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

doi:10.11983/CBB17169

Abstract

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

Liu Wei, Tong Yong’ao, Bai Jie. Bioinformatics Analysis of tRNA-derived Fragments in Rice Male Gametophyte Development[J]. Chinese Bulletin of Botany, 2018, 53(5): 625-633.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB17169

https://www.chinbullbotany.com/EN/Y2018/V53/I5/625

Figures/Tables 5

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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