植物研究 ›› 2021, Vol. 41 ›› Issue (1): 119-129.doi: 10.7525/j.issn.1673-5102.2021.01.015
收稿日期:
2020-03-07
出版日期:
2021-01-20
发布日期:
2021-01-05
通讯作者:
鲁黎明
E-mail:louis_luliming@126.com
作者简介:
鲁琳(1965—),女,副教授,主要从事园林植物研究。
基金资助:
Lin LU1, Shang-Yu YANG2, Wei-Dong LIU1, Li-Ming LU2()
Received:
2020-03-07
Online:
2021-01-20
Published:
2021-01-05
Contact:
Li-Ming LU
E-mail:louis_luliming@126.com
About author:
LU Lin(1965—),female,associate professor,major in landscape plants study.
Supported by:
摘要:
为了鉴定参与花烟草低温胁迫的转录因子,对花烟草幼苗进行了4℃低温处理,并在处理后12 h采集其幼苗样本,提取总RNA后,采用高通量测序技术,进行了转录组测序。在对差异表达基因进行GO及KEGG分析的基础上,对参与其中的转录因子进行了挖掘,并采用qRT-PCR的方法,对转录组测序的结果进行了验证。结果表明,低温处理后,花烟草基因表达量变化在2倍以上的基因有8 388个(P<0.01),其中,上调表达4 229个,下调表达4 159个。这些差异表达基因的功能归类于生物过程、细胞组分及分子功能3大类69个GO条目,并显著富集在40条KEGG代谢通路中。同时,在低温胁迫下,花烟草有118个转录因子的表达发生了显著改变,其中,上调表达82个,下调表达36个。这些转录因子属于28个家族,其中,数量最多的为NAC家族19个,其次为ERF家族16个、MYB家族15个、WRKY家族15个。本研究的结果为花烟草低温响应分子机制的研究提供了借鉴。
中图分类号:
鲁琳, 杨尚谕, 刘维东, 鲁黎明. 基于转录组测序的花烟草低温胁迫响应转录因子挖掘[J]. 植物研究, 2021, 41(1): 119-129.
Lin LU, Shang-Yu YANG, Wei-Dong LIU, Li-Ming LU. To Explore the Transcription Factor in Response to Low Temperature Stress in Nicotiana alata by Transcriptome Sequencing[J]. Bulletin of Botanical Research, 2021, 41(1): 119-129.
表1
qPCR反应所用引物
序号 ID | 引物名称 Primers | 引物序列 Sequence(5′—3′) |
---|---|---|
1 | IAA17-F | TGTTGGAGATGTTCCTTGGAAA |
IAA17-R | GGCTTCCGAGCTCTTCATCA | |
2 | NAC2-F | CCCAGAGGAATCAAAACCAA |
NAC2-R | CCAATCGTCAAGCCTCAAGTTA | |
3 | P450-F | TGGCTTTGGTGACGCTAAAT |
P450-R | GCTGCCAGTCCTGTATTTCC | |
4 | WRKY6-F | TGTCCCCGAGCTTATTATCG |
WRKY6-R | TGGTAGGGGGTGGTTATGTG | |
5 | CIPK6-F | AAGCTATGGATTCATCTGTTACATTG |
CIPK6-R | TTTCATTTCAAGAGACATACCTCAA | |
6 | ERF025-F | CAGATTGGCTAGAAGCACCA |
ERF025-R | ACAAACTGGGAGCCACTACC | |
7 | Actin-F | CCAAGCAGCATGAAGATCAA |
Actin-R | CGTACTCGGCCTTTGAAATC |
表2
各样品测序质量
Sample name | Raw reads | Clean reads | Total mapped | Multiple mapped | Uniquely mapped | Q30(%) | GC content(%) |
---|---|---|---|---|---|---|---|
CK_1 | 49 583 710 | 47 599 094 | 4 4085 400(92.62%) | 969 397(2.04%) | 43 116 003(90.58%) | 90.32 | 42.98 |
CK_2 | 56 621 858 | 54 483 002 | 5 0100 087(91.96%) | 1 130 193(2.07%) | 48 969 894(89.88%) | 90.99 | 43.03 |
CK_3 | 50 230 428 | 47 972 778 | 4 4659 130(93.09%) | 965 148(2.01%) | 43 693 982(91.08%) | 90.53 | 43.03 |
F12_1 | 59 737 702 | 57 148 708 | 4 7984 291(83.96%) | 1 208 247(2.11%) | 46 776 044(81.85%) | 89.15 | 39.37 |
F12_2 | 60 120 416 | 57 845 042 | 4 9904 446(86.27%) | 1 231 084(2.13%) | 48 673 362(84.14%) | 90.09 | 40.06 |
F12_3 | 50 761 464 | 48 721 146 | 4 2563 180(87.36%) | 1 011 326(2.08%) | 41 551 854(85.29%) | 89.78 | 40.68 |
表3
上调差异表达基因的GO功能注释分析
功能描述 Description | 分类 Term_type | 差异基因数量 DEG_item |
---|---|---|
Cellular carbohydrate metabolic process | Biological process | 256 |
Cellular carbohydrate biosynthetic process | 212 | |
Single-organism carbohydrate metabolic process | 371 | |
Carbohydrate biosynthetic process | 232 | |
Cellular polysaccharide metabolic process | 205 | |
Phosphorylation | 521 | |
Cellular polysaccharide biosynthetic process | 184 | |
Polysaccharide metabolic process | 222 | |
Phosphate-containing compound metabolic process | 761 | |
Polysaccharide biosynthetic process | 185 | |
Photosynthetic electron transport chain | 19 | |
Lipopolysaccharide metabolic process | 128 | |
Lipopolysaccharide biosynthetic process | 128 | |
Phosphorus metabolic process | 761 | |
Protein phosphorylation | 447 | |
Cellular lipid metabolic process | 337 | |
Lipid biosynthetic process | 292 | |
Lipid metabolic process | 471 | |
Coenzyme metabolic process | 147 | |
Carbohydrate metabolic process | 537 | |
Cellular protein modification process | 634 | |
Protein modification process | 634 | |
Carbohydrate catabolic process | 77 | |
Oxidoreduction coenzyme metabolic process | 84 | |
Nucleoside diphosphate phosphorylation | 49 | |
Nucleotide phosphorylation | 49 | |
Nucleoside diphosphate metabolic process | 49 | |
Pyridine-containing compound metabolic process | 78 | |
Pyruvate metabolic process | 44 | |
Glycolytic process | 43 | |
ATP generation from ADP | 43 | |
Purine nucleoside diphosphate metabolic process | 43 | |
Purine ribonucleoside diphosphate metabolic process | 43 | |
Ribonucleoside diphosphate metabolic process | 43 | |
ADP metabolic process | 43 | |
Pyridine nucleotide metabolic process | 74 | |
Nicotinamide nucleotide metabolic process | 74 | |
Liposaccharide metabolic process | 167 | |
Response to hormone | 37 | |
Single-organism carbohydrate catabolic process | 56 | |
Cellulose metabolic process | 33 | |
Macromolecule modification | 683 | |
Carbohydrate derivative biosynthetic process | 287 | |
Photosynthetic electron transport in photosystem II | 9 | |
Response to endogenous stimulus | 38 | |
Inositol metabolic process | 9 | |
Cofactor metabolic process | 229 | |
Cellulose biosynthetic process | 29 | |
Carbohydrate derivative metabolic process | 409 | |
beta-glucan metabolic process | 39 | |
Inositol biosynthetic process | 6 | |
Polyol biosynthetic process | 6 | |
beta-glucan biosynthetic process | 35 | |
Protein kinase activity | Molecular function | 503 |
Kinase activity | 638 | |
Phosphotransferase activity, alcohol group as acceptor | 599 | |
Chlorophyll binding | 13 | |
Inorganic phosphate transmembrane transporter activity | 8 | |
Fructose-bisphosphate aldolase activity | 13 | |
Intramolecular lyase activity | 13 | |
Transferase activity, transferring phosphorus-containing groups | 948 | |
Transferase activity | 1 558 | |
Inositol-3-phosphate synthase activity | 6 |
表4
下调差异表达基因的GO功能注释分析
功能描述 Description | 分类 Term_type | 差异基因数量 DEG_item |
---|---|---|
Nuclear ubiquitin ligase complex | Cellular component | 96 |
Anaphase-promoting complex | 96 | |
Cullin-RING ubiquitin ligase complex | 101 | |
Ubiquitin ligase complex | 125 | |
Ubiquitin-protein transferase activity | Molecular function | 128 |
Ubiquitin-like protein transferase activity | 128 |
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