Bioinformatics analysis of miR169 gene family in Brassica napus L. and prediction of their target genes

doi:10.3969/j.issn.1004-1524.2018.08.01

›› 2018, Vol. 30 ›› Issue (8): 1273-1280.DOI: 10.3969/j.issn.1004-1524.2018.08.01

• Crop Science • Previous Articles Next Articles

Bioinformatics analysis of miR169 gene family in Brassica napus L. and prediction of their target genes

RUAN Xianle, WANG Junsheng, LIU Hongzhan, CHEN Liangbing, ZHAO Jinhui

College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou 466001, China

Received:2017-09-30 Online:2018-08-25 Published:2018-08-28

Abstract

Abstract: To understand the miR169 gene family in oilseed rape, the bioinformatics method was used to analyze the chromosomal location, molecular evolution, conservatism of the precursor sequence, promoter and target gene of the members of the miR169 gene family. The results showed that miR169 gene family members were distributed in 9 chromosomes. Evolution analysis showed that these genes were divided into two groups. The precursor sequence was highly conserved at the position where the mature miRNA was formed. There were 13 main elements in the upstream promoter of the miR169 genes, endosperm expression element, anaerobic stress component, thermal response element and MBS had the most quantities. miR169 gene family had a total of 16 target genes, most of which belong to the NF-YA gene family. The results laid a good foundation for further research on the function of miR169 gene family in oilseed rape.

Key words: Brassica napus L., miR169 gene family, target gene, bioinformatics

CLC Number:

S565.4

RUAN Xianle, WANG Junsheng, LIU Hongzhan, CHEN Liangbing, ZHAO Jinhui. Bioinformatics analysis of miR169 gene family in Brassica napus L. and prediction of their target genes[J]. , 2018, 30(8): 1273-1280.

References

[1] JONESRHOADES M W, BARTEL D P, BARTEL B.MicroRNAS and their regulatory roles in plants[J]. Annual Review of Plant Biology, 2006, 57(1): 19-53.
[2] JUNG J H, SEO P J, PARK C M.MicroRNA biogenesis and function in higher plants[J]. Plant Biotechnology Reports, 2009, 3(2): 111-126.
[3] JONESRHOADES M W, BARTEL D P.Computational identification of plant microRNAs and their targets, including a stress-induced miRNA[J]. Molecular Cell, 2004, 14(6): 787-799.
[4] LELANDAISBRIERE C, SORIN C, DECLERCK M, et al.Small RNA diversity in plants and its impact in development[J]. Current Genomics, 2010, 11(1): 14-23.
[5] CHEN X.Small RNAs and their roles in plant development[J]. Annual Review of Cell and Developmental Biology, 2009, 25(1): 21-44.
[6] 熊雪梅. 盐芥冷响应miRNA表达模式分析及tsa-miR396功能初探[D]. 哈尔滨: 东北林业大学, 2014.
XIONG X M.Profiling of chilling-stress-responsive miRNAs and preliminary study on tsa-miR396 in Thellungiella salsuginea [D]. Harbin: Northeast Forestry University, 2014. (in Chinese with English abstract)
[7] LIU H H, TIAN X, LI Y J, et al.Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana[J]. RNA, 2008, 14(5): 836-843.
[8] 杨凤玺. MIR396在烟草中的功能分析[D]. 北京:中国科学院研究生院, 2009.
YANG F X.The function analysis of miR396 in tobacco [D]. Beijing: Graduate University of Chinese Academy of Sciences, 2009. (in Chinese with English abstract)
[9] 张晓娜. 枳(Poncirus trifoliata)低温相关microRNAs鉴定及ptf-miR396b抗寒功能研究[D]. 武汉: 华中农业大学, 2015.
ZHANG X N.Identification of cold responsive microRNAs and characterization of ptf-miR396b Poncirus trifoliate[D]. Wuhan: Huazhong Agricultural University, 2015. (in Chinese with English abstract)
[10] 高鹏. 水稻冷胁迫相关miRNA基因的预测及冷胁迫相关性验证[D].哈尔滨:东北农业大学,2008.
GAO P.Prediction of rice cold stress related miRNA genes and verification of their relativity with cold stress[D]. Haerbing: Northeast Agricultural University, 2008. (in Chinese with English abstract)
[11] 肖霞. 落叶松miR396对体细胞胚发育的调控及GRF基因的表达研究[D]. 北京: 中国林业科学研究院, 2015.
XIAO X.The regulation of miR396 and expression analysis of GRF gene in somatic embryo development of Larix leptolepis[D]. Beijing: Chinese Academy of Forestry, 2015. (in Chinese with English abstract)
[12] MIYASHIMA S, HONDA M, HASHIMOTO K, et al.A comprehensive expression analysis of the Arabidopsis MICRORNA165/6 gene family during embryogenesis reveals a conserved role in meristem specification and a non-cell-autonomous function[J]. Plant and Cell Physiology, 2013, 54(3): 375-384.
[13] KNAUER S, HOLT A L, RUBIO-SOMOZA I, et al.A protodermal miR394 signal defines a region of stem cell competence in the Arabidopsis shoot meristem[J]. Developmental Cell, 2013, 24(2): 125-132.
[14] 徐妙云, 朱佳旭, 张敏,等. 植物miR169/NF-YA调控模块研究进展[J]. 遗传, 2016, 38(8): 700-706.
XU M Y, ZHU J X, ZHANG M, et al.Advances on plant miR169/NF-YA regulation modules[J]. Hereditas, 2016, 38(8): 700-706. (in Chinese with English abstract)
[15] LI Y J,FU Y R,JI L S, et al.Characterization and expression analysis of the Arabidopsis miR169 family[J]. Plant Science, 2010, 178(3) : 271-280.
[16] PANG B D, MUSIALAK-LANGE M, NUC P, et al.Identification of nutrient responsive Arabidosis and rapeseed microRNAs by comprehensive real time polymerase china reaction profiling and small RNA sequecing[J]. Plant and Physiology, 2009, 150(3): 1541-1555.
[17] LI W X, OONO Y, ZHU J, et al.The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance[J]. Plant Cell, 2008, 20(8): 2238-2251.
[18] ZHAO B, GE L, LIANG R, et al.Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor[J]. BMC Molecular Biology, 2009, 10(1): 1-10.
[19] CALVIÑO M, MESSING J. Discovery of microRNA169 gene copies in genomes of flowering plants through positional information[J]. Genome Biology and Evolution, 2013, 5(2): 402-417.
[20] 栾明达. 玉米miR169及其靶基因NFYA转录因子功能的初步研究[D]. 绵阳: 西南科技大学, 2014.
LUAN M D.Research of zma-miR169s and their targeted trandcription factor ZmNFYAs in Maize [D]. Mianyang: Southwest University of Science and Technology, 2014. (in Chinese with English abstract)
[21] 舒李露, 孙志超, 张玮, 等. 山核桃miR169克隆及功能分析[J]. 核农学报, 2017, 31(8): 1453-1462.
SHU L L, SUN Z C, ZHANG W, et al.Cloning and functional analysis of miR169 from Carya cathayensis[J]. Journal of Nuclear Agricultural Sciences, 2017, 31(8): 1453-1462. (in Chinese with English abstract)
[22] 尹海龙. 大豆miR169d的表达分析及功能验证[D]. 长春: 吉林农业大学,2013.
YIN H L.Expression analysis and characterization of Gma-miR169d[D]. Changchun: Jilin Agricultural University, 2013. (in Chinese with English abstract)
[23] 刘志祥, 曾超珍, 谭晓风. 杨树MIR169 基因家族分子进化分析[J]. 遗传, 2013, 35(11) : 1307-1316.
LIU Z X, ZENG C Z, TAN X F.Molecular evolution of the poplar MIR169 gene family[J]. Hereditas, 2013, 35(11) : 1307-1316. (in Chinese with English abstract)
[24] 李会. 甘蓝型油菜(Brassica napus)miR394 a/b/c及其靶基因F-box的克隆、载体构建和转化[D]. 南京: 南京农业大学, 2010.
LI H.Clonging, construction and transformation of miR394 a/b/c and its target F-bor from Brassica napus[D]. Nanjing: Nanjing Agricultural University, 2010. (in Chinese with English abstract)
[25] 张芸. 镉胁迫下油菜(Brassica napus)miRNA的表达分析、miR395d过表达载体的构建及转化[D]. 南京: 南京农业大学, 2009.
ZHANG Y.Transcript analysis of Cd-regulated miRNAs from Brassica napus and miR395d vector construction and transformation[D]. Nanjing: Nanjing Agricultural University, 2009. (in Chinese with English abstract)
[26] 张柳伟. miR395调节油菜(Brassica napus)耐镉功能的研究[D]. 南京: 南京农业大学, 2012.
ZHANG L W.Functional characterization of miR395 in regulation of tolerance of Brassica napus to cadmium [D]. Nanjing: Nanjing Agricultural University, 2012. (in Chinese with English abstract)
[27] 黄思齐. 镉胁迫下水稻和油菜中microRNA的克隆、鉴定与miR395功能分析[D]. 南京: 南京农业大学, 2010.
HUANG S Q.Isolation and identification of microRNA in Oryza sativa and Branssica napus under Cd stress and functional characterization of miR395[D]. Nanjing: Nanjing Agricultural University, 2010. (in Chinese with English abstract)
[28] 董云. 油菜(Brassica napus)miRNA的鉴定及Bna-miR1140表达调控机制研究[D]. 石河子: 石河子大学, 2012.
DONG Y.Identification of miRNAs from Brassica napus and expression regulation of Bna-miR1140 [D]. Shihezi: Shihezi University, 2012. (in Chinese with English abstract)
[29] 董云, 王毅, 靳丰蔚, 等. 油菜Bna-miR169d基因的分离与过表达初步分析[J]. 西北农业学报, 2016, 25(12): 1809-1815.
DONG Y, WANG Y, JIN F W, et al.Isolation and preliminary overexpression of bna-miR169d gene in Oilseed rape[J]. Acta Agriculturae Boreali-occidentalis Sinica, 2016, 25(12): 1809-1815. (in Chinese with English abstract)
[30] 陶庆. 油菜抗逆响应bna-miR169及其靶基因BnNF-YA的表达分析[D]. 南京: 南京农业大学, 2015.
TAO Q.Characterization of stress responsive bna-miR169 and its targer genes BnNF-YA in canola (Brassica napus) [D]. Nanjing: Nanjing Agricultural University, 2015. (in Chinese with English abstract)
[31] 吴金海, 焦靖芝, 谢伶俐, 等. 氧化石墨烯处理对甘蓝型油菜生长发育的影响[J]. 基因组学与应用生物学, 2015, 34(12): 2738-3742.
WU J H, JIAO J Z, XIE L L, et al.Effects of graphene oxide on growth and development of Brassica napus L.[J]. Genomics and Applied Biology, 2015, 34(12): 2738-3742. (in Chinese with English abstract)
[32] FAHLGREN N, HOWELL M D, KASSCHAU K D, et al.High-throughput sequencing of, Arabidopsis, microRNAs: Evidence for frequent birth and death of, MIRNA, genes[J]. Plos One, 2007, 2(2): e219.
[33] 方辉, 曲俊杰, 孙嘉曼, 等. 葡萄miR169及其靶基因的生物信息学分析[J]. 南方农业学报, 2017, 48(8): 1329-1334.
FANG H, QU J J, SUN J M, et al.Bioinformatics analysis for miR169 and its target gene in Vitis vinifera[J]. Journal of Southern Agriculture, 2017, 48(8): 1329-1334. (in Chinese with English abstract)
[34] ZHAO B, GE L, LIANG R, et al.Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor[J]. BMC Molecular Biology, 2009, 10(1): 1-10.
[35] SINHA S, MAITY S N, LU J, et al.Recombinant rat CBF-C, the third subunit of CBF/NFY, allows formation of a protein-DNA complex with CBF-A and CBF-B and with yeast HAP2 and HAP3[J]. Proceedings of the National Academy of Sciences of the United States of America, 1995, 92(5): 1624-1628.

Bioinformatics analysis of miR169 gene family in Brassica napus L. and prediction of their target genes

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