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Int. J. Mol. Sci. 2017, 18(12), 2599; doi:10.3390/ijms18122599

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

1,2,†
,
1,†
,
3,†
,
4
,
4,†
,
3,* and 4,5,*
1
College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
2
National Agro-Tech Extension and Service Center, Beijing 100125, China
3
National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
4
College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
5
Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, Beijing 102206, China
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 23 October 2017 / Revised: 23 November 2017 / Accepted: 27 November 2017 / Published: 13 December 2017
(This article belongs to the Section Molecular Botany)
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Abstract

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. View Full-Text
Keywords: auxin; degradome; fruit development; microRNA; peach auxin; degradome; fruit development; microRNA; peach
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Shi, M.; Hu, X.; Wei, Y.; Hou, X.; Yuan, X.; Liu, J.; Liu, Y. Genome-Wide Profiling of Small RNAs and Degradome Revealed Conserved Regulations of miRNAs on Auxin-Responsive Genes during Fruit Enlargement in Peaches. Int. J. Mol. Sci. 2017, 18, 2599.

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