植物学报 ›› 2018, Vol. 53 ›› Issue (5): 625-633.doi: 10.11983/CBB17169

• 研究报告 • 上一篇    下一篇

水稻雄配子体发育过程中tRNA片段的生物信息学分析

刘魏1, 童永鳌1,2, 白洁1,*()   

  1. 1四川大学生命科学学院, 生物资源与生态环境教育部重点实验室, 成都 610064
    2成都无糖信息技术有限公司, 成都 610041
  • 收稿日期:2017-09-06 接受日期:2017-11-16 出版日期:2018-09-01 发布日期:2018-11-29
  • 通讯作者: 白洁 E-mail:baijie@scu.edu.cn
  • 作者简介:

    作者简介: 路安民(图中左), 植物系统分类学家。20世纪60-70年代编著《中国植物志》等, 后从事植物系统发育和进化研究。“七五”以来主持了4项中科院、国家自然科学基金委重大和重点项目。1991年获国务院颁发的有突出贡献科学家荣誉证书。1987年8月-1990年12月担任中科院植物所所长。

  • 基金资助:
    国家自然科学基金(No.31070276)

Bioinformatics Analysis of tRNA-derived Fragments in Rice Male Gametophyte Development

Liu Wei1, Tong Yong’ao1,2, Bai Jie1,*()   

  1. 1Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
    2Chengdu WuTang Information Technology Co Ltd, Chengdu 610041, China
  • Received:2017-09-06 Accepted:2017-11-16 Online:2018-09-01 Published:2018-11-29
  • Contact: Bai Jie E-mail:baijie@scu.edu.cn
  • About author:

    † These authors contributed equally to this paper

摘要:

tRNA片段(tRF)是tRNA通过非随机剪切产生的RNA片段, 其产生和功能机制尚不明确; 而在水稻(Oryza sativa)雄配子体发育过程中, 人们对tRNA更是知之甚少。通过高通量测序, 在水稻雄配子体发育过程中发现了长度范围较大的tRFs; 进一步采用logo对tRFs两端的序列进行分析, 发现了4个有序列特征(其中3个未见报道)和1个无序列特征的酶切位点; 通过NCBI Blast预测了tRF靶基因, 发现其大多靶向转座因子。研究结果对揭示tRF产生机制以及水稻雄配子体发育研究有一定的参考价值。

关键词: 水稻, 雄配子体, 花粉, tRNA片段, 生物信息学

Abstract:

tRNA derived fragments (termed tRFs) are functional RNAs produced by non-random cleavage of tRNAs. The knowledge of tRNAs’ production and function is being studied but is unknown in the rice male gametophyte. Using high-throughput sequencing with 3 stages in the rice male gametophyte development, we found tRFs with a large range of length. Next, we determined four sequence-specific and one non-sequence-specific ribonuclease cleaving sites. We also summarized the distribution profile of tRFs in the three stages. Finally, a NCBI blast search was carried out to predict the tRF target gene, revealing that the major class of targets was transposable elements. This results provid new clues for rice male gametophyte research.

Key words: rice, male gametophyte, pollen, tRFs, bioinformatics

图1

水稻雄配子三类花粉中的tRF长度分布 unm: 单核小孢子; bcp: 二细胞花粉; tcp: 三细胞花粉; RPM: 每百万条读段里的(目标)读段数"

图2

水稻雄配子三类花粉的tRF起始和终止位点在四叶草结构中的分布 (A) tRNA二级结构示意图; (B) tRF起点分布; (C) tRF终点分布。*代表图2A中数字的位置, 不代表碱基编号。unm、bcp、tcp及RPM同图1。"

图3

水稻雄配子三类花粉的tRF 5’端碱基分布偏好性(A) 起始于tRNA各个位置的tRF起点碱基分布情况(纵坐标各点相对位置进行了1/2次幂变形处理); (B) bcp样品中tRF起始于tRNA第1位时, 对应宿主tRNA前8个碱基logo图; (C) bcp样品中tRF起始于tRNA第2位时, 对应宿主tRNA前8个碱基logo图; (D) tcp样品中tRF起始于tRNA第1位时, 对应宿主tRNA前8个碱基logo图; (E) tcp样品中tRF起始于tRNA第2位时, 对应宿主tRNA前8个碱基logo图。unm、bcp、tcp和RPM同图1。"

图4

水稻雄配子三类花粉的tRNA剪切位置周围碱基分布(A), (D) 所有tRNA的D环和反密码子环上前7个碱基分布logo图; (B) bcp于D环第3个碱基终止的tRF对应tRNA序列logo图; (C) tcp于D环第7个碱基起始的tRF对应tRNA序列logo图; (E) bcp于反密码子环第1个碱基终止的tRF对应tRNA序列logo图; (F) tcp于反密码子环第6个碱基起始的tRF对应tRNA序列logo图。除了图A和D, 各图横轴4和5之间为“剪切发生位置”。"

表1

被靶向的非TE基因和TE数的对比"

Sample No. of non-TE
genes
No. of genic
TEs
No. of
intergenic
TEs
TE
Percentage
(%)
unm 317 166 506 67.95
bcp 728 403 905 64.24
tcp 529 287 736 65.91
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