Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp.
Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp.
复制标题
Argonaute、Dicer 样和 RNA 依赖性 RNA 聚合酶基因家族的全基因组鉴定和表征及其在草莓属中的表达分析。
作者：
在植物的生长发育过程中，一些非编码小RNA （non-coding small RNA, sRNAs）不仅在转录后水平介导RNA干扰，而且在转录水平对染色质修饰也起着重要的调控作用。在这些过程中，蛋白因子Argonaute （AGO）、Dicer-like （DCL）和RNA依赖性RNA聚合酶（RDR）分别在sRNAs的合成中起着非常重要的作用。虽然在许多植物中已经发现了这些基因家族，但对草莓中这些基因家族的信息知之甚少。本研究利用全基因组分析和系统发育方法，从二倍体草莓Fragaria vesca中鉴定出13个AGO基因、6个DCL基因和9个RDR基因。在八倍体草莓Fragaria x ananassa中鉴定出33个AGO、18个DCL和28个RDR基因，研究了这些基因在草莓不同组织和发育阶段的表达模式，并研究了这些基因对某些激素的响应，发现几乎所有基因都对5种激素胁迫有响应。本研究首次报道了Fragaria spp. AGO， DCL和RDR基因家族的全基因组分析，提供了这些基因的基本基因组信息和表达模式。此外，本研究为进一步研究这些基因的功能提供了基础，并为二倍体和八倍体草莓的进化提供了一些证据。
In the growth and development of plants, some non-coding small RNAs (sRNAs) not only mediate RNA interference at the post-transcriptional level, but also play an important regulatory role in chromatin modification at the transcriptional level. In these processes, the protein factors Argonaute (AGO), Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) play very important roles in the synthesis of sRNAs respectively. Though they have been identified in many plants, the information about these gene families in strawberry was poorly understood. In this study, using a genome-wide analysis and a phylogenetic approach, 13 AGO, six DCL, and nine RDR genes were identified in diploid strawberry Fragaria vesca. We also identified 33 AGO, 18 DCL, and 28 RDR genes in octoploid strawberry Fragaria × ananassa, studied the expression patterns of these genes in various tissues and developmental stages of strawberry, and researched the response of these genes to some hormones, finding that almost all genes respond to the five hormone stresses. This study is the first report of a genome-wide analysis of AGO, DCL, and RDR gene families in Fragaria spp., in which we provide basic genomic information and expression patterns for these genes. Additionally, this study provides a basis for further research on the functions of these genes and some evidence for the evolution between diploid and octoploid strawberries.
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