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Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches

Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we perfor...

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Autores principales: Shi, Mengya, Hu, Xiao, Wei, Yu, Hou, Xu, Yuan, Xue, Liu, Jun, Liu, Yueping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751202/
https://www.ncbi.nlm.nih.gov/pubmed/29236054
http://dx.doi.org/10.3390/ijms18122599
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author Shi, Mengya
Hu, Xiao
Wei, Yu
Hou, Xu
Yuan, Xue
Liu, Jun
Liu, Yueping
author_facet Shi, Mengya
Hu, Xiao
Wei, Yu
Hou, Xu
Yuan, Xue
Liu, Jun
Liu, Yueping
author_sort Shi, Mengya
collection PubMed
description Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA). Our analyses identified 24 evolutionarily conserved miRNA genes as well as 16 predicted genes. Experimental verification showed that the expression levels of miR398 and miR408b were significantly upregulated after NAA treatment, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were significantly downregulated. Degradome sequencing coupled with miRNA target prediction analyses detected 119 significant cleavage sites on several mRNA targets, including SQUAMOSA promoter binding protein–like (SPL), ARF, (NAM, ATAF1/2 and CUC2) NAC, Arabidopsis thaliana homeobox protein (ATHB), the homeodomain-leucine zipper transcription factor revoluta(REV), (teosinte-like1, cycloidea and proliferating cell factor1) TCP and auxin signaling F-box protein (AFB) family genes. Our systematic profiling of miRNAs and the degradome in peach fruit suggests the existence of a post-transcriptional regulation network of miRNAs that target auxin pathway genes in fruit development.
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spelling pubmed-57512022018-01-08 Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches Shi, Mengya Hu, Xiao Wei, Yu Hou, Xu Yuan, Xue Liu, Jun Liu, Yueping Int J Mol Sci Article Auxin has long been known as a critical phytohormone that regulates fruit development in plants. However, due to the lack of an enlarged ovary wall in the model plants Arabidopsis and rice, the molecular regulatory mechanisms of fruit division and enlargement remain unclear. In this study, we performed small RNA sequencing and degradome sequencing analyses to systematically explore post-transcriptional regulation in the mesocarp at the hard core stage following treatment of the peach (Prunus persica L.) fruit with the synthetic auxin α-naphthylacetic acid (NAA). Our analyses identified 24 evolutionarily conserved miRNA genes as well as 16 predicted genes. Experimental verification showed that the expression levels of miR398 and miR408b were significantly upregulated after NAA treatment, whereas those of miR156, miR160, miR166, miR167, miR390, miR393, miR482, miR535 and miR2118 were significantly downregulated. Degradome sequencing coupled with miRNA target prediction analyses detected 119 significant cleavage sites on several mRNA targets, including SQUAMOSA promoter binding protein–like (SPL), ARF, (NAM, ATAF1/2 and CUC2) NAC, Arabidopsis thaliana homeobox protein (ATHB), the homeodomain-leucine zipper transcription factor revoluta(REV), (teosinte-like1, cycloidea and proliferating cell factor1) TCP and auxin signaling F-box protein (AFB) family genes. Our systematic profiling of miRNAs and the degradome in peach fruit suggests the existence of a post-transcriptional regulation network of miRNAs that target auxin pathway genes in fruit development. MDPI 2017-12-13 /pmc/articles/PMC5751202/ /pubmed/29236054 http://dx.doi.org/10.3390/ijms18122599 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Shi, Mengya
Hu, Xiao
Wei, Yu
Hou, Xu
Yuan, Xue
Liu, Jun
Liu, Yueping
Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title_full Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title_fullStr Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title_full_unstemmed Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title_short Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches
title_sort genome-wide profiling of small rnas and degradome revealed conserved regulations of mirnas on auxin-responsive genes during fruit enlargement in peaches
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5751202/
https://www.ncbi.nlm.nih.gov/pubmed/29236054
http://dx.doi.org/10.3390/ijms18122599
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