Chin Bull Bot ›› 2018, Vol. 53 ›› Issue (5): 625-633.doi: 10.11983/CBB17169

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

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:2018-11-29 Published:2018-09-01
  • Contact: Bai Jie E-mail:baijie@scu.edu.cn
  • About author:

    † These authors contributed equally to this paper

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

Figure 1

Length distribution of tRFs in three types of pollens in rice male gameteunm: Uni-nucleate microspore; bcp: Bi-cellular pollen; tcp : Tri-cellular pollen; RPM: Reads per million"

Figure 2

tRFs’ starting and ending site distribution in tRNAs’ universal cloverleaf structure sections in three types of pollens in rice male gamete(A) Schematic view of tRNAs’ cloverleaf-like secondary structure; (B) tRFs’ starting site positions in tRNA; (C) tRFs’ ending site positions in tRNA. * indicate that the numbers before can only be regarded as a positions represented in Figure 2A instead of base ID. unm, bcp, tcp and RPM see Figure 1."

Figure 3

tRFs’ 5’ end base bias in three types of pollens in rice male gamete(A) tRF starting site’s distribution in each position of their host tRNA (The vertical axis labels’ positions were transferred according to their square root number); (B) First 8 base logo of the tRNAs that produce tRFs from the 1st base in bcp; (C) First 8 base logo of tRNAs that produce tRFs from the 2nd base in bcp; (D) First 8 base logo of the tRNAs that produce tRFs from the 1st base in tcp; (E) First 8 base logo of tRNAs that produce tRFs from the 2nd base in tcp. unm, bcp, tcp and RPM see Figure 1."

Figure 4

Sequence motif logo for tRNA 8 mer around cleavage sites in three types of pollens in rice male gamete(A), (D) Sequence logo of all tRNA’s first 7 bases of D loop and Anticodon loop; (B) For bcp tRFs ended at the 3rd base of D loop; (C) For tcp tRFs started at the 7th base of D loop; (E) For bcp tRFs ended at the 1st base of Anticodon loop; (F) For tcp tRFs started at the 6th base of Anticodon loop. The position between 4 and 5 in X axis of Figure B, C, E and F stand for cleavage site."

Table 1

tRFs targeted loci of non-TE and TE genes"

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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