chinese)
[9] 张四维, 岑凯, 刘艳, 等. 青藏高原野生冬虫夏草子实体发育时期的宏转录组研究[J]. 中国科学:生命科学, 2018, 48(5): 562-570.
ZHANG S W, CEN K, LIU Y, et al.Metatranscriptomics analysis of the fruiting caterpillar fungus collected from the Qinghai-Tibetan plateau[J]. Scientia Sinica(Vitae), 2018, 48(5): 562-570.(in Chinese with English abstract)
[10] 康亚璇, 陈武, 庞晓明, 等. 枣不同组织提取RNA方法的比较及优化[J]. 分子植物育种, 2015, 13(12): 2871-2882.
KANG Y X, CHEN W, PANG X M, et al.The comparison and improvement of RNA extraction methods in different tissues in Chinese jujube (Ziziphus jujuba Mill.)[J]. Molecular Plant Breeding, 2015, 13(12): 2871-2882. (in Chinese with English abstract)
[11] COCK P J A, FIELDS C J, GOTO N, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants[J]. Nucleic Acids Research, 2010, 38(6): 1767-1771.
[12] 王华, 汪王微, 王冬良, 等. 杜鹃花叶片转录组测序数据组装及功能注释[J]. 浙江农业学报, 2018, 30(7): 1149-1159.
WANG H, WANG W W, WANG D L, et al.De novo assembly and functional annotation of transcriptome data of Rhododendron pulchurum cv. Baifeng 4 leaf[J]. Acta Agriculturae Zhejiangensis, 2018, 30(7): 1149-1159.(in Chinese with English abstract)
[13] ZHANG J, KUO C C, CHEN L.WemIQ: an accurate and robust isoform quantification method for RNA-seq data[J]. Bioinformatics, 2015, 31(6): 878-885.
[14] MCCARTHY D J, CHEN Y, SMYTH G K.Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation[J]. Nucleic Acids Research, 2012, 40(10): 4288-4297.
[15] ZOUARI I, SALVIOLI A, CHIALVA M, et al.From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism[J]. BMC Genomics, 2014, 15: 221.
[16] 李海录, 宋艳艳, 冯浩, 等. 苹果褐斑病菌侵染苹果属山定子的转录组学分析[J]. 农业生物技术学报, 2017, 25(1): 32-42.
LI H L, SONG Y Y, FENG H, et al.Transcriptome analysis of the Malus baccata infected with Diplocarpon mali[J]. Journal of Agricultural Biotechnology, 2017, 25(1): 32-42.(in Chinese with English abstract)
[17] 唐贤, 丁祥, 董明明, 等. 棒瑚菌子实体不同发育时期的转录组分析[J]. 生物技术通报, 2019(10): 119-129.
TANG X, DING X, DONG M M, et al.Transcriptome analysis of Clavariadelphus pistillaris fruiting bodies at different development stages[J]. Biotechnology Bulletin, 2019(10): 119-129.(in Chinese with English abstract)
[18] KANEHISA M, ARAKI M, GOTO S, et al.KEGG for linking genomes to life and the environment[J]. Nucleic Acids Research, 2007, 36(Database): D480-D484.
[19] LEHNINGER A L, WADKINS C L.Oxidative phosphorylation[J]. Annual Review of Biochemistry, 1962, 31(1): 47-78.
[20] 关丫丫, 章小英, 王辉, 等. 线粒体ATP合酶抑制因子(ATPIF1)在能量代谢中的作用[J]. 生理科学进展, 2018,49(3): 230-236.
GUAN Y Y, ZHANG X Y, WANG H, et al.Mitochondrial ATP synthase inhibitor (ATPIF1) role in energy metabolism[J]. Progress in Physiological Sciences, 2018, 49(3): 230-236. (in Chinese with English abstract)
[21] 王鹏, 沈允钢. 还原型二(三)磷酸吡啶核苷酸[NAD(P)H]脱氢酶复合体及叶绿体呼吸研究进展[J]. 植物生理与分子生物学学报, 2007, 33(2): 91-100.
WANG P, SHEN Y G.The progress in research on the reduced nicotinamide adenine di(tri)nucleotide phosophate [NAD(P)H] dehydrogenase complex and chlororespiration[J]. Journal of Plant Physiology and Molecular Biology, 2007, 33(2): 91-100.(in Chinese with English abstract)
[22] 王金利, 史胜青, 贾利强, 等. 植物泛素结合酶E2功能研究进展[J]. 生物技术通报, 2010(4): 7-10.
WANG J L, SHI S Q, JIA L Q, et al.Progress on functions of ubiquitin-conjugating enzyme(E2) in plants[J]. Biotechnology Bulletin, 2010(4): 7-10.(in Chinese with English abstract)
[23] HUEN M S Y, HUANG J, YUAN J, et al. Noncanonical E2 variant-independent function of UBC13 in promoting checkpoint protein assembly[J]. Molecular and Cellular Biology, 2008, 28(19): 6104-6112.
[24] 黄艳, 周政. H2A-H2B类型组蛋白及其伴侣蛋白的研究进展[J]. 生物化学与生物物理进展, 2018, 45(9): 971-980.
HUANG Y, ZHOU Z.Recent progress in histone chaperones associated with H2A-H2B type histones[J]. Progress in Biochemistry and Biophysics, 2018, 45(9): 971-980.(in Chinese with English abstract)
[25] 王海英. 草菇不同发育时期菌柄基因表达谱差异初步分析[D]. 福州: 福建农林大学, 2011.
WANG H Y.Analysis of the differential stipe expression profiles of Volvariella volvacea[D]. Fuzhou: Fujian Agriculture and Forestry University, 2011.(in Chinese with English abstract)
[26] 武红霞, 姚全胜, 王松标, 等. ‘KRS’芒果发育过程中糖积累与代谢相关酶活性的关系[J]. 安徽农业科学, 2016, 44(17): 24-26, 55.
WU H X, YAO Q S, WANG S B, et al.The relationship between sugar accumulation and related enzyme activities during the development process of ‘KRS’ mango fruits[J]. Journal of Anhui Agricultural Sciences, 2016, 44(17): 24-26, 55.(in Chinese with English abstract)
[27] 吴亚召, 张文隽, 雷萍, 等. 茶树菇生长发育过程中几种胞外酶活性的变化[J]. 西北农林科技大学学报(自然科学版), 2018,46(11): 115-120.
WU Y Z, ZHAN W J, LEI P, et al.Changes of extracellular enzymes activities during development of Agrocybe aegerita[J]. Journal of Northwest A & F University (Natural Science Edition), 2018,46(11): 115-120. (in Chinese with English abstract)
[28] 高爽, 查笑君, 潘建伟. 真核翻译延伸因子eEF1A功能研究进展[J]. 浙江师范大学学报(自然科学版), 2013, 36(4): 444-449.
GAO S, ZHA X J, PAN J W.Research advances on the biological functions of eukaryotic translation elongation factor[J]. Journal of Zhejiang Normal University(Natural Sciences), 2013, 36(4): 444-449.(in Chinese with English abstract)
[29] 唐蜻. 植物RNA结合蛋白的研究进展[J]. 安徽农业科学, 2010, 38(1): 38-41.
TANG Q.Research progress on the plant RNA-binding proteins[J]. Journal of Anhui Agricultural Sciences, 2010, 38(1): 38-41.(in Chinese with English abstract)
[30] 杨超, 胡红涛, 吴平, 等. 高等植物铁氧还蛋白-NADP+氧化还原酶研究进展[J]. 植物生理学报, 2014, 50(9): 1353-1366.
YANG C, HU H T, WU P, et al.Advances in the research of ferredoxin-NADP+ oxidoreductase in higher plants[J]. Plant Physiology Journal, 2014, 50(9): 1353-1366.(in Chinese with English abstract)
[31] 姜铨, 童汉兴, 陆维祺. 琥珀酸脱氢酶缺陷型胃肠间质瘤研究进展[J]. 中国实用外科杂志, 2016, 36(3): 344-347.
JIANG Q, TONG X H, LU W Q.Advances in succinate dehydrogenase deficient gastrointestinal stromal tumors[J]. Chinese Journal of Practical Surgery, 2016, 36(3): 344-347. (in Chinese)
[32] 刘宝宝, 张士璀. 多胺氧化酶在多胺代谢中的作用[J]. 鲁东大学学报(自然科学版), 2014, 30(4): 336-341.
LIU B B, ZHANG S C.Roles of polyamine oxidases in polyamine catabolism[J]. Ludong University Journal(Natural Science Edition), 2014, 30(4): 336-341.(in Chinese with English abstract)
[33] 李勇, 李登科, 李凯明, 等. 基于分子模拟技术何首乌中蒽醌类法尼基转移酶抑制剂的筛选[J]. 中国新药杂志, 2018, 27(18): 2164-2172.
LI Y, LI D K, LI K M, et al.Discovery of potential FTase inhibitors from anthraquinones of Polygoni multiflori radix based on molecular simulation[J]. Chinese Journal of New Drugs, 2018, 27(18): 2164-2172.(in Chinese with English abstract)
[34] SANTOS M, REBELO S, DA CRUZ E SILVA O A B, et al. Immunolocalization of PPP1C isoforms in SH-SY5Y cells during the cell cycle[J]. Microscopy and Microanalysis, 2012, 18(S5): 41-42.
[35] 于定群, 汤浩茹, 张勇, 等. 高等植物葡萄糖-6-磷酸脱氢酶的研究进展[J]. 生物工程学报, 2012, 28(7): 800-812.
YU D Q, TANG H R, ZHANG Y, et al.Research progress in glucose-6-phosphate dehydrogenase in higher plants[J]. Chinese Journal of Biotechnology, 2012, 28(7): 800-812.(in Chinese with English abstract)
[36] MIACHKE M D, CHANT J.The shape of things to come: morphogenesis in yeast and related patterns in other systems[J]. Canadian Journal of Botany, 2011, 73(S1): 234-242.
[37] 荣成博, 赵爽, 宋爽, 等. 白灵侧耳子实体发育相关基因的挖掘[J]. 生物技术通报, 2018(4): 115-120.
RONG C B, ZHAO S, SONG S, et al.Identification of candidate genes related to the development of Pleurotus tuoliensis fruiting bodies[J]. Biotechnology Bulletin, 2018(4): 115-120.(in Chinese with English abstract)
[38] 施肖堃, 蔡志欣, 郭仲杰, 等. 双孢蘑菇As2796子实体发育转录组测序分析[J]. 福建农业学报, 2018, 33(3): 282-287.
SHI X K, CAI Z X, GUO Z J, et al.Transcriptome sequencing on fruiting body of Agaricus bisporus in developing stages[J]. Fujian Journal of Agricultural Sciences, 2018, 33(3): 282-287.(in Chinese with English abstract)

松乳菇子实体两个发育时期的转录组分析

Transcriptome analysis of fruiting bodies of Lactarius deliciosus at two developmental stages

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 2

编辑推荐

Metrics

本文评价

[1]	杜宇, 熊翠玲, 史秀丽, 郑燕珍, 付中民, 徐细建, 陈大福, 郭睿. 意大利蜜蜂6日龄幼虫肠道内球囊菌的差异表达基因分析[J]. 浙江农业学报, 2017, 29(7): 1119-1128.
[2]	张真真1，邱立军1，李玲2，陈文荣2，应海良1，郭卫东2，*. 低温胁迫差异表达基因在佛手和枳中的半定量RT\\|PCR分析[J]. 浙江农业学报, 2015, 27(12): 2105-.