Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean

Abstract Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3′ and 5′ ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many c...

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Autores principales:	Wei Zhao, Yihui Cheng, Chi Zhang, Qingbo You, Xinjie Shen, Wei Guo, Yongqing Jiao
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6ee2d3830f0b414db81824671532d8fc
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spelling	oai:doaj.org-article:6ee2d3830f0b414db81824671532d8fc2021-12-02T15:06:14ZGenome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean10.1038/s41598-017-05922-92045-2322https://doaj.org/article/6ee2d3830f0b414db81824671532d8fc2017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05922-9https://doaj.org/toc/2045-2322Abstract Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3′ and 5′ ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.Wei ZhaoYihui ChengChi ZhangQingbo YouXinjie ShenWei GuoYongqing JiaoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Wei Zhao Yihui Cheng Chi Zhang Qingbo You Xinjie Shen Wei Guo Yongqing Jiao Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
description	Abstract Circular RNAs (circRNAs) arise during pre-mRNA splicing, in which the 3′ and 5′ ends are linked to each other by a covalent bond. Soybean is an ancient tetraploid, which underwent two whole genome duplications. Most of soybean genes are paralogous genes with multiple copies. Although many circRNAs have been identified in animals and plants, little is known about soybean circRNAs, especially about circRNAs derived from paralogous genes. Here, we used deep sequencing technology coupled with RNase R enrichment strategy and bioinformatic approach to uncover circRNAs in soybean. A total of 5,372 circRNAs were identified, approximately 80% of which were paralogous circRNAs generated from paralogous genes. Despite high sequence homology, the paralogous genes could produce different paralogous circRNAs with different expression patterns. Two thousand and one hundred thirty four circRNAs were predicted to be 92 miRNAs target mimicry. CircRNAs and circRNA isoforms exhibited tissue-specific expression patterns in soybean. Based on the function of circRNA-host genes, the soybean circRNAs may participate in many biological processes such as developmental process, multi-organism process, and metabolic process. Our study not only provided a basis for research into the function of circRNAs in soybean but also new insights into the plant circRNA kingdom.
format	article
author	Wei Zhao Yihui Cheng Chi Zhang Qingbo You Xinjie Shen Wei Guo Yongqing Jiao
author_facet	Wei Zhao Yihui Cheng Chi Zhang Qingbo You Xinjie Shen Wei Guo Yongqing Jiao
author_sort	Wei Zhao
title	Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
title_short	Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
title_full	Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
title_fullStr	Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
title_full_unstemmed	Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean
title_sort	genome-wide identification and characterization of circular rnas by high throughput sequencing in soybean
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/6ee2d3830f0b414db81824671532d8fc
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_version_	1718388518289408000

Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean

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