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Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes

Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post‐transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue‐specific miRNAs respon...

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Detalles Bibliográficos
Autores principales: Candar‐Cakir, Bilgin, Arican, Ercan, Zhang, Baohong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067666/
https://www.ncbi.nlm.nih.gov/pubmed/26857916
http://dx.doi.org/10.1111/pbi.12533
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author Candar‐Cakir, Bilgin
Arican, Ercan
Zhang, Baohong
author_facet Candar‐Cakir, Bilgin
Arican, Ercan
Zhang, Baohong
author_sort Candar‐Cakir, Bilgin
collection PubMed
description Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post‐transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue‐specific miRNAs responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought‐responsive tomato genotypes (Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved miRNAs belonging to 578 families were determined and 688 miRNAs were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 miRNA families. Drought‐related miRNAs and their targets were enriched functionally by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Totally, 53 miRNAs targeted 23 key drought stress‐ and tissue development‐related genes, including DRP (dehydration‐responsive protein), GTs (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II) protein, HD‐ZIP (homeodomain‐leucine zipper), MYB and NAC‐domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key miRNAs functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of miRNAs in drought response with plant hormone signal transduction and drought‐tolerant tomato breeding.
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spelling pubmed-50676662016-11-01 Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes Candar‐Cakir, Bilgin Arican, Ercan Zhang, Baohong Plant Biotechnol J Research Articles Drought stress has adverse impacts on plant production and productivity. MicroRNAs (miRNAs) are one class of noncoding RNAs regulating gene expression post‐transcriptionally. In this study, we employed small RNA and degradome sequencing to systematically investigate the tissue‐specific miRNAs responsible to drought stress, which are understudied in tomato. For this purpose, root and upground tissues of two different drought‐responsive tomato genotypes (Lycopersicon esculentum as sensitive and L. esculentum var. cerasiforme as tolerant) were subjected to stress with 5% polyethylene glycol for 7 days. A total of 699 conserved miRNAs belonging to 578 families were determined and 688 miRNAs were significantly differentially expressed between different treatments, tissues and genotypes. Using degradome sequencing, 44 target genes were identified associated with 36 miRNA families. Drought‐related miRNAs and their targets were enriched functionally by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Totally, 53 miRNAs targeted 23 key drought stress‐ and tissue development‐related genes, including DRP (dehydration‐responsive protein), GTs (glycosyltransferases), ERF (ethylene responsive factor), PSII (photosystem II) protein, HD‐ZIP (homeodomain‐leucine zipper), MYB and NAC‐domain transcription factors. miR160, miR165, miR166, miR171, miR398, miR408, miR827, miR9472, miR9476 and miR9552 were the key miRNAs functioning in regulation of these genes and involving in tomato response to drought stress. Additionally, plant hormone signal transduction pathway genes were differentially regulated by miR169, miR172, miR393, miR5641, miR5658 and miR7997 in both tissues of both sensitive and tolerant genotypes. These results provide new insight into the regulatory role of miRNAs in drought response with plant hormone signal transduction and drought‐tolerant tomato breeding. John Wiley and Sons Inc. 2016-02-09 2016-08 /pmc/articles/PMC5067666/ /pubmed/26857916 http://dx.doi.org/10.1111/pbi.12533 Text en © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution (http://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Candar‐Cakir, Bilgin
Arican, Ercan
Zhang, Baohong
Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title_full Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title_fullStr Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title_full_unstemmed Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title_short Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
title_sort small rna and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5067666/
https://www.ncbi.nlm.nih.gov/pubmed/26857916
http://dx.doi.org/10.1111/pbi.12533
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