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Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing

BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs)...

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Autores principales: Wan, Li-Chuan, Wang, Feng, Guo, Xiangqian, Lu, Shanfa, Qiu, Zongbo, Zhao, Yuanyuan, Zhang, Haiyan, Lin, Jinxing
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462689/
https://www.ncbi.nlm.nih.gov/pubmed/22894611
http://dx.doi.org/10.1186/1471-2229-12-146
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author Wan, Li-Chuan
Wang, Feng
Guo, Xiangqian
Lu, Shanfa
Qiu, Zongbo
Zhao, Yuanyuan
Zhang, Haiyan
Lin, Jinxing
author_facet Wan, Li-Chuan
Wang, Feng
Guo, Xiangqian
Lu, Shanfa
Qiu, Zongbo
Zhao, Yuanyuan
Zhang, Haiyan
Lin, Jinxing
author_sort Wan, Li-Chuan
collection PubMed
description BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. RESULTS: To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. CONCLUSIONS: We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution.
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spelling pubmed-34626892012-10-03 Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing Wan, Li-Chuan Wang, Feng Guo, Xiangqian Lu, Shanfa Qiu, Zongbo Zhao, Yuanyuan Zhang, Haiyan Lin, Jinxing BMC Plant Biol Research Article BACKGROUND: Small non-coding RNAs (sRNAs) play key roles in plant development, growth and responses to biotic and abiotic stresses. At least four classes of sRNAs have been well characterized in plants, including repeat-associated siRNAs (rasiRNAs), microRNAs (miRNAs), trans-acting siRNAs (tasiRNAs) and natural antisense transcript-derived siRNAs. Chinese fir (Cunninghamia lanceolata) is one of the most important coniferous evergreen tree species in China. No sRNA from Chinese fir has been described to date. RESULTS: To obtain sRNAs in Chinese fir, we sequenced a sRNA library generated from seeds, seedlings, leaves, stems and calli, using Illumina high throughput sequencing technology. A comprehensive set of sRNAs were acquired, including conserved and novel miRNAs, rasiRNAs and tasiRNAs. With BLASTN and MIREAP we identified a total of 115 conserved miRNAs comprising 40 miRNA families and one novel miRNA with precursor sequence. The expressions of 16 conserved and one novel miRNAs and one tasiRNA were detected by RT-PCR. Utilizing real time RT-PCR, we revealed that four conserved and one novel miRNAs displayed developmental stage-specific expression patterns in Chinese fir. In addition, 209 unigenes were predicted to be targets of 30 Chinese fir miRNA families, of which five target genes were experimentally verified by 5' RACE, including a squamosa promoter-binding protein gene, a pentatricopeptide (PPR) repeat-containing protein gene, a BolA-like family protein gene, AGO1 and a gene of unknown function. We also demonstrated that the DCL3-dependent rasiRNA biogenesis pathway, which had been considered absent in conifers, existed in Chinese fir. Furthermore, the miR390-TAS3-ARF regulatory pathway was elucidated. CONCLUSIONS: We unveiled a complex population of sRNAs in Chinese fir through high throughput sequencing. This provides an insight into the composition and function of sRNAs in Chinese fir and sheds new light on land plant sRNA evolution. BioMed Central 2012-08-15 /pmc/articles/PMC3462689/ /pubmed/22894611 http://dx.doi.org/10.1186/1471-2229-12-146 Text en Copyright ©2012 Wan et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Wan, Li-Chuan
Wang, Feng
Guo, Xiangqian
Lu, Shanfa
Qiu, Zongbo
Zhao, Yuanyuan
Zhang, Haiyan
Lin, Jinxing
Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title_full Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title_fullStr Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title_full_unstemmed Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title_short Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing
title_sort identification and characterization of small non-coding rnas from chinese fir by high throughput sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462689/
https://www.ncbi.nlm.nih.gov/pubmed/22894611
http://dx.doi.org/10.1186/1471-2229-12-146
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