Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles

Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles

<i>Fusarium</i> wilt (<i>FW</i>) of cucumber (<i>Cucumis sativus</i> L.) caused by <i>Fusarium oxysporum</i> f. sp. <i>cucumerinum</i> (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. M...

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Autores principales: Jun Xu, Qianqian Xian, Ningyuan Zhang, Ke Wang, Xin Zhou, Yansong Li, Jingping Dong, Xuehao Chen
Formato: article
Lenguaje:EN
Publicado: MDPI AG 2021
Materias:
cucumber
miRNA
transcriptome
<i>Fusarium</i> wilt
resistance
Microbiology
QR1-502
Acceso en línea:https://doaj.org/article/948aad17fb994374bb2ca81c0283fdff
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spelling oai:doaj.org-article:948aad17fb994374bb2ca81c0283fdff2021-11-25T16:52:52ZIdentification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles10.3390/biom111116202218-273Xhttps://doaj.org/article/948aad17fb994374bb2ca81c0283fdff2021-11-01T00:00:00Zhttps://www.mdpi.com/2218-273X/11/11/1620https://doaj.org/toc/2218-273X<i>Fusarium</i> wilt (<i>FW</i>) of cucumber (<i>Cucumis sativus</i> L.) caused by <i>Fusarium oxysporum</i> f. sp. <i>cucumerinum</i> (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to <i>FW</i> remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar ‘Rijiecheng’, which is resistant to <i>FW</i>. The integrated analysis identified <i>FW</i>-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that <i>JRL3</i> (<i>Csa2G362470</i>), which is targeted by <i>miR319a</i>, and <i>BEE1</i> (<i>Csa1G024150</i>), <i>DAHP1</i> (<i>Csa2G369040</i>), and <i>PERK2</i> (<i>Csa4G642480</i>), which are targeted by <i>miR6300</i>, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that <i>miR319a</i>-<i>JRL3</i>, <i>miR6300</i>-<i>BEE1</i>, <i>miR6300</i>-<i>DAHP1</i> and <i>miR6300</i>-<i>PERK2</i> regulate cucumber defenses against <i>FW</i>, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to <i>FW</i>.Jun XuQianqian XianNingyuan ZhangKe WangXin ZhouYansong LiJingping DongXuehao ChenMDPI AGarticlecucumbermiRNAtranscriptome<i>Fusarium</i> wiltresistanceMicrobiologyQR1-502ENBiomolecules, Vol 11, Iss 1620, p 1620 (2021)
institution DOAJ
collection DOAJ
language EN
topic cucumber
miRNA
transcriptome
<i>Fusarium</i> wilt
resistance
Microbiology
QR1-502
spellingShingle cucumber
miRNA
transcriptome
<i>Fusarium</i> wilt
resistance
Microbiology
QR1-502
Jun Xu
Qianqian Xian
Ningyuan Zhang
Ke Wang
Xin Zhou
Yansong Li
Jingping Dong
Xuehao Chen
Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
description <i>Fusarium</i> wilt (<i>FW</i>) of cucumber (<i>Cucumis sativus</i> L.) caused by <i>Fusarium oxysporum</i> f. sp. <i>cucumerinum</i> (Foc) is a destructive soil-borne disease that severely decreases cucumber yield and quality worldwide. MicroRNAs (miRNAs) are small non-coding RNAs (sRNAs) that are important for regulating host immunity because they affect target gene expression. However, the specific miRNAs and the miRNA/target gene crosstalk involved in cucumber resistance to <i>FW</i> remain unknown. In this study, we compared sRNA-seq and RNA-seq data for cucumber cultivar ‘Rijiecheng’, which is resistant to <i>FW</i>. The integrated analysis identified <i>FW</i>-responsive miRNAs and their target genes. On the basis of verified expression levels, we detected two highly expressed miRNAs with down-regulated expression in response to Foc. Moreover, an analysis of 21 target genes in cucumber inoculated with Foc indicated that <i>JRL3</i> (<i>Csa2G362470</i>), which is targeted by <i>miR319a</i>, and <i>BEE1</i> (<i>Csa1G024150</i>), <i>DAHP1</i> (<i>Csa2G369040</i>), and <i>PERK2</i> (<i>Csa4G642480</i>), which are targeted by <i>miR6300</i>, are expressed at high levels, but their expression is further up-regulated after Foc inoculation. These results imply that <i>miR319a</i>-<i>JRL3</i>, <i>miR6300</i>-<i>BEE1</i>, <i>miR6300</i>-<i>DAHP1</i> and <i>miR6300</i>-<i>PERK2</i> regulate cucumber defenses against <i>FW</i>, and provide the gene resources that may be useful for breeding programs focused on developing new cucumber varieties with enhanced resistance to <i>FW</i>.
format article
author Jun Xu
Qianqian Xian
Ningyuan Zhang
Ke Wang
Xin Zhou
Yansong Li
Jingping Dong
Xuehao Chen
author_facet Jun Xu
Qianqian Xian
Ningyuan Zhang
Ke Wang
Xin Zhou
Yansong Li
Jingping Dong
Xuehao Chen
author_sort Jun Xu
title Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
title_short Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
title_full Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
title_fullStr Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
title_full_unstemmed Identification of miRNA-Target Gene Pairs Responsive to <i>Fusarium</i> Wilt of Cucumber via an Integrated Analysis of miRNA and Transcriptome Profiles
title_sort identification of mirna-target gene pairs responsive to <i>fusarium</i> wilt of cucumber via an integrated analysis of mirna and transcriptome profiles
publisher MDPI AG
publishDate 2021
url https://doaj.org/article/948aad17fb994374bb2ca81c0283fdff
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