Comprehensive Characterization of miRNA and PHAS Loci in the Diploid Strawberry (Fragaria vesca) Genome
Comprehensive Characterization of miRNA and PHAS Loci in the Diploid Strawberry (Fragaria vesca) Genome
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二倍体草莓 (Fragaria vesca) 基因组中 miRNA 和 PHAS 位点的综合表征
DOI：
10.1016/j.hpj.2019.11.004
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发表时间：
2019-11-01
影响因子：
5.7
通讯作者：
Liu, Yuanlong
中科院分区：
文献类型：
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作者：
Feng, Lei;Xia, Rui;Liu, Yuanlong
小分子RNA（smallRNAs，sRNAs）是基因表达的重要调控因子，参与多种生物学过程。其中，microRNA（miRNAs）和phased small interfering RNAs（phasiRNAs）在过去几十年中得到了很好的定义和研究。开发了一系列脚本或管道来注释miRNAs和phasiRNAs。然而，一些计算注释是粗糙的，没有仔细的人工检查，导致低质量的注释。本研究收集了19份草莓（Fragaria uesca）9种不同组织的sRNA测序数据，对F.维斯卡经过生物信息学分析和仔细的手工检查，准确注释了167种已知的miRNA、27种丰度较高的miRNA*、54种新的miRNA。分别使用miRN 47和miR 3627 h从miR 477 b和miR 5225校正两种miRNAs的项。除了21个核苷酸（nt）的miR 390外，草莓中11个长度为22-nt的miRNAs负责触发来自110个PHAS位点的21-nt phasiRNAs的生物合成。特别是，我们发现几个PHAS基因座被两种不同的miRNA靶向（类似于“两次击中”模型），并且phasiRNA产生区域位于两个靶位点之间。我们推测一个靶位点控制触发phasiRNA生物发生，而另一个靶位点限定了phasiRNA生物发生区域的边界，这可能为phasiRNA的产生提供了准确的方法。总的来说，我们提供了一个全面和准确的注释的miRNA和PHAS基因座在F。vesca基因组
Small RNAs (sRNAs) are vital regulators of gene expression and involved in various biological processes. Among them, microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) have been well defined and studied in the past decades. A bunch of scripts or pipelines were developed to annotate miRNAs and phasiRNAs. However, some computational annotations are rough and without careful manual check, resulting in low quality annotation. In this study, 19 public strawberry (Fragaria uesca) sRNA sequencing data from nine different tissues were collected to annotate miRNAs and PHAS loci in F. vesca. After bioinformatics analysis and careful manual checking, 167 known miRNAs, 27 miRNA*s with notable abundance, 54 novel miRNAs were accurately annotated. The terms of two miRNAs were corrected from miR477b and miR5225 using miRN47 and miR3627h, respectively. Besides 21 nucleotides (nt) miR390, eleven miRNAs with a length of 22-nt are in charge of triggering the biogenesis of 21-nt phasiRNAs from 110 PHAS loci in strawberry. In particular, we found several PHAS loci were targeted by two different miRNAs (similar to the "two-hit" model) and the phasiRNA generating region located between two target sites. We speculate that one target site is in control of triggering phasiRNA biogenesis and the other target site define the boundary of the region of phasiRNA biogenesis, which likely provide an accurate way for phasiRNA generation. Overall, we provided a comprehensive and accurate annotation of miRNAs and PHAS loci in the F. vesca genome.