Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20–24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been exten...

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Autores principales:	Jinqiang Yan, Min Wang, Wenrui Liu, Dasen Xie, Xiaoming He, Qingwu Peng, Biao Jiang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	wax gourd high-throughput sequencing microRNAs target genes Technology T Engineering (General). Civil engineering (General) TA1-2040 Biology (General) QH301-705.5 Physics QC1-999 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/fd0f0302e38f4ba3926c9150888e8395
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spelling	oai:doaj.org-article:fd0f0302e38f4ba3926c9150888e83952021-11-11T15:08:19ZIdentification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing10.3390/app1121100682076-3417https://doaj.org/article/fd0f0302e38f4ba3926c9150888e83952021-10-01T00:00:00Zhttps://www.mdpi.com/2076-3417/11/21/10068https://doaj.org/toc/2076-3417MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20–24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (<i>Benincasa hispida</i>). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.Jinqiang YanMin WangWenrui LiuDasen XieXiaoming HeQingwu PengBiao JiangMDPI AGarticlewax gourdhigh-throughput sequencingmicroRNAstarget genesTechnologyTEngineering (General). Civil engineering (General)TA1-2040Biology (General)QH301-705.5PhysicsQC1-999ChemistryQD1-999ENApplied Sciences, Vol 11, Iss 10068, p 10068 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	wax gourd high-throughput sequencing microRNAs target genes Technology T Engineering (General). Civil engineering (General) TA1-2040 Biology (General) QH301-705.5 Physics QC1-999 Chemistry QD1-999
spellingShingle	wax gourd high-throughput sequencing microRNAs target genes Technology T Engineering (General). Civil engineering (General) TA1-2040 Biology (General) QH301-705.5 Physics QC1-999 Chemistry QD1-999 Jinqiang Yan Min Wang Wenrui Liu Dasen Xie Xiaoming He Qingwu Peng Biao Jiang Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
description	MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20–24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (<i>Benincasa hispida</i>). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.
format	article
author	Jinqiang Yan Min Wang Wenrui Liu Dasen Xie Xiaoming He Qingwu Peng Biao Jiang
author_facet	Jinqiang Yan Min Wang Wenrui Liu Dasen Xie Xiaoming He Qingwu Peng Biao Jiang
author_sort	Jinqiang Yan
title	Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
title_short	Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
title_full	Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
title_fullStr	Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
title_full_unstemmed	Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing
title_sort	identification and characterization of known and novel micrornas in five tissues of wax gourd (<i>benincasa hispida</i>) based on high-throughput sequencing
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/fd0f0302e38f4ba3926c9150888e8395
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Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (<i>Benincasa hispida</i>) Based on High-Throughput Sequencing

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