Genome-Wide Identification and Analysis of Small Nucleolar RNAs and Their Roles in Regulating Latex Regeneration in the Rubber Tree (Hevea brasiliensis).

Xiang Chen,Zhi Deng,Dingwei Yu,Wenguan Wu,Xiao Huang,Huasun Huang,Xiaofei Zhang,Qun Liang,Zewei An,Han Cheng

doi:10.3389/fpls.2021.731484

Abstract

Small nucleolar RNAs (snoRNAs) are a class of conserved nuclear RNAs that play important roles in the modification of ribosomal RNAs (rRNAs) in plants. In rubber trees, rRNAs are run off with latex flow during tapping and need to be regenerated for maintaining the functions of the laticifer cells. SnoRNAs are expected to play essential roles in the regeneration of rRNAs. However, snoRNAs in the rubber tree have not been sufficiently characterized thus far. In this study, we performed nuclear RNA sequencing (RNA-seq) to identify snoRNAs globally and investigate their roles in latex regeneration. We identified a total of 3,626 snoRNAs by computational prediction with nuclear RNA-seq data. Among these snoRNAs, 50 were highly expressed in latex; furthermore, the results of reverse transcription polymerase chain reaction (RT-PCR) showed the abundant expression of 31 of these snoRNAs in latex. The correlation between snoRNA expression and adjusted total solid content (TSC/C) identified 13 positively yield-correlated snoRNAs. To improve the understanding of latex regeneration in rubber trees, we developed a novel insulated tapping system (ITS), which only measures the latex regenerated in specific laticifers. Using this system, a laticifer-abundant snoRNA, HbsnoR28, was found to be highly correlated with latex regeneration. To the best of our knowledge, this is the first report to globally identify snoRNAs that might be involved in latex regeneration regulation and provide new clues for unraveling the mechanisms underlying the regulation of latex regeneration.

Highlights

Small nucleolar RNAs, which range from 50 to 300 nt in size (Kiss, 2002), are a distinct class of non-coding RNAs that play important roles in ribosomal RNA maturation by guiding ribose 2 -O-methylation or pseudouridylation modification of the precursor ribosomal RNAs (rRNAs) (Tollervey and Kiss, 1997; Bachellerie et al, 2002; Watkins and Bohnsack, 2012)
We identified a total of 3,626 snoRNAs by this extensive analysis, and showed that 50 of them were highly expressed in latex; the expression of 31 out of the 50 snoRNAs in latex was confirmed by reverse transcription polymerase chain reaction (RT-PCR)
To identify snoRNAs globally in the rubber tree, we constructed two complementary DNA (cDNA) libraries using the total RNAs extracted from the nuclei of the latex (Figure 1A) and leaves (Figure 1B) of the rubber tree

Summary

Introduction

Small nucleolar RNAs (snoRNAs), which range from 50 to 300 nt in size (Kiss, 2002), are a distinct class of non-coding RNAs (ncRNAs) that play important roles in ribosomal RNA (rRNA) maturation by guiding ribose 2 -O-methylation or pseudouridylation modification of the precursor rRNA (Tollervey and Kiss, 1997; Bachellerie et al, 2002; Watkins and Bohnsack, 2012). SnoRNAs Related to Latex Regeneration and 3 -end D box sequence (CUGA), and some contain less conserved internal copies of each box, known as C’ box and D’ box, respectively (Watkins et al, 2000; Kiss, 2002; Lui and Lowe, 2013). This subclass of snoRNAs guides methylation at the 2 -hydroxyl group (2 -O-ribose methylation) in rRNAs, transfer RNAs (tRNAs), and small nuclear RNAs (snRNAs) (Brown et al, 2003). H/ACA box snoRNAs guide pseudouridine modification in rRNAs and snRNAs, which convert uridine into pseudouridine ( ) (Tollervey and Kiss, 1997; Watkins and Bohnsack, 2012)

Methods

Results

Conclusion