野生稻CBF/DREB1转录因子的鉴定与生物信息学分析

doi:10.11686/cyxb2023251

草业学报 ›› 2024, Vol. 33 ›› Issue (6): 126-144.DOI: 10.11686/cyxb2023251

• 研究论文 • 上一篇

野生稻CBF/DREB1转录因子的鉴定与生物信息学分析

霍晨敏¹(), 袁敏³, 张宝文², 王瑞菊²()

^1.河北经贸大学生物科学与工程学院，河北石家庄 050061
^2.分子细胞生物学教育部重点实验室，河北省细胞生物学基础学科研究中心，河北省细胞信号与环境适应协同创新中心，河北省分子细胞生物学重点实验室，河北师范大学生命科学学院，河北石家庄 050024
^3.华北理工大学生命科学学院，河北唐山 063210

收稿日期:2023-07-19 修回日期:2023-09-28 出版日期:2024-06-20 发布日期:2024-03-20
通讯作者: 王瑞菊
作者简介:E-mail： ruijuw@hebtu.edu.cn
霍晨敏（1978-），女，河北井陉人，副教授，博士。E-mail： huochenmin@163.com
基金资助:
河北省自然科学基金优秀青年科学基金项目(C2021205011);河北省重点研发计划项目(20326513D);河北经贸大学校内科研基金项目(2019ZD05);河北省教育厅科学研究项目(BJ2021029)

Genome-wide identification and bioinformatics analysis of CBF/DREB1 transcription factors in wild rice

Chen-min HUO¹(), Min YUAN³, Bao-wen ZHANG², Rui-ju WANG²()

^1.College of Bioscience and Engineering，Hebei University of Economics and Business，Shijiazhuang 050061，China
^2.Ministry of Education Key Laboratory of Molecular and Cellular Biology，Hebei Research Center of the Basic Discipline of Cell Biology，Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation，Hebei Key Laboratory of Molecular and Cellular Biology，College of Life Sciences，Hebei Normal University，Shijiazhuang 050024，China
^3.College of Life Sciences，North China University of Science and Technology，Tangshan 063210，China

Received:2023-07-19 Revised:2023-09-28 Online:2024-06-20 Published:2024-03-20
Contact: Rui-ju WANG

摘要/Abstract

摘要：

低温冷害是限制栽培稻地域分布和产量的重要因素之一，严重影响我国的粮食安全。以CBF/DREB1为核心的C-重复结合因子-冷调节基因（CBF-COR）途径是水稻适应低温的重要信号传导途径。基于稻属9种植物的全基因测序结果和隐马尔可夫模型（HMM）搜索，共鉴定出71个CBF/DREB1基因序列。所有基因均无内含子，由单个外显子组成。大部分DREB1s呈弱酸性，所有DREB1s亲水性平均值<0。进化树分析进一步将其分为3个组：DREB1A/1B/1H、DREB1C/1E/1F/1G和DREB1D/1I/1J，各组成员除AP2保守结构域和侧翼序列外，其他保守基序组成差别较大。适应性进化分析粳亚种和其他水稻的直系同源基因对，发现OsDREB1A/ObDREB1A、 OsDREB1D/OnDREB1D、OsDREB1I/OsIDREB1I和OsDREB1J/OsIDREB1J四对基因非同义替换/同义替换（Ka/Ks）值均>1，受到正选择压力。旁系同源基因之间启动子顺式元件种类和数量差异较大，直系同源基因的启动子顺式元件种类和数量很相似。对日本晴、93-11和东乡野生稻7 d幼苗4 ℃ 冷处理2 h的实时荧光定量PCR分析发现早期冷响应基因可分为激活型（DREB1A/1B/1C/1E/1F/1G/1H）和抑制型（DREB1D/1I/1J）。在日本晴、93-11和东乡野生稻冷激活型基因中，DREB1B/1G/1H均是冷处理后响应最快的一级冷响应因子，且启动子均含有至少一个拷贝的CAMTA转录因子结合元件CM2（CCGCGT）。OrDREB1B/1C/1E/1F/1G/1H在东乡野生稻4 ℃冷处理4 h后的表达量均高于栽培稻同源基因的表达量。9种稻属植物的CBF/DREB1基因亚家族的分子进化分析结果为低温抗性基因的挖掘和利用提供了前期基础。

关键词: 野生稻, CBF/DREB1, 保守基序, 选择压力, 启动子分析

Abstract:

Low temperature and cold damage are important factors limiting the regional distribution and yield of cultivated rice， and this seriously affects food security in China. The C-repeat binding factor cold-regulated gene （CBF-COR） pathway with CBF/DREB1 transcription factors as the core component is an important signal transduction pathway involved in the cold acclimation of rice. A total of 71 members of the CBF/DREB1 gene subfamily were identified based on whole genome sequencing results and hidden markov model （HMM） searches of nine species in the rice （Oryza） genus. All genes were intron-free and consisted of a single exon. Most of them encoded weakly acidic proteins. All putative DREB1 proteins had a grand average of hydropathicity （GRAVY） of <0. A phylogenetic analysis divided into three groups： Group I （DREB1A/1B/1H）， Group Ⅱ（DREB1C/1E/1F/1G）， and Group Ⅲ （DREB1D/1I/1J）. The motif composition differed among the groups， although all of the putative proteins contained the characteristic AP2 domain and flanking sequence. An adaptive evolutionary analysis of japonica subspecies and other rice orthologuous gene pairs showed that the nonsynonymous nucleotide substitution rate/synonymous nucleotide substitution rate （Ka/Ks） values for the gene pairs OsDREB1A/ObDREB1A， OsDREB1D/OnDREB1D，OsDREB1I/OsIDREB1I， and OsDREB1J/OsIDREB1J were greater than 1， indicating that they were under positive selection pressure. The types and numbers of promoter elements were similar in orthologs， but differed between paralogs. Real-time quantitative PCR analyses were conducted for 7-day-old seedlings of Nipponbare， 93-11 and Dongxiang wild rice after 2 hours of cold treatment at 4 ℃. The results showed that， during the early cold response， some DREB genes were activated （DREB1A/1B/1C/1E/1F/1G/1H） and others were inhibited （DREB1D/1I/1J）. Among the cold-activated genes in Nipponbare， 93-11， and Dongxiang wild rice， DREB1B/1G/1H were the first and the fastest to respond to cold. All of these three genes had at least one copy of the CAMTA transcription factor binding element CM2 （CCGCGT） in their promoter regions. The transcript levels of OrDREB1B/1C/1E/1F/1G/1H in Dongxiang wild ricewere higher than those of their homologs in cultivated rice after 4 hours of cold treatment at 4℃. The results of this molecular evolutionary study on the CBF/DREB1 gene subfamily in nine species in the Oryza genus provide a preliminary basis for the mining and utilization of low-temperature resistance genes.

Key words: wild rice, CBF/DREB1, motif, selective pressure, promoter analysis

霍晨敏, 袁敏, 张宝文, 王瑞菊. 野生稻CBF/DREB1转录因子的鉴定与生物信息学分析[J]. 草业学报, 2024, 33(6): 126-144.

Chen-min HUO, Min YUAN, Bao-wen ZHANG, Rui-ju WANG. Genome-wide identification and bioinformatics analysis of CBF/DREB1 transcription factors in wild rice[J]. Acta Prataculturae Sinica, 2024, 33(6): 126-144.

图/表 12

参考文献 49

1	Ding Y， Shi Y， Yang S. Molecular regulation of plant responses to environmental temperatures. Molecular Plant， 2020， 13（4）： 544-564.
2	Liu Y， Dang P， Liu L， et al. Cold acclimation by the CBF-COR pathway in a changing climate： Lessons from Arabidopsis thaliana. Plant Cell Reports， 2019， 38（5）： 511-519.
3	Zhang H， Zhu J， Gong Z， et al. Abiotic stress responses in plants. Nature Reviews Genetics， 2022， 23（2）： 104-119.
4	Park S， Gilmour S J， Grumet R， et al. CBF-dependent and CBF-independent regulatory pathways contribute to the differences in freezing tolerance and cold-regulated gene expression of two Arabidopsis ecotypes locally adapted to sites in Sweden and Italy. PLoS One， 2018， 13（12）： e0207723.
5	Stockinger E J， Gilmour S J， Thomashow M F. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE， a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proceedings of the National Academy of Sciences of the United States of America， 1997， 94（3）： 1035-1040.
6	Gilmour S J， Zarka D G， Stockinger E J， et al. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. The Plant Journal， 1998， 16（4）： 433-442.
7	Thomashow M F. Plant cold acclimation： Freezing tolerance genes and regulatory mechanisms. Annual Review of Plant Physiology and Plant Molecular Biology， 1999， 50： 571-599.
8	Hwarari D， Guan Y， Ahmad B， et al. ICE-CBF-COR signaling cascade and its regulation in plants responding to cold stress. International Journal of Molecular Sciences， 2022， 23（3）：1549.
9	Jaglo-Ottosen K R， Gilmour S J， Zarka D G， et al. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science， 1998， 280（5360）： 104-106.
10	Liu Q， Kasuga M， Sakuma Y， et al. Two transcription factors， DREB1 and DREB2， with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression， respectively， in Arabidopsis. The Plant Cell， 1998， 10（8）： 1391-1406.
11	Zhao C， Zhang Z， Xie S， et al. Mutational evidence for the critical role of CBF transcription factors in cold acclimation in Arabidopsis. Plant Physiology， 2016， 171（4）： 2744-2759.
12	Jia Y， Ding Y， Shi Y， et al. The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis. The New Phytologist， 2016， 212（2）： 345-353.
13	Wang L， Ma H， Lin J. Angiosperm-wide and family-level analyses of AP2/ERF genes reveal differential retention and sequence divergence after whole-genome duplication. Frontiers in Plant Science， 2019， 10： 196.
14	Nie Y， Guo L， Cui F， et al. Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms. Journal of Integrative Plant Biology， 2022， 64（11）： 2111-2125.
15	Canella D， Gilmour S J， Kuhn L A， et al. DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence. Biochimica et Biophysica Acta， 2010， 1799（5/6）： 454-462.
16	Li W， Chen Y， Ye M， et al. Evolutionary history of the C-repeat binding factor/dehydration-responsive element-binding 1 （CBF/DREB1） protein family in 43 plant species and characterization of CBF/DREB1 proteins in Solanum tuberosum. BMC Evolutionary Biology， 2020， 20（1）： 142.
17	Han J， Xie X， Zhang Y， et al. Evolution of the Dehydration-responsive element-binding protein subfamily in green plants. Plant Physiology， 2022， 190（1）： 421-440.
18	Skinner J S， Von Zitzewitz J， Szucs P， et al. Structural， functional， and phylogenetic characterization of a large CBF gene family in barley. Plant Molecular Biology， 2005， 59（4）： 533-551.
19	Dubouzet J G， Sakuma Y， Ito Y， et al. OsDREB genes in rice， Oryza sativa L.， encode transcription activators that function in drought-， high-salt- and cold-responsive gene expression. The Plant Journal， 2003， 33（4）： 751-763.
20	Ito Y， Katsura K， Maruyama K， et al. Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant & Cell Physiology， 2006， 47（1）： 141-153.
21	Chen J Q， Meng X P， Zhang Y， et al. Over-expression of OsDREB genes lead to enhanced drought tolerance in rice. Biotechnology Letters， 2008， 30（12）： 2191-2198.
22	Wang Q， Guan Y， Wu Y， et al. Overexpression of a rice OsDREB1F gene increases salt， drought， and low temperature tolerance in both Arabidopsis and rice. Plant Molecular Biology， 2008， 67（6）： 589-602.
23	Zhang Y， Chen C， Jin X F， et al. Expression of a rice DREB1 gene， OsDREB1D， enhances cold and high-salt tolerance in transgenic Arabidopsis. BMB Reports， 2009， 42（8）： 486-492.
24	Moon S J， Min M K， Kim J A， et al. Ectopic expression of OsDREB1G， a member of the OsDREB1 subfamily， confers cold stress tolerance in rice. Frontiers in Plant Science， 2019， 10： 297.
25	Wei S， Li X， Lu Z， et al. A transcriptional regulator that boosts grain yields and shortens the growth duration of rice. Science （New York， N.Y.）， 2022， 377（6604）： eabi8455.
26	Wing R A， Ammiraju J S， Luo M， et al. The Oryza map alignment project： the golden path to unlocking the genetic potential of wild rice species. Plant Molecular Biology， 2005， 59（1）： 53-62.
27	Tello-Ruiz M K， Naithani S， Gupta P， et al. Gramene 2021： Harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research， 2021， 49（D1）： 1452-1463.
28	Chen C， Chen H， Zhang Y， et al. TBtools： An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant， 2020， 13（8）： 1194-1202.
29	Letunic I， Bork P. Interactive tree of life （iTOL） v5： An online tool for phylogenetic tree display and annotation. Nucleic Acids Research， 2021， 49（W1）： 293-296.
30	Chen H， Song X， Shang Q， et al. CFVisual： An interactive desktop platform for drawing gene structure and protein architecture. BMC Bioinformatics， 2022， 23（1）： 178.
31	Wang Y， Tang H， Debarry J D， et al. MCScanX： A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research， 2012， 40（7）： e49.
32	Hurst L D. The Ka/Ks ratio： diagnosing the form of sequence evolution. Trends in Genetics， 2002， 18（9）： 486.
33	Wang D， Xiao Y， Chen H， et al. Combination of genomics， transcriptomics identifies candidate loci related to cold tolerance in Dongxiang wild rice. Plants （Basel）， 2022， 11（18）： 2329.
34	Brozynska M， Copetti D， Furtado A， et al. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal， 2017， 15（6）： 765-774.
35	Stein J C， Yu Y， Copetti D， et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation， turnover and innovation across the genus Oryza. Nature Genetics， 2018， 50（2）： 285-296.
36	Mao D， Chen C. Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway. PLoS One， 2012， 7（10）： e47275.
37	Doherty C J， Van Buskirk H A， Myers S J， et al. Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. The Plant Cell， 2009， 21（3）： 972-984.
38	Fay J C， Wu C I. Sequence divergence， functional constraint， and selection in protein evolution. Annual Review of Genomics and Human Genetics， 2003， 4： 213-235.
39	Zhang Z， Li J， Zhao X Q， et al. KaKs_Calculator： calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics， 2006， 4（4）： 259-263.
40	Li J， Zhang Z， Vang S， et al. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. Journal of Molecular Evolution， 2009， 68（4）： 414-423.
41	Zhang J， Luo W， Zhao Y， et al. Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice. New Phytologist， 2016， 211（4）： 1295-1310.
42	Salse J， Bolot S， Throude M， et al. Identification and characterization of shared duplications between rice and wheat provide new insight into grass genome evolution. The Plant Cell， 2008， 20（1）： 11-24.
43	Jiao Y， Li J， Tang H， et al. Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. The Plant Cell， 2014， 26（7）： 2792-2802.
44	Wang H， Lu S， Guan X， et al. Dehydration-responsive element binding protein 1C， 1E， and 1G promote stress tolerance to chilling， heat， drought， and salt in rice. Frontiers in Plant Science， 2022， 13： 851731.
45	Que Z， Lu Q， Shen C. Chromosome-level genome assembly of Dongxiang wild rice （Oryza rufipogon） provides insights into resistance to disease and freezing. Frontiers in Genetics， 2022， 13： 1029879.
46	Chinnusamy V， Ohta M， Kanrar S， et al. ICE1： A regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes & Development， 2003， 17（8）： 1043-1054.
47	Fursova O V， Pogorelko G V， Tarasov V A. Identification of ICE2， a gene involved in cold acclimation which determines freezing tolerance in Arabidopsis thaliana. Gene， 2009， 429（1/2）： 98-103.
48	Kidokoro S， Maruyama K， Nakashima K， et al. The phytochrome-interacting factor PIF7 negatively regulates DREB1 expression under circadian control in Arabidopsis. Plant Physiology， 2009， 151（4）： 2046-2057.
49	Choi M S， Kim M C， Yoo J H， et al. Isolation of a calmodulin-binding transcription factor from rice （Oryza sativa L.）. Journal of Biological Chemistry， 2005， 280（49）： 40820-40831.

元件名称Element name	序列 Sequence	重命名Rename
ABRE	ACGTG， CACGTG， CGCACGTGTC， GACACGTGGC， TACGGTC	ABA响应元件ABA responsive element
ABRE2	CCACGTGG	ABA响应元件ABA responsive element
ABRE3a	TACGTG	ABA响应元件ABA responsive element
ABRE4	CACGTA	ABA响应元件ABA responsive element
ARE	AAACCA	厌氧响应元件Anaerobic responsive element
TGA-element	AACGAC	生长素响应元件Auxin responsive element
DRE core	GCCGAC	CRT/DRE核心元件CRT/DRE core element
AAGAA-motif	GAAAGAA， gGTAAAGAAA	生长发育相关元件Development related element
as-1	TGACG	生长发育相关元件Development related element
ERE	ATTTTAAA	乙烯响应元件Ethylene-responsive element
P-box	CCTTTTG	赤霉素响应元件Gibberellin responsive element
AAAC-motif	CAATCAAAACCT	光响应元件Light responsive element
ACE	GACACGTATG	光响应元件Light responsive element
G-box	ACACGTGGC， ACACGTGT， CACGAC， CACGTG， CACGTT， CAGACGTGGCA， CCACGTAA， GCCACGTGGA， TACGTG	光响应元件Light responsive element
GT1-motif	GGTTAA， GGTTAAT	光响应元件Light responsive element
Sp1	GGGCGG， GGTTAAT， GTGTGTGAA	光响应元件Light responsive element
LTR	CCGAAA	低温响应元件Low-temperature responsive element
CGTCA-motif	CGTCA	茉莉酸甲酯响应元件MeJA responsive element
TGACG-motif	TGACG	茉莉酸甲酯响应元件MeJA responsive element
MRE	AACCTAA	MYB类转录因子结合位点MYB binding site
MBS	CAACTG	MYB类转录因子结合位点MYB binding site
MBSI	TTTTTACGGTTA， aaaAaaC（G/C）GTTA	MYB类转录因子结合位点MYB binding site
MYB	CAACAG， TAACCA	MYB类转录因子结合位点MYB binding site
Myb	CAACTG， TAACTG	MYB类转录因子结合位点MYB binding site
MYB recognition site	aaaAaaC（G/C）GTTA， CAACAG， CAACCA， CAACTG， CCGTTG， TAACCA， TAACTG， TTTTTACGGTTA	MYB类转录因子结合位点MYB binding site
Myb-binding site	CAACAG	MYB类转录因子结合位点MYB binding site
MYB-like sequence	TAACCA	MYB类转录因子结合位点MYB binding site
MYC	CATGTG， CATTTG	MYC类转录因子结合位点MYC binding site
Myc	TCTCTTA	MYC类转录因子结合位点MYC binding site
MYC binding site	CATTTG	MYC类转录因子结合位点MYC binding site
Sanaerobic responsive element	TTCGACCATCTT	水杨酸响应元件Salicylic acid responsive element
TCA-element	CCATCTTTTT， TCAGAAGAGG	水杨酸响应元件Salicylic acid responsive element
WUN-motif	AAATTACT， AAATTACTA， AAATTTCTT， CAATTACAT， CCATTTCAA， TAATTACTC， TTATTACAT	伤害反应元件Wounding responsive element
W box	TTGACC	WRKY类转录因子结合位点WRKY binding site

元件名称Element name	序列 Sequence	重命名Rename
ABRE	ACGTG， CACGTG， CGCACGTGTC， GACACGTGGC， TACGGTC	ABA响应元件ABA responsive element
ABRE2	CCACGTGG	ABA响应元件ABA responsive element
ABRE3a	TACGTG	ABA响应元件ABA responsive element
ABRE4	CACGTA	ABA响应元件ABA responsive element
ARE	AAACCA	厌氧响应元件Anaerobic responsive element
TGA-element	AACGAC	生长素响应元件Auxin responsive element
DRE core	GCCGAC	CRT/DRE核心元件CRT/DRE core element
AAGAA-motif	GAAAGAA， gGTAAAGAAA	生长发育相关元件Development related element
as-1	TGACG	生长发育相关元件Development related element
ERE	ATTTTAAA	乙烯响应元件Ethylene-responsive element
P-box	CCTTTTG	赤霉素响应元件Gibberellin responsive element
AAAC-motif	CAATCAAAACCT	光响应元件Light responsive element
ACE	GACACGTATG	光响应元件Light responsive element
G-box	ACACGTGGC， ACACGTGT， CACGAC， CACGTG， CACGTT， CAGACGTGGCA， CCACGTAA， GCCACGTGGA， TACGTG	光响应元件Light responsive element
GT1-motif	GGTTAA， GGTTAAT	光响应元件Light responsive element
Sp1	GGGCGG， GGTTAAT， GTGTGTGAA	光响应元件Light responsive element
LTR	CCGAAA	低温响应元件Low-temperature responsive element
CGTCA-motif	CGTCA	茉莉酸甲酯响应元件MeJA responsive element
TGACG-motif	TGACG	茉莉酸甲酯响应元件MeJA responsive element
MRE	AACCTAA	MYB类转录因子结合位点MYB binding site
MBS	CAACTG	MYB类转录因子结合位点MYB binding site
MBSI	TTTTTACGGTTA， aaaAaaC（G/C）GTTA	MYB类转录因子结合位点MYB binding site
MYB	CAACAG， TAACCA	MYB类转录因子结合位点MYB binding site
Myb	CAACTG， TAACTG	MYB类转录因子结合位点MYB binding site
MYB recognition site	aaaAaaC（G/C）GTTA， CAACAG， CAACCA， CAACTG， CCGTTG， TAACCA， TAACTG， TTTTTACGGTTA	MYB类转录因子结合位点MYB binding site
Myb-binding site	CAACAG	MYB类转录因子结合位点MYB binding site
MYB-like sequence	TAACCA	MYB类转录因子结合位点MYB binding site
MYC	CATGTG， CATTTG	MYC类转录因子结合位点MYC binding site
Myc	TCTCTTA	MYC类转录因子结合位点MYC binding site
MYC binding site	CATTTG	MYC类转录因子结合位点MYC binding site
Sanaerobic responsive element	TTCGACCATCTT	水杨酸响应元件Salicylic acid responsive element
TCA-element	CCATCTTTTT， TCAGAAGAGG	水杨酸响应元件Salicylic acid responsive element
WUN-motif	AAATTACT， AAATTACTA， AAATTTCTT， CAATTACAT， CCATTTCAA， TAATTACTC， TTATTACAT	伤害反应元件Wounding responsive element
W box	TTGACC	WRKY类转录因子结合位点WRKY binding site

引物名称Primers name	序列 Sequence （5'-3'）	引物名称Primers name	序列 Sequence （5'-3'）
DREB1A-qFP	ACCGACGACGACGAGGAGTC	DREB1H-qFP	CGAAATGGACTACGACACGTACTA
DREB1A-qRP	GCCAAGCTCGCGTAGTACAGGT	DREB1H-qRP	GAGACAGTGTCAGAGCTCAGTAGC
DREB1B-qFP	GGCGACGAAGAAGAAGACAACAAG	DREB1I-qFP	GAGCCTGTACTACGCGAGCTTA
DREB1B-qRP	GTAGTACGACCCGGCGTCCATC	DREB1I-qRP	TCAGCGATGTCGCTTGAGTC
DREB1C-qFP	GAGTTGGAGCTAGCAGTTTTGAG	DREB1J-qFP	ATGCGCACCGATCTGTACTT
DREB1C-qRP	TAGCTGTATAGGAGGAGCAAAGC	DREB1J-qRP	ACAAACGATCCTTTTGTGTTCTG
DREB1D-qFP	CAAAGCTTATCAGCAGTAGC	OsIDREB1A-qFP	ACCGACGACGAGGAGGAGTCCG
DREB1D-qRP	GGTTAGTAGCAGAAAGACTTG	OsIDREB1G-qRP	GCCACCTACGGCAGGATCAC
DREB1E-qFP	GAATTCGAAATGCAGGGGTA	OrDREB1I-qRP	TCAGCGATGTCGCCTGAGTC
DREB1E-qRP	CTCGCAGTCGTAGTCCTCCT	OsIDREB1J-qFP	ATGCGCGCCGATCTGTACTACG
DREB1F-qFP	AGGACGCCATCTTCGACAT	OrDREB1J-qFP	ATGCGCGCCGATCTGTACTA
DREB1F-qRP	GTCGAGAGATCTCCCAATCG	OrDREB1J-qRP	ACACAACGATCCTTTTGTGTTCTG
DREB1G-qFP	CCCGTACTACGAGGTCATGG	ACTIN1-qF659	ACATCGCCCTGGACTATGACCA
DREB1G-qRP	GCTACCTACGGCAGGATCAC	ACTIN1-qR1095	GTCGTACTCAGCCTTGGCAAT

引物名称Primers name	序列 Sequence （5'-3'）	引物名称Primers name	序列 Sequence （5'-3'）
DREB1A-qFP	ACCGACGACGACGAGGAGTC	DREB1H-qFP	CGAAATGGACTACGACACGTACTA
DREB1A-qRP	GCCAAGCTCGCGTAGTACAGGT	DREB1H-qRP	GAGACAGTGTCAGAGCTCAGTAGC
DREB1B-qFP	GGCGACGAAGAAGAAGACAACAAG	DREB1I-qFP	GAGCCTGTACTACGCGAGCTTA
DREB1B-qRP	GTAGTACGACCCGGCGTCCATC	DREB1I-qRP	TCAGCGATGTCGCTTGAGTC
DREB1C-qFP	GAGTTGGAGCTAGCAGTTTTGAG	DREB1J-qFP	ATGCGCACCGATCTGTACTT
DREB1C-qRP	TAGCTGTATAGGAGGAGCAAAGC	DREB1J-qRP	ACAAACGATCCTTTTGTGTTCTG
DREB1D-qFP	CAAAGCTTATCAGCAGTAGC	OsIDREB1A-qFP	ACCGACGACGAGGAGGAGTCCG
DREB1D-qRP	GGTTAGTAGCAGAAAGACTTG	OsIDREB1G-qRP	GCCACCTACGGCAGGATCAC
DREB1E-qFP	GAATTCGAAATGCAGGGGTA	OrDREB1I-qRP	TCAGCGATGTCGCCTGAGTC
DREB1E-qRP	CTCGCAGTCGTAGTCCTCCT	OsIDREB1J-qFP	ATGCGCGCCGATCTGTACTACG
DREB1F-qFP	AGGACGCCATCTTCGACAT	OrDREB1J-qFP	ATGCGCGCCGATCTGTACTA
DREB1F-qRP	GTCGAGAGATCTCCCAATCG	OrDREB1J-qRP	ACACAACGATCCTTTTGTGTTCTG
DREB1G-qFP	CCCGTACTACGAGGTCATGG	ACTIN1-qF659	ACATCGCCCTGGACTATGACCA
DREB1G-qRP	GCTACCTACGGCAGGATCAC	ACTIN1-qR1095	GTCGTACTCAGCCTTGGCAAT

物种 Species	基因 Gene	基因号 Gene ID	定位 Location	起始 Start	终止 Stop	方向 Strand	蛋白长度Protein length （aa）	分子量Molecular weight （Da）	等电点pI	亲水性平均值GRAVY
粳亚种 O. sativa subsp. japonica	OsDREB1A	Os09g0522200	chr09	20403413	20404332	-	238	25390.11	5.05	-0.39
	OsDREB1B	Os09g0522000	chr09	20395262	20395703	-	218	23237.90	5.22	-0.30
	OsDREB1C	Os06g0127100	chr06	1434770	1435533	+	214	23110.47	5.01	-0.54
	OsDREB1D	Os06g0165600	chr06	3310919	3311822	+	253	27668.15	10.18	-0.03
	OsDREB1E	Os04g0572400	chr04	28820861	28821520	+	219	23899.74	5.44	-0.48
	OsDREB1F	Os01g0968800	chr01	42727426	42728261	+	219	23817.55	5.80	-0.68
	OsDREB1G	Os02g0677300	chr02	27652935	27654206	+	224	23946.50	5.14	-0.54
	OsDREB1H	Os09g0522100	chr09	20399458	20400198	-	246	25491.17	5.29	-0.34
	OsDREB1I	Os08g0545500	chr08	27320678	27325475	-	251	26811.70	4.64	-0.28
	OsDREB1J	Os08g0545400	chr08	27320517	27321388	-	236	24470.15	5.54	-0.32
籼亚种 O. sativa subsp. indica	OsIDREB1A	BGIOSGA029415	chr09	19178562	19179278	-	238	25404.14	5.06	-0.39
	OsIDREB1B	BGIOSGA029417	chr09	19170261	19170917	-	218	23238.88	5.10	-0.30
	OsIDREB1C	BGIOSGA022219	chr06	1598848	1599492	+	214	23110.47	5.01	-0.54
	OsIDREB1E	BGIOSGA016950	chr04	27628706	27629365	+	219	23899.74	5.44	-0.48
	OsIDREB1F	BGIOSGA005257	chr01	46762939	46763598	+	219	23817.55	5.80	-0.68
	OsIDREB1G	BGIOSGA008804	chr02	29450768	29451442	+	224	23962.56	5.14	-0.52
	OsIDREB1H	BGIOSGA029416	chr09	19174204	19174944	-	246	25491.17	5.29	-0.34
	OsIDREB1I	NA	chr08	29128839	29129559	-	243	27931.30	12.24	-0.93
	OsIDREB1J	BGIOSGA026545	chr08	29120126	29121120	-	236	24534.21	5.54	-0.35
普通野生稻 O. rufipogon	OrDREB1A	ORUFI09G18210	chr09	17999596	18000312	-	238	25390.11	5.05	-0.39
	OrDREB1B	ORUFI09G18190	chr09	17991615	17992271	-	218	23238.88	5.10	-0.30
	OrDREB1C	ORUFI06G01550	chr06	1230570	1231214	+	214	23046.38	4.92	-0.54
	OrDREB1E	ORUFI04G23890	chr04	24364699	24365358	+	219	23899.74	5.44	-0.48
	OrDREB1F	ORUFI01G48730	chr01	39412759	39413418	+	219	23817.55	5.80	-0.68
	OrDREB1G	ORUFI02G29230	chr02	25864920	25865594	+	224	23916.48	5.14	-0.53
	OrDREB1H	ORUFI09G18200	chr09	17995213	17995953	-	246	25530.23	5.47	-0.35
	OrDREB1I	NA	chr08	24822909	24823679	-	256	27386.35	4.66	-0.31
	OrDREB1J	NA	chr08	24819129	24819836	-	235	24341.05	5.35	-0.31
尼瓦拉野生稻 O. nivara	OnDREB1A	ONIVA09G17900	chr09	18116554	18117270	-	238	25390.11	5.05	-0.39
	OnDREB1B	ONIVA09G17880	chr09	18108246	18108902	-	218	23238.88	5.10	-0.30
	OnDREB1C	ONIVA06G01850	chr06	1249828	1250472	+	214	23046.38	4.92	-0.54
	OnDREB1D	NA	chr06	3798236	3798798	+	173	18310.85	10.76	-0.25
	OnDREB1E	ONIVA04G20840	chr04	21515072	21515731	+	219	23899.74	5.44	-0.48
	OnDREB1F	ONIVA01G51530	chr01	42411945	42412604	+	219	23817.55	5.80	-0.68
	OnDREB1G	ONIVA02G30790	chr02	27408992	27409666	+	224	23962.56	5.14	-0.52
	OnDREB1H	ONIVA09G17890	chr09	18112192	18112932	-	246	25588.26	5.30	-0.36
	OnDREB1I	NA	chr08	25758472	25759224	-	251	26781.67	4.64	-0.28
	OnDREB1J	NA	chr08	25754653	25755363	-	236	24462.08	5.54	-0.33
短舌野生稻 O. barthii	ObDREB1A	OBART09G16830	chr09	16640128	16644591	-	312	33320.37	4.26	-0.40
	ObDREB1B	OBART09G16810	chr09	16632280	16632819	-	179	19948.40	10.60	-0.64
	ObDREB1E	OBART04G22220	chr04	21530282	21530941	+	219	23899.74	5.44	-0.48
	ObDREB1F	OBART01G45260	chr01	36416371	36417081	+	236	24506.98	5.06	-0.36
	ObDREB1G	OBART02G27760	chr02	24261105	24261779	+	224	23946.50	5.14	-0.55
非洲栽培稻 O. glaberrima	OgDREB1B	ORGLA09G0133000	chr09	15159598	15160254	-	218	23266.93	5.10	-0.29
	OgDREB1E	ORGLA04G0192900	chr04	20672896	20673555	+	219	23899.74	5.44	-0.48
	OgDREB1F	ORGLA01G0390500	chr01	32189602	32190261	+	219	23817.55	5.80	-0.68
	OgDREB1H	ORGLA09G0133100	chr09	15163537	15164277	-	246	25517.20	5.29	-0.35
	OgDREB1I	ORGLA08G0220100	chr08	441680	442435	+	251	26795.70	4.64	-0.28
	OgDREB1J	ORGLA08G0220200	chr08	445553	446263	+	236	24486.15	5.54	-0.32
展颖野生稻 O. glumipatula	OglDREB1A	OGLUM09G17430	chr09	20529148	20529864	-	238	25390.11	5.05	-0.39
	OglDREB1E	OGLUM04G22260	chr04	26252832	26253491	+	219	23899.74	5.44	-0.48
	OglDREB1G	OGLUM02G28340	chr02	28942831	28943505	+	224	23916.48	5.14	-0.53
	OglDREB1H	OGLUM09G17420	chr09	20525066	20525806	-	246	25536.23	5.47	-0.32
	OglDREB1J	OGLUM08G23770	chr08	25986834	25987544	-	236	24456.12	5.54	-0.32
南方野生稻 O. meridionalis	OmDREB1A	OMERI09G12490	chr09	16142040	16142759	-	239	25577.27	4.90	-0.42
	OmDREB1C	OMERI06G01670	chr06	1429888	1430526	+	212	22852.15	4.82	-0.58
	OmDREB1D	OMERI12G13360	chr12	18179855	18180932	+	228	25010.51	11.78	-0.47
	OmDREB1E	OMERI04G18770	chr04	23800496	23801143	+	215	23629.56	5.59	-0.47
	OmDREB1F	OMERI01G42070	chr01	41472214	41472876	+	220	23919.72	5.64	-0.67
	OmDREB1G	OMERI02G26980	chr02	29016115	29016789	+	224	23930.50	5.14	-0.54
	OmDREB1H	OMERI09G12480	chr09	16137270	16137995	-	241	25299.09	5.61	-0.36
	OmDREB1I	NA	chr08	20572535	20573305	-	256	27354.35	4.66	-0.28
	OmDREB1J	NA	chr08	20569698	20573305	-	236	24530.23	5.36	-0.34
斑点野生稻 O. punctata	OpDREB1A	OPUNC09G15290	chr09	23779185	23779904	-	239	25478.09	4.87	-0.38
	OpDREB1B	OPUNC09G15260	chr09	23772250	23772933	-	227	24492.23	4.74	-0.34
	OpDREB1C	OPUNC06G01430	chr06	895238	895870	+	210	22853.28	5.02	-0.54
	OpDREB1E	OPUNC04G19970	chr04	27121978	27122628	+	216	23735.51	5.43	-0.57
	OpDREB1F	OPUNC01G44220	chr01	45661375	45662049	+	224	24248.14	6.44	-0.64
	OpDREB1G	OPUNC02G25480	chr02	30411907	30412581	+	224	23890.42	5.25	-0.52
	OpDREB1H	OPUNC09G15280	chr09	23775668	23776438	-	256	27201.04	5.48	-0.46
	OpDREB1J	NA	chr08	28670355	28671059	-	234	24164.03	6.21	-0.22

野生稻CBF/DREB1转录因子的鉴定与生物信息学分析

Genome-wide identification and bioinformatics analysis of CBF/DREB1 transcription factors in wild rice

RichHTML

PDF (PC)

可视化

摘要/Abstract

引用本文

使用本文

图/表 12

参考文献 49

相关文章 0

编辑推荐

Metrics

基因1 Gene 1	基因2 Gene 2	Ka	Ks	Ka/Ks
OsDREB1A	ObDREB1A	0.075375	0.049444	1.52445763
OsIDREB1A	ObDREB1A	0.077660	0.055665	1.39514429
OglDREB1A	ObDREB1A	0.075375	0.055665	1.35408984
OnDREB1A	ObDREB1A	0.075375	0.049444	1.52445763
OrDREB1A	ObDREB1A	0.075375	0.049444	1.52445763
OsDREB1D	OnDREB1D	2.309537	1.229761	1.87803706
OmDREB1D	OnDREB1D	2.198006	1.180527	1.86188509
OgDREB1H	OglDREB1H	0.011198	0.010161	1.10202539
OsDREB1I	OsIDREB1I	0.098510	0.094181	1.04597363
OsIDREB1I	OnDREB1I	0.098510	0.094181	1.04597363
OsDREB1J	OsIDREB1J	0.009646	0.005386	1.79101378
OsIDREB1J	OnDREB1J	0.009653	0.005376	1.79538389