Cargando…

Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa

RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dep...

Descripción completa

Detalles Bibliográficos
Autores principales: Yun, Shiyu, Zhang, Xin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985633/
https://www.ncbi.nlm.nih.gov/pubmed/36871121
http://dx.doi.org/10.1038/s41598-023-30827-1
_version_ 1784900999731740672
author Yun, Shiyu
Zhang, Xin
author_facet Yun, Shiyu
Zhang, Xin
author_sort Yun, Shiyu
collection PubMed
description RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant.
format Online
Article
Text
id pubmed-9985633
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-99856332023-03-06 Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa Yun, Shiyu Zhang, Xin Sci Rep Article RNA interference is a highly conserved mechanism wherein several types of non-coding small RNAs regulate gene expression at the transcriptional or post-transcriptional level, modulating plant growth, development, antiviral defence, and stress responses. Argonaute (AGO), DCL (Dicer-like), and RNA-dependent RNA polymerase (RDR) are key proteins in this process. Here, these three protein families were identified in Chenopodium quinoa. Further, their phylogenetic relationships with Arabidopsis, their domains, three-dimensional structure modelling, subcellular localization, and functional annotation and expression were analysed. Whole-genome sequence analysis predicted 21 CqAGO, eight CqDCL, and 11 CqRDR genes in quinoa. All three protein families clustered into phylogenetic clades corresponding to those of Arabidopsis, including three AGO clades, four DCL clades, and four RDR clades, suggesting evolutionary conservation. Domain and protein structure analyses of the three gene families showed almost complete homogeneity among members of the same group. Gene ontology annotation revealed that the predicted gene families might be directly involved in RNAi and other important pathways. Largely, these gene families showed significant tissue-specific expression patterns, RNA-sequencing (RNA-seq) data revealed that 20 CqAGO, seven CqDCL, and ten CqRDR genes tended to have preferential expression in inflorescences. Most of them being downregulated in response to drought, cold, salt and low phosphate stress. To our knowledge, this is the first study to elucidate these key protein families involved in the RNAi pathway in quinoa, which are significant for understanding the mechanisms underlying stress responses in this plant. Nature Publishing Group UK 2023-03-04 /pmc/articles/PMC9985633/ /pubmed/36871121 http://dx.doi.org/10.1038/s41598-023-30827-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Yun, Shiyu
Zhang, Xin
Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title_full Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title_fullStr Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title_full_unstemmed Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title_short Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa
title_sort genome-wide identification, characterization and expression analysis of ago, dcl, and rdr families in chenopodium quinoa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9985633/
https://www.ncbi.nlm.nih.gov/pubmed/36871121
http://dx.doi.org/10.1038/s41598-023-30827-1
work_keys_str_mv AT yunshiyu genomewideidentificationcharacterizationandexpressionanalysisofagodclandrdrfamiliesinchenopodiumquinoa
AT zhangxin genomewideidentificationcharacterizationandexpressionanalysisofagodclandrdrfamiliesinchenopodiumquinoa