食品与发酵工业 >

2021 , Vol. 47 >Issue 4: 102 - 109

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.024863

研究报告

不同培养条件下酿酒酵母菌的转录组差异分析

  • 杨新 ,
  • 陈莉 ,
  • 杨双全 ,
  • 卢红梅 ,
  • 章之柱
展开
  • 1(贵州大学,贵州省发酵工程与生物制药重点实验室,贵州 贵阳, 550025)
    2(贵州大学 酿酒与食品工程学院,贵州 贵阳, 550025)
    3(贵州大学 化学与化工学院,贵州 贵阳, 550025)
    4(开阳县市场监督管理局,贵州 贵阳, 550300)
硕士研究生(陈莉副教授和杨双全副教授为共同通讯作者,E-mail:3152539622@qq.com;441221916@qq.com)

收稿日期: 2020-06-27

  修回日期: 2020-09-01

  网络出版日期: 2021-03-16

基金资助

贵州省科技支撑计划项目(黔科合支撑[2019]2317号)

收起

Transcriptome analysis of Saccharomyces cerevisiae under different culture conditions

  • YANG Xin ,
  • CHEN Li ,
  • YANG Shuangquan ,
  • LU Hongmei ,
  • ZHANG Zhizhu
Expand
  • 1(Guizhou Key Lab of Fermentation Engineering and Biological Pharmacy, Guizhou University, Guiyang 550025, China)
    2(School of Liquor-making and Food Engineering, Guizhou University, Guiyang 550025, China)
    3(School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China)
    4(Market Supervision Administration of KaiYang, Guiyang 550300, China)

Received date: 2020-06-27

  Revised date: 2020-09-01

  Online published: 2021-03-16

Fold

摘要

从组学水平分析富硒条件下酿酒酵母菌(Saccharomyces cerevisiae)内在分子机制,为酿酒酵母菌富硒研究及富硒基因的挖掘利用提供理论依据。该研究以不加硒培养的酿酒酵母菌作为对照组Kb,以加20 μg/mL硒培养的酿酒酵母菌为实验组Se,利用Illumina高通量测序平台对两组进行转录组测序,通过生物信息学方法对数据进行分析处理。结果表明,转录组测序共获得6 445个Unigenes,分别有1 401个(21.74%)、3 665个(56.87%)、5 630个(87.35%)、6 112个(94.83%)、6 077个(94.29%)、5 059个(78.49%) Unigenes被注释到GO、KEGG、COG、NR、Swiss Prot和Pfam数据库,共有6 150个(95.42%)Unigenes得到注释。在GO功能注释中,共得到41个GO功能小类,在KEGG代谢通路分析时,获得了113条KEGG通路。该转录组测序数据质量高,结果覆盖面广,为酿酒酵母菌富硒基因挖掘和研究提供了一定的理论参考。

关键词： 酿酒酵母菌; 富硒培养; 转录组学; 生物信息学; 差异分析

本文引用格式

杨新 , 陈莉 , 杨双全 , 卢红梅 , 章之柱 . 不同培养条件下酿酒酵母菌的转录组差异分析[J]. 食品与发酵工业, 2021 , 47(4) : 102 -109 . DOI: 10.13995/j.cnki.11-1802/ts.024863

Abstract

To analyze the internal molecular mechanism of Saccharomyces cerevisiae under selenium-enriched conditions from the omics level and provide a theoretical basis for the study of selenium-enriched S. cerevisiae and the mining and utilization of selenium-enriched genes, S. cerevisiae cultured without selenium was used as the control group Kb, and S. cerevisiae cultured with 20 μg/mL selenium was used as the experimental group Se. Illumina high-throughput sequencing platform was used to sequence the transcriptome. Data were analyzed and processed by a variety of bioinformatics methods. The results showed that a total of 6 445 Unigenes were obtained by transcriptome sequencing, including 1 401 (21.74%), 3 665 (56.87%), 5 630 (87.35%), 6 112 (94.83%), 6 077 (94.29%) and 5 059 (78.49%) Unigenes were annotated to GO, KEGG, COG, NR, Swiss Prot and Pfam databases, and a total of 6 150 (95.42%) Unigenes were annotated. In the GO functional annotation, a total of 41 GO functional subclasses were obtained, and 113 KEGG pathways were obtained in the KEGG metabolic pathway analysis. The high-quality transcriptome sequencing data and wide coverage provide a certain theoretical reference for selenium-enriched gene mining and research of S. cerevisiae.

Key words： Saccharomyces cerevisiae; selenium-rich culture; transcriptomics; bioinformatics; variance analysis

参考文献

[1] TSAI C F, OU B R, LIANG Y C, et al.Growth inhibition and antioxidative status induced by selenium-enriched broccoli extract and selenocompounds in DNA mismatch repair-deficient human colon cancer cells[J].Food Chemistry, 2013, 139(1):267-273.
[2] FAIRWEATHER-TAIT S, BAO Y, BROADLEY M R, et al.Selenium in human health and disease[J].Antioxidants & Redox Signaling, 2011,14(7):1 337-1 383.
[3] El-DEMERDASH F M.Antioxidant effect of vitamin E and selenium on lipid peroxidation, enzyme activities and biochemical parameters in rats exposed to aluminium[J].Journal of Trace Elements in Medicine and Biology, 2004, 18(1):113-121.
[4] BRYSZEWSKA M A, MAGE A.Determination of selenium and its compounds in marine organisms[J].Journal of Trace Elements in Medicine and Biology, 2015, 29(1):91-98.
[5] 王磊,杜菲,孙卉,等.人体硒代谢与硒营养研究进展[J].生物技术进展,2015,5(4):285-290.
WANG L, DU F, SUN H, et al.Progress on selenium metabolism and nutrition in human[J].Current Biotechnology, 2015, 5(4):285-290.
[6] IP C, DONG Y, GANTHER H.New concepts in seleniu chemoprevention[J].Cancer and Metastasis Reviews, 2002, (21):281-289.
[7] XUE M, CARLSON B A, GRIMM T A, et a1.Rhesus monkey simian immunodeficiency virus infection as a model for assessing the role of selenium in AIDS[J].Journal of Acquired Immune Deficiency Syndromes, 2002, 31(5):453-463.
[8] TAN J, ZHU W, Wang W, et a1.Selenium in soil and endemic diseases in China[J].Science of The Total Environment, 2002, 284:227-235.
[9] HOU J, WANG T, LIU M F, et al.Suboptimal selenium supply:A continuing problem in Keshan disease areas in Heilongjiang province[J].Biological Trace Element Research, 2011, 143(3):1 255-1 263.
[10] LIN Y L, CHANG Y Y, YANG D J, et al.Beneficial effects of noni (Morinda citrifolia L.) juice on livers of high-fat dietary hamsters[J].Food chemistry, 2013, 140(1):31-38.
[11] CRISTALDI L A, MCDOWELL L R, BUERGELT C D, et al.Tolerance of inorganic selenium in wether sheep[J].Small Ruminant Research, 2005, 56(1):205-213.
[12] ABBOTT D A, ZELLE R M, PRONK J T, et al.Metabolic engineering of Saccharomyces cerevisiae for production of carboxylic acids:Current status and challenges[J].FEMS Yeast Research, 2009, 9:1 123-1 136.
[13] LIAN J, MISHRA S, ZHAO H.Recent advances in metabolic engineering of Saccharomyces cerevisiae:New tools and their applications[J].Metabolic Engineering, 2018, 50:85-108.
[14] SULTAN M, SCHULZ M H, RICHARD H, et al.A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome[J].Science, 2008, 321(5 891):956-960.
[15] SCHUSTER S C.Next-generation sequencing transforms today's biology[J].Nature Methods, 2008, 5(1):16-18.
[16] 聂文强,吴天祥,钟敏,等.真菌灰树花菌丝体转录组测序及分析[J].食品科学,2017,38(20):6-11.
NIE W Q, WU T X, ZHONG M, et al.Transcriptome sequencing and analysis of grifola frondosa mycelia[J].Food Science, 2017, 38(20):6-11.
[17] 宋雪飞,郭晶晶,姜静,等.植物乳杆菌FS5-5在盐胁迫下的转录组学分析[J].食品科学,2017,38(6):20-26.
SONG X F, GUO J J, JIANG J, et al.Transcriptomic analyses of Lactobacillus plantarum FS5-5 against salt stress[J].Food Science, 2017, 38(6):20-26.
[18] QI Y X, LIU Y B, RONG W H.RNA-Seq and its applications:A new technology for transcriptomics[J].Hereditas, 2011, 33(11):1 191-1 202.
[19] 周华,张新,刘腾云,等.高通量转录组测序的数据分析与基因发掘[J].江西科学,2012,30(5):607-611.
ZHOU H, ZHANG X, LIU T Y, et al.Data processing and gene discovery of high-throughput transcriptome sequencing[J].Jiangxi Science, 2012, 30(5):607-611.
[20] 许波,张伟强,冯晓曦,等.转录组测序技术在玉米中的应用研究进展[J].玉米科学,2014,22(1):67-72;78.
XU B, ZHANG W Q, FENG X X, et al.Application progress of transcriptome sequencing technology in maize[J].Journal of Maize Sciences, 2014, 22(1):67-72;78.
[21] QI Y X, LIU Y B, RONG W H.RNA-Seq and its applications:A new technology for transcriptomics[J].Hereditas(Beijing), 2011, 33(11):1 191-1 202.
[22] 石浩然. 基于二代测序的转录组数据分析方法的比较研究[D].雅安:四川农业大学,2016.
SHI H R.Comparison of transcriptome analysis methods based on next-generation sequencing technologies[D].Ya'an:Sichuan Agricultural University, 2016.
[23] 姚娜,刘秀明,董园园,等.转录组的测序方法及应用研究概述[J].北方园艺,2017(12):192-198.
YAO N, LIU X M, DONG Y Y, et al.Advances in application and seguencing methods of transcriptome[J].Northern Horticulture, 2017(12):192-198.
[24] WANG J, DEAN D C, HORNICEK F J, et al.RNA sequencing (RNA-Seq) and its application in ovarian cancer[J].Gynecologic oncology,2019,152(1):194-201.
[25] SALIBA A E, C SANTOS S, VOGEL J.New RNA-seq approaches for the study of bacterial pathogens[J].Current Opinion in Microbiology, 2017, 35:78-87.
[26] 叶美玲. 南极酵母AN5重金属Cu2+胁迫的转录组学研究[D].哈尔滨:哈尔滨工业大学,2015.
YE M L.Transcriptomics of antarctic yeast an5 under heavy metal(Cu2+)Stress[D].Harbin:Harbin Institute of Technology, 2015.
[27] TRAPNELL C, PACHTER L, SALZBERG S L.TopHat:Discovering splice junctions with RNA-Seq[J].Bioinformatics, 2009, 25(9):1 105-1 111.
[28] PATIL K V, CANLON B, CEDERROTH C R.High quality RNA extraction of the mammalian cochlea for qRT-PCR and transcriptome analyses[J].Hearing Research, 2015, 325(7):42-48.
[29] ANDERS S, HUBER W.Differential expression analysis for sequence count data[J].Genome Biology, 2010, 11(10):106-107.
[30] LOVE M I, HUBER W, ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome Biology, 2014, 15(12):550-553.
Options
文章导航

/

〈 〉

技术支持：北京玛格泰克科技发展有限公司