Cargando…

Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum

RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stres...

Descripción completa

Detalles Bibliográficos
Autores principales: Cui, Dong-Li, Meng, Jian-Yu, Ren, Xiao-Yan, Yue, Jing-Jing, Fu, Hua-Ying, Huang, Mei-Ting, Zhang, Qing-Qi, Gao, San-Ji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413343/
https://www.ncbi.nlm.nih.gov/pubmed/32764599
http://dx.doi.org/10.1038/s41598-020-70061-7
_version_ 1783568774810566656
author Cui, Dong-Li
Meng, Jian-Yu
Ren, Xiao-Yan
Yue, Jing-Jing
Fu, Hua-Ying
Huang, Mei-Ting
Zhang, Qing-Qi
Gao, San-Ji
author_facet Cui, Dong-Li
Meng, Jian-Yu
Ren, Xiao-Yan
Yue, Jing-Jing
Fu, Hua-Ying
Huang, Mei-Ting
Zhang, Qing-Qi
Gao, San-Ji
author_sort Cui, Dong-Li
collection PubMed
description RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stress-resistance genes in modern sugarcane cultivars (Saccharum spp.) were originated from wild species of Saccharum, for example S. spontaneum. Here, we used genome-wide analysis and a phylogenetic approach to identify four DCL, 21 AGO and 11 RDR genes in the S. spontaneum genome (termed SsDCL, SsAGO and SsRDR, respectively). Several genes, particularly some of the SsAGOs, appeared to have undergone tandem or segmental duplications events. RNA-sequencing data revealed that four SsAGO genes (SsAGO18c, SsAGO18b, SsAGO10e and SsAGO6b) and three SsRDR genes (SsRDR2b, SsRDR2d and SsRDR3) tended to have preferential expression in stem tissue, while SsRDR5 was preferentially expressed in leaves. qRT-PCR analysis showed that SsAGO10c, SsDCL2 and SsRDR6b expressions were strongly upregulated, whereas that of SsAGO18b, SsRDR1a, SsRDR2b/2d and SsRDR5 was significantly depressed in S. spontaneum plants exposed to PEG-induced dehydration stress or infected with Xanthomonas albilineans, causal agent of leaf scald disease of sugarcane, suggesting that these genes play important roles in responses of S. spontaneum to biotic and abiotic stresses.
format Online
Article
Text
id pubmed-7413343
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-74133432020-08-10 Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum Cui, Dong-Li Meng, Jian-Yu Ren, Xiao-Yan Yue, Jing-Jing Fu, Hua-Ying Huang, Mei-Ting Zhang, Qing-Qi Gao, San-Ji Sci Rep Article RNA silencing is a conserved mechanism in eukaryotic organisms to regulate gene expression. Argonaute (AGO), Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) proteins are critical components of RNA silencing, but how these gene families’ functions in sugarcane were largely unknown. Most stress-resistance genes in modern sugarcane cultivars (Saccharum spp.) were originated from wild species of Saccharum, for example S. spontaneum. Here, we used genome-wide analysis and a phylogenetic approach to identify four DCL, 21 AGO and 11 RDR genes in the S. spontaneum genome (termed SsDCL, SsAGO and SsRDR, respectively). Several genes, particularly some of the SsAGOs, appeared to have undergone tandem or segmental duplications events. RNA-sequencing data revealed that four SsAGO genes (SsAGO18c, SsAGO18b, SsAGO10e and SsAGO6b) and three SsRDR genes (SsRDR2b, SsRDR2d and SsRDR3) tended to have preferential expression in stem tissue, while SsRDR5 was preferentially expressed in leaves. qRT-PCR analysis showed that SsAGO10c, SsDCL2 and SsRDR6b expressions were strongly upregulated, whereas that of SsAGO18b, SsRDR1a, SsRDR2b/2d and SsRDR5 was significantly depressed in S. spontaneum plants exposed to PEG-induced dehydration stress or infected with Xanthomonas albilineans, causal agent of leaf scald disease of sugarcane, suggesting that these genes play important roles in responses of S. spontaneum to biotic and abiotic stresses. Nature Publishing Group UK 2020-08-06 /pmc/articles/PMC7413343/ /pubmed/32764599 http://dx.doi.org/10.1038/s41598-020-70061-7 Text en © The Author(s) 2020 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Cui, Dong-Li
Meng, Jian-Yu
Ren, Xiao-Yan
Yue, Jing-Jing
Fu, Hua-Ying
Huang, Mei-Ting
Zhang, Qing-Qi
Gao, San-Ji
Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title_full Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title_fullStr Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title_full_unstemmed Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title_short Genome-wide identification and characterization of DCL, AGO and RDR gene families in Saccharum spontaneum
title_sort genome-wide identification and characterization of dcl, ago and rdr gene families in saccharum spontaneum
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413343/
https://www.ncbi.nlm.nih.gov/pubmed/32764599
http://dx.doi.org/10.1038/s41598-020-70061-7
work_keys_str_mv AT cuidongli genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT mengjianyu genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT renxiaoyan genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT yuejingjing genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT fuhuaying genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT huangmeiting genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT zhangqingqi genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum
AT gaosanji genomewideidentificationandcharacterizationofdclagoandrdrgenefamiliesinsaccharumspontaneum