《植物生理学报》 2014, 50(4): 483-487

萱草microRNAs生物信息学及与冷冻相关microRNAs的分析

安凤霞^1,2, 卢宝伟³, 梁鸣², 唐焕伟², 李富恒^1,*

¹东北农业大学生命科学学院, 哈尔滨150030; ²黑龙江省科学院自然与生态研究所, 湿地与生态保育国家地方联合工程实验室, 黑龙江省特色动植物利用工程技术研究中心, 哈尔滨150040; ³黑龙江生态工程职业学院, 哈尔滨150025

通信作者：李富恒；E-mail: an_fengxia@163.com；Tel: 0451-86050321

摘　要：

microRNA是一类长度为16~29 nt的非蛋白质编码的内源小分子RNA (sRNA), 在植物生长发育以及逆境胁迫响应等过程中发挥着重要作用。本文利用基于HiSeq原理的sRNA深度测序技术, 结合生物信息学方法对萱草根系中已知miRNA的类型、丰度以及部分与冷冻胁迫相关的已知miRNA的功能进行了分析。结果表明, 在10 ℃常温和–25 ℃低温条件下萱草根系中分别有14 843 184和16 072 575条序列信息, 代表14 064 385和15 309 725种sRNA片段, 且sRNA均呈现正态分布特征; 在非编码RNA中转运RNA (tRNA)、核糖体RNA (rRNA)所占比例较大。低温sRNA组中得到注释的sRNA有67 411种, 共计799 994条sRNA片段; 常温sRNA组中, 得到注释的sRNA有66 524种, 共计1 055 466条sRNA片段。冷冻胁迫下, 萱草通过提高miR393、miR397、miR396的表达量和降低miR319的表达量来增强其抗冻性。本研究为后续揭示萱草低温应答蛋白合成的调控机理, 筛选抗冻关键调控基因提供了丰富的数据。

关键词：萱草; miRNA; 生物信息学; 低温; 深度测序

收稿：2013-12-04   修定：2014-03-25

资助：黑龙江省森工总局科技计划项目(sgzjY2010026)和黑龙江省科学院科学研究基金项目。

Bioinformatics, Expression and Functional Analysis of microRNAs in Response to Low Temperature in Hemerocallis fulva (L.) L.

AN Feng-Xia^1,2, LU Bao-Wei³, LIANG Ming², TANG Huan-Wei², LI Fu-Heng^1,*

¹School of Life Sciences, Northeast Agricultural University, Harbin 150030, China; ²Natural and Ecological Institute, Heilongjiang Academy of Sciences, National and Provincial Joint Engineering Laboratory of Wetlands and Ecological Conservation, Characteristic Animal and Plant Utilization Engineering Technology Research Center of Heilongjiang Province, Harbin 150040, China; ³Heilongjiang Vocational Institute of Ecological Engineering, Harbin 150025, China

Corresponding author: LI Fu-Heng; E-mail: an_fengxia@163.com; Tel: 0451-86050321

Abstract:

MicroRNAs (miRNAs), as endogenous small non-coding single-stranded RNAs of 16–29 nt, play a prominent role in the process of growth, development and responses to environmental stresses in plants. The miRNAs in response to low temperature in Hemerocallis fulva roots were identified using deep-sequencing technique in combination with bioinformatics prediction. A total of 14 843 184 and 16 072 575 RNA sequences were explored under normal and low temperature conditions, which represented 14 064 385 and 15 309 725 types of small RNA (sRNA), respectively. The sRNA showed a normal distribution. Through GenBank and Rfam comparison analysis, rRNA and tRNA accounts for a larger proportion in non-coding RNA. Totally 799 994 sRNA in 67 411 types were annotated under low temperature, and 1 055 466 sRNAs in 66 524 types were annotated under normal temperature. miR393, miR397 and miR396 were up-regulated and miR319 was downregulated at low temperature. This research provides rich data for illuminating the regulatory mechanism of protein synthesis and screening the key regulatory genes in response to low temperature.

Key words: Hemerocallis fulva; miRNA; bioinformatics; low temperature; deep-sequencing