Long noncoding RNAs in Brassica rapa L. following vernalization

Abstract Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNA...

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Autores principales:	Daniel J. Shea, Namiko Nishida, Satoko Takada, Etsuko Itabashi, Satoshi Takahashi, Ayasha Akter, Naomi Miyaji, Kenji Osabe, Hasan Mehraj, Motoki Shimizu, Motoaki Seki, Tomohiro Kakizaki, Keiichi Okazaki, Elizabeth S. Dennis, Ryo Fujimoto
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/79fb42c157a748fb85a51ba484810885
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spelling	oai:doaj.org-article:79fb42c157a748fb85a51ba4848108852021-12-02T15:08:19ZLong noncoding RNAs in Brassica rapa L. following vernalization10.1038/s41598-019-45650-w2045-2322https://doaj.org/article/79fb42c157a748fb85a51ba4848108852019-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-45650-whttps://doaj.org/toc/2045-2322Abstract Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.Daniel J. SheaNamiko NishidaSatoko TakadaEtsuko ItabashiSatoshi TakahashiAyasha AkterNaomi MiyajiKenji OsabeHasan MehrajMotoki ShimizuMotoaki SekiTomohiro KakizakiKeiichi OkazakiElizabeth S. DennisRyo FujimotoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-11 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Daniel J. Shea Namiko Nishida Satoko Takada Etsuko Itabashi Satoshi Takahashi Ayasha Akter Naomi Miyaji Kenji Osabe Hasan Mehraj Motoki Shimizu Motoaki Seki Tomohiro Kakizaki Keiichi Okazaki Elizabeth S. Dennis Ryo Fujimoto Long noncoding RNAs in Brassica rapa L. following vernalization
description	Abstract Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding RNAs (lincRNAs), 551 natural antisense transcripts (NATs), and 93 intronic noncoding RNAs (incRNAs); 549 of the 2,088 lncRNAs significantly altered their expression in response to four weeks of cold treatment. Most differentially expressed lncRNAs did not lead to a change of expression levels in mRNAs covering or near lncRNAs, suggesting that the transcriptional responses to four weeks of cold treatment in lncRNA and mRNA are independent. However, some differentially expressed mRNAs had NATs with expression altered in the same direction. These genes were categorized as having an abiotic stress response, suggesting that the paired-expression may play a role in the transcriptional response to vernalization or cold treatment. We also identified short-term cold treatment induced NATs in BrFLC and BrMAF genes, which are involved in vernalization. The lncRNAs we identified differed from those reported in Arabidopsis thaliana, suggesting the role of lncRNAs in vernalization differ between these two species.
format	article
author	Daniel J. Shea Namiko Nishida Satoko Takada Etsuko Itabashi Satoshi Takahashi Ayasha Akter Naomi Miyaji Kenji Osabe Hasan Mehraj Motoki Shimizu Motoaki Seki Tomohiro Kakizaki Keiichi Okazaki Elizabeth S. Dennis Ryo Fujimoto
author_facet	Daniel J. Shea Namiko Nishida Satoko Takada Etsuko Itabashi Satoshi Takahashi Ayasha Akter Naomi Miyaji Kenji Osabe Hasan Mehraj Motoki Shimizu Motoaki Seki Tomohiro Kakizaki Keiichi Okazaki Elizabeth S. Dennis Ryo Fujimoto
author_sort	Daniel J. Shea
title	Long noncoding RNAs in Brassica rapa L. following vernalization
title_short	Long noncoding RNAs in Brassica rapa L. following vernalization
title_full	Long noncoding RNAs in Brassica rapa L. following vernalization
title_fullStr	Long noncoding RNAs in Brassica rapa L. following vernalization
title_full_unstemmed	Long noncoding RNAs in Brassica rapa L. following vernalization
title_sort	long noncoding rnas in brassica rapa l. following vernalization
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/79fb42c157a748fb85a51ba484810885
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Long noncoding RNAs in Brassica rapa L. following vernalization

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