Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp

Xiaotong Jing; Linlin Xu; Xinjia Huai; Hong Zhang; Fengli Zhao; Yushan Qiao

doi:10.3390/genes14010121

Genome-Wide Identification and Characterization of Argonaute, Dicer-like and RNA-Dependent RNA Polymerase Gene Families and Their Expression Analyses in Fragaria spp

Genes (Basel). 2023 Jan 1;14(1):121. doi: 10.3390/genes14010121.

Authors

Xiaotong Jing¹, Linlin Xu², Xinjia Huai¹, Hong Zhang¹, Fengli Zhao¹, Yushan Qiao^{1

2}

Affiliations

¹ Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China.
² Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China.

Abstract

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.

Keywords: AGO; DCL; RDR; evolution; expression; identification; strawberries.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Fragaria* / metabolism
Genes, Plant
Phylogeny
RNA-Dependent RNA Polymerase* / genetics
RNA-Dependent RNA Polymerase* / metabolism

Substances

RNA-Dependent RNA Polymerase

Grants and funding

This research was funded by the National Natural Science Foundation of China, grant number 31872056 and 32072540, the Fundamental Research Funds for the Central Universities, grant number KYZZ2022004, the Key Research and Development Program of Ningxia Hui Autonomous Region, grant number 2021BBF02016, and the Jiangsu Province Agricultural Science and Technology Innovation Fund Projects, grant number CX(20)2021.