Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied ...Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.31872063)。
文摘Small RNAs(sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, micro RNAs(mi RNAs) and phased small interfering RNAs(phasi RNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate mi RNAs and phasi RNAs. However, some computational annotations are rough and without careful manual check,resulting in low quality annotation. In this study, 19 public strawberry(Fragaria vesca) s RNA sequencing data from nine different tissues were collected to annotate mi RNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known mi RNAs, 27 mi RNA*s with notable abundance, 54 novel mi RNAs were accurately annotated. The terms of two mi RNAs were corrected from mi R477 b and mi R5225 using mi RN47 and mi R3627 h, respectively. Besides 21 nucleotides(nt) mi R390, eleven mi RNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasi RNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different mi RNAs(similar to the "two-hit" model) and the phasi RNA generating region located between two target sites. We speculate that one target site is in control of triggering phasi RNA biogenesis and the other target site define the boundary of the region of phasi RNA biogenesis,which likely provide an accurate way for phasi RNA generation. Overall, we provided a comprehensive and accurate annotation of mi RNAs and PHAS loci in the F. vesca genome.
